Contacts of the helix formed by residues 93 - 108 (chain G) in PDB entry 2X86
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 ASN 93 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G GLY 5.7 0.7 - - - -
77G ALA* 3.4 12.5 - - + +
78G CYS* 2.8 45.8 + - - +
89G MET* 2.9 28.6 + - - +
92G ASN* 1.3 84.8 + - - +
94G TYR* 1.3 62.8 + - - +
95G GLN 3.7 0.2 - - - -
97G SER* 2.8 32.8 + - - -
140G PHE* 4.0 8.5 - - - -
143G SER* 3.2 28.2 + - - +
144G LYS* 4.6 7.4 - - + +
147G PHE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G MET 3.7 0.2 + - - -
90G MET* 3.2 37.1 + - + +
93G ASN* 1.3 75.1 - - - +
95G GLN* 1.3 73.4 + - - +
97G SER* 3.2 6.4 + - - -
98G LYS* 2.9 41.1 + - + +
143G SER* 4.1 10.1 - - - +
146G LEU* 3.5 43.8 - - + +
147G PHE* 3.6 28.2 - + + -
150G TYR* 3.7 15.6 - - + +
48H ALA 4.3 0.7 + - - -
49H ASP* 2.4 39.9 + - - -
50H TYR* 3.7 14.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G MET 2.8 14.8 + - - +
91G ASP* 3.3 26.7 - - - +
94G TYR* 1.3 76.9 - - + +
96G TYR* 1.3 64.1 + - - +
98G LYS* 3.0 41.3 + - - +
99G GLU* 3.0 47.8 + - - +
50H TYR 4.1 9.7 - - - +
51H MET* 5.4 6.1 - - - +
55H ASP* 5.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G THR* 5.4 0.4 - - + -
53G LYS* 2.7 40.6 + - + -
54G GLU* 5.4 1.3 - - - -
56G PHE* 3.5 19.3 - + - -
57G LEU* 3.6 34.2 + - + -
74G HIS* 3.9 15.9 - + - +
91G ASP 2.9 12.1 + - - +
92G ASN* 3.1 26.2 - - - +
93G ASN 4.0 0.2 - - - +
94G TYR 3.3 0.2 - - - -
95G GLN* 1.3 74.6 - - - +
97G SER* 1.3 63.5 + - - +
99G GLU* 3.0 17.4 + - - +
100G LEU* 3.0 31.6 + - + +
400G NAP 3.2 37.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G HIS* 2.8 33.1 + - - -
93G ASN* 2.8 21.7 + - - -
94G TYR 3.5 4.0 - - - -
96G TYR* 1.3 79.2 - - - +
98G LYS* 1.3 62.4 + - - +
100G LEU* 3.3 2.9 + - - +
101G LEU* 2.9 24.4 + - - +
111G PHE* 4.1 1.0 - - - -
113G TYR* 5.9 0.5 - - - -
144G LYS* 5.7 2.9 + - - -
147G PHE* 3.6 33.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G TYR* 2.9 28.8 + - + +
95G GLN* 3.0 45.7 + - - +
97G SER* 1.3 76.0 - - - +
99G GLU* 1.3 64.3 + - - +
101G LEU* 3.2 2.8 + - - +
102G HIS* 3.0 37.2 + - + +
147G PHE* 3.5 13.0 - - + -
150G TYR* 3.6 45.0 + - + +
49H ASP* 2.9 31.8 + - - +
50H TYR 4.1 2.6 + - - -
51H MET* 5.2 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G LEU* 4.0 14.6 - - + -
60G ILE* 3.9 7.9 - - + +
61G MET* 3.4 45.0 - - + +
95G GLN* 3.0 38.1 + - - +
96G TYR 3.0 10.5 + - - +
98G LYS* 1.3 80.8 - - - +
100G LEU* 1.3 61.7 + - - +
102G HIS* 3.4 8.1 + - - +
103G TYR* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G THR* 4.1 14.1 - - + -
56G PHE* 3.7 24.9 - - + -
57G LEU* 5.2 2.7 - - + -
60G ILE* 3.9 18.4 - - + -
72G ILE* 4.5 12.8 - - + -
74G HIS* 3.3 46.2 - - + +
96G TYR* 3.0 25.0 + - + +
97G SER 3.6 7.2 - - - +
99G GLU* 1.3 74.5 - - - +
101G LEU* 1.3 65.7 - - - +
103G TYR* 3.1 6.9 + - - +
104G CYS* 2.9 26.3 + - - -
111G PHE* 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G SER 2.9 18.1 + - - +
98G LYS 3.5 3.8 - - - +
100G LEU* 1.3 76.2 - - - +
102G HIS* 1.3 59.5 + - + +
104G CYS* 3.3 1.4 + - - +
105G LEU* 2.8 40.7 + - + +
111G PHE* 3.8 31.1 - - + -
147G PHE* 4.0 20.2 - - + -
150G TYR* 4.0 27.8 - - + -
151G VAL* 4.3 9.9 - - + -
154G ILE* 4.3 14.4 - - + -
162G ILE* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G LYS* 3.0 34.9 + - + +
99G GLU* 3.9 8.5 - - - +
101G LEU* 1.3 75.1 - - + +
103G TYR* 1.3 67.4 + - - +
105G LEU* 3.3 13.6 + - + +
106G GLU* 3.0 30.0 + - - +
150G TYR* 2.6 37.8 + + - -
154G ILE* 4.5 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G ILE* 3.5 58.3 - - + -
63G GLY* 4.3 0.9 - - - -
64G GLU 2.6 28.1 + - - -
65G GLU* 3.8 5.0 + - - -
66G PHE* 3.3 18.1 + + - -
69G VAL* 5.6 3.2 - - + +
72G ILE* 4.7 7.4 - - + -
99G GLU 3.2 13.3 + - - +
100G LEU* 3.1 8.9 + - - +
102G HIS* 1.3 77.4 - - - +
104G CYS* 1.3 72.5 + - - +
106G GLU* 4.8 1.3 - - - -
107G ARG* 3.1 81.1 + - - +
109G ILE* 4.1 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ILE* 3.4 36.8 - - - -
100G LEU 2.9 14.9 + - - +
101G LEU* 3.6 7.6 - - + +
103G TYR* 1.3 78.7 - - - +
105G LEU* 1.3 54.5 + - + +
107G ARG 3.0 2.1 + - - -
108G GLU 2.7 31.9 + - - -
109G ILE* 2.9 41.7 + - - +
111G PHE* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G LEU* 2.8 31.7 + - + +
102G HIS* 3.3 15.9 + - - +
104G CYS* 1.3 77.6 - - + +
106G GLU* 1.3 61.9 + - - +
108G GLU* 3.3 17.7 + - - +
109G ILE 6.1 0.2 - - - +
111G PHE* 6.3 0.7 - - + -
154G ILE* 3.6 32.5 - - + -
158G ALA* 4.4 12.6 - - + -
159G ASN* 5.2 2.8 - - - +
160G SER* 4.3 15.0 + - - +
161G GLN 5.7 0.2 - - - +
162G ILE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G HIS* 3.0 18.1 + - - +
103G TYR* 3.8 5.4 - - - +
105G LEU* 1.3 77.2 - - - +
107G ARG* 1.3 79.2 + - + +
108G GLU* 3.4 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G GLY* 3.5 28.9 + - - -
65G GLU* 3.3 37.6 + - - +
103G TYR* 3.1 64.4 + - - +
104G CYS 3.0 2.0 + - - -
106G GLU* 1.3 101.5 + - + +
108G GLU* 1.3 71.5 + - - +
109G ILE* 3.2 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G CYS 2.7 5.0 + - - -
105G LEU 3.3 10.8 + - - +
106G GLU 4.9 2.9 - - - +
107G ARG* 1.3 80.7 - - - +
109G ILE* 1.3 57.5 + - - +
110G PRO* 3.4 10.7 - - - +
159G ASN* 3.9 31.2 + - + +
160G SER* 3.4 26.8 - - - +
----------------------------------------------------------
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