Contacts of the helix formed by residues 95 - 122 (chain G) in PDB entry 1QGH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 95 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D HIS* 5.3 2.7 - - + -
34G MET* 3.8 36.8 - - + -
35G ARG 3.6 28.6 + - - +
36G GLY* 4.8 2.0 - - - -
38G ASN* 3.9 16.2 - - + +
39G PHE* 3.8 26.2 - - - +
42G LEU* 3.5 29.2 - - + -
93G LYS 3.8 0.6 + - - -
94G THR* 1.3 74.3 + - - +
96G ASP* 1.3 61.8 + - - +
98G LEU* 3.2 8.9 + - - +
99G MET* 2.9 32.6 + - + +
149G PHE* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D HIS* 2.7 43.4 + - - -
94G THR* 2.9 11.5 - - + +
95G MET* 1.3 73.9 - - - +
97G GLN* 1.3 67.9 + - + +
99G MET* 3.2 1.3 + - - +
100G GLU* 2.8 35.5 + - - +
149G PHE* 3.6 12.6 - - - -
150G LEU* 3.6 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G PRO 4.7 1.8 + - - +
93G LYS* 3.8 31.2 - - + +
94G THR* 2.9 47.7 + - + +
96G ASP* 1.3 80.0 - - - +
98G LEU* 1.3 63.8 + - - +
100G GLU* 3.3 12.9 + - - +
101G ASP* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G GLN* 5.3 3.1 - - + +
30G ILE* 3.7 28.2 - - + +
33G TYR 4.6 3.1 - - - +
34G MET* 3.8 37.0 - - + +
35G ARG 5.2 0.2 - - - +
89G TYR* 4.3 12.6 - - + -
93G LYS* 3.8 43.5 - - + +
94G THR 3.0 18.9 + - - +
95G MET* 3.2 9.2 + - - +
97G GLN* 1.3 73.5 - - - +
99G MET* 1.3 77.6 + - + +
101G ASP* 3.1 8.5 + - + +
102G LEU* 2.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ILE* 3.5 33.0 - - + -
34G MET* 4.6 7.9 - - + -
42G LEU* 4.1 12.6 - - + -
46G MET* 4.3 10.8 - - + -
95G MET* 2.9 22.1 + - + +
96G ASP 3.8 3.8 - - - +
98G LEU* 1.3 81.2 - - + +
100G GLU* 1.3 51.5 + - - +
102G LEU* 3.0 6.7 + - + +
103G VAL* 2.7 38.5 + - + +
146G PHE* 3.6 34.3 - - + -
149G PHE* 3.5 26.0 - - + -
150G LEU* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G ASP* 2.8 26.4 + - - +
97G GLN* 3.6 14.6 - - - +
99G MET* 1.3 76.2 - - - +
101G ASP* 1.3 57.4 + - - +
103G VAL* 3.8 3.6 - - - +
104G GLY* 2.9 25.6 + - - -
150G LEU* 3.7 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LYS* 3.3 37.9 + - - +
29G GLN* 4.7 5.0 + - - -
30G ILE* 5.3 3.1 - - + +
93G LYS* 4.0 18.9 + - - +
97G GLN 3.1 11.6 + - - +
98G LEU* 3.1 12.7 + - + +
100G GLU* 1.3 73.4 - - - +
102G LEU* 1.3 66.6 + - - +
104G GLY* 3.2 1.8 + - - -
105G THR* 3.1 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G PHE* 3.5 32.8 - - + -
26G LYS* 5.2 1.8 - - - -
27G ILE* 4.8 2.0 - - + -
30G ILE* 3.9 21.2 - - + +
46G MET* 4.1 6.5 - - + -
49G LEU* 3.7 22.0 - - + -
98G LEU 2.9 12.6 + - - +
99G MET* 3.1 12.6 - - + +
101G ASP* 1.3 77.4 - - - +
103G VAL* 1.3 63.3 + - - +
105G THR* 3.1 5.8 + - - -
106G LEU* 2.9 25.4 + - + +
146G PHE* 3.7 43.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G MET 2.7 22.0 + - - +
100G GLU* 3.9 6.7 - - - +
102G LEU* 1.3 73.3 - - - +
104G GLY* 1.3 65.0 + - - +
106G LEU* 3.3 11.1 + - + +
107G GLU* 2.9 33.2 + - + +
143G ILE* 5.1 7.2 - - + +
146G PHE* 3.3 41.3 - - + -
147G LYS* 3.8 30.5 - - + +
150G LEU* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G GLU 2.9 18.0 + - - -
101G ASP* 3.2 1.5 + - - -
102G LEU 3.2 0.2 - - - -
103G VAL* 1.3 77.7 - - - +
105G THR* 1.3 57.9 + - - +
107G GLU* 3.0 16.7 + - - +
108G LEU* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G PHE* 3.5 36.6 - - + -
26G LYS* 3.5 19.5 - - - -
84G VAL* 3.9 29.4 - - + +
85G GLU 5.0 0.3 + - - -
101G ASP* 3.1 15.4 + - - -
102G LEU 3.6 6.5 - - - -
104G GLY* 1.3 73.6 - - - +
106G LEU* 1.3 67.9 + - - +
108G LEU* 3.2 7.9 + - + +
109G LEU* 2.9 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G PHE* 3.8 20.0 - - + -
49G LEU* 5.6 2.0 - - + -
53G PHE* 3.9 24.7 - - + -
102G LEU* 2.9 31.0 + - + +
103G VAL* 3.6 14.6 - - + +
104G GLY 3.2 0.2 - - - -
105G THR* 1.3 76.5 - - - +
107G GLU* 1.3 58.0 + - - +
109G LEU* 3.0 6.9 + - + +
110G ARG* 2.7 31.0 + - - +
139G ILE* 3.7 13.4 - - + +
142G HIS* 3.9 25.6 - - + +
143G ILE* 3.8 21.8 - - + +
146G PHE* 4.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G VAL* 2.9 29.3 + - + +
104G GLY* 3.0 14.8 + - - +
106G LEU* 1.3 75.9 - - - +
108G LEU* 1.3 62.2 + - - +
110G ARG* 3.2 26.4 + - - +
111G ASP* 2.9 32.1 + - - +
143G ILE* 4.0 19.6 - - + +
147G LYS* 3.4 27.6 + - - -
154G PRO 4.4 5.4 - - - +
155G LEU* 5.9 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ASN* 4.1 2.5 - - - +
83G SER* 3.6 31.6 - - - +
84G VAL* 4.0 23.1 - - + -
85G GLU 5.2 0.9 - - - +
104G GLY 2.9 12.0 + - - +
105G THR* 3.5 11.0 - - - +
107G GLU* 1.3 75.9 - - - +
109G LEU* 1.3 69.4 + - - +
111G ASP* 3.1 7.4 + - - +
112G GLU* 2.9 56.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G GLN* 3.7 22.7 - - - +
19G ASN* 4.0 22.2 - - + +
20G LEU* 4.1 17.7 - - + -
23G PHE* 3.5 38.4 - - + -
53G PHE* 4.6 7.6 - - + -
84G VAL* 4.5 1.3 - - + -
105G THR* 2.9 24.5 + - + +
106G LEU* 3.6 7.6 - - + +
108G LEU* 1.3 79.7 - - + +
110G ARG* 1.3 65.6 + - - +
112G GLU* 3.8 1.7 - - - +
113G TYR* 2.9 35.7 + - + +
139G ILE* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 110 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G LEU 2.7 17.9 + - - +
107G GLU* 3.4 33.2 + - - +
109G LEU* 1.3 73.9 - - - +
111G ASP* 1.3 89.9 + - - +
113G TYR* 3.3 5.8 + - - +
114G LYS* 3.0 22.3 + - + +
136G LYS* 4.1 22.3 - - + +
139G ILE* 3.9 16.5 - - + +
140G ASP* 3.2 26.4 + - - +
143G ILE* 3.8 18.5 - - + +
154G PRO 5.2 0.2 + - - -
155G LEU* 3.8 27.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G GLU* 2.9 23.2 + - - +
108G LEU* 3.8 5.5 - - - +
110G ARG* 1.3 109.5 + - - +
112G GLU* 1.3 62.9 + - + +
114G LYS* 3.1 14.7 + - - +
115G GLN* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G PHE* 3.1 10.6 - - + -
15G HIS* 3.0 9.4 + - - -
16G GLN* 3.0 21.5 + - - +
19G ASN* 2.9 21.1 + - - -
83G SER* 2.5 28.3 + - - -
108G LEU* 2.9 34.5 + - + +
109G LEU* 3.9 4.0 - - - +
111G ASP* 1.3 77.3 - - + +
113G TYR* 1.3 65.0 + - - +
115G GLN* 3.0 13.6 + - + +
116G GLY 2.9 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G PHE* 3.9 10.7 - + - -
16G GLN* 3.6 34.0 - - + +
20G LEU* 3.5 25.6 - - - +
56G GLN* 2.9 19.2 + - - -
60G VAL* 4.9 1.0 - - + +
109G LEU* 2.9 28.9 + - + +
110G ARG* 3.6 5.8 - - - +
112G GLU* 1.3 77.6 - - - +
114G LYS* 1.3 52.0 + - - +
116G GLY* 2.9 2.3 + - - -
117G ILE* 2.6 48.9 + - + +
132G LEU* 4.0 19.1 - - + +
135G PHE* 3.4 41.4 - + + -
136G LYS* 4.2 6.5 - - + -
139G ILE* 3.7 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLY* 3.6 13.1 + - - -
126B ASP* 2.5 37.4 + - - +
110G ARG* 3.0 13.6 + - + +
111G ASP* 3.3 14.6 - - - +
112G GLU 3.1 0.2 - - - -
113G TYR* 1.3 76.6 - - - +
115G GLN* 1.3 67.5 + - - +
117G ILE* 3.0 20.4 + - + +
118G GLU* 3.0 54.3 + - - +
136G LYS* 4.7 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G PHE* 4.7 4.9 - - + -
111G ASP* 2.9 29.7 + - - +
112G GLU* 3.0 15.7 + - + +
114G LYS* 1.3 84.3 - - - +
116G GLY* 1.3 63.3 + - - +
117G ILE 3.2 0.2 + - - -
118G GLU* 3.3 10.8 + - - +
119G LEU* 3.0 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G PHE* 3.4 36.3 - - - -
112G GLU 2.9 7.5 + - - -
113G TYR 2.9 6.0 + - - -
115G GLN* 1.3 76.5 - - - +
117G ILE* 1.3 63.5 + - - +
119G LEU* 4.1 6.3 - - - -
120G THR* 2.9 29.6 + - - -
132G LEU* 4.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 3.7 32.5 - - + +
113G TYR* 2.6 28.0 + - + +
114G LYS* 3.0 13.0 + - + +
116G GLY* 1.3 74.5 - - - +
118G GLU* 1.3 64.3 + - + +
120G THR* 4.5 1.1 - - - -
121G ASP* 3.1 10.7 + - + +
129G ASN* 2.9 35.8 + - - +
132G LEU* 3.6 25.4 - - + +
133G ILE* 3.8 31.0 - - + +
136G LYS* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 5.8 0.2 - - - +
114G LYS* 3.0 51.8 + - - +
115G GLN* 4.0 11.0 - - - +
117G ILE* 1.3 75.0 - - + +
119G LEU* 1.3 66.4 + - - +
121G ASP* 3.1 8.6 + - - +
122G LYS* 2.9 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 3.7 22.2 - - + +
8G ASP 4.0 8.7 - - - -
9G THR* 3.9 7.0 - - - +
12G PHE* 3.8 31.2 - - + -
115G GLN* 3.0 14.3 + - + +
116G GLY* 3.7 11.0 - - - +
118G GLU* 1.3 76.8 - - - +
120G THR* 1.3 56.7 + - - +
122G LYS* 3.0 9.7 + - - +
123G GLU* 2.8 66.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G THR* 4.1 16.9 + - - +
12G PHE* 5.8 1.0 - - - -
116G GLY* 2.9 19.1 + - - -
117G ILE* 3.7 1.6 - - - -
119G LEU* 1.3 81.4 - - - +
121G ASP* 1.3 57.2 + - - +
123G GLU* 3.8 1.7 - - - -
124G GLY 3.0 5.7 + - - -
125G ASP* 2.8 46.3 + - + +
128G THR* 3.7 18.8 - - - +
129G ASN* 2.8 46.0 - - + +
132G LEU* 3.9 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ILE* 3.1 16.9 + - + +
118G GLU* 3.3 6.3 - - - +
120G THR* 1.3 79.2 - - - +
122G LYS* 1.3 85.3 + - - +
124G GLY* 3.1 14.0 + - - -
125G ASP 5.8 0.2 - - - -
126G ASP* 6.4 0.2 - - - +
129G ASN* 3.8 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G GLU* 2.9 34.3 + - + +
119G LEU* 3.6 9.9 - - - +
121G ASP* 1.3 99.7 + - - +
123G GLU* 1.3 60.5 + - + +
124G GLY* 3.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il