Contacts of the helix formed by residues 86 - 109 (chain G) in PDB entry 2PWZ
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 ASP 86 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G GLY 3.4 4.4 + - - +
85G MET* 1.3 75.4 - - - +
87G ARG* 1.3 71.9 + - + +
88G SER* 3.2 19.0 + - - -
89G ASP* 3.3 21.1 + - - +
90G LEU* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ASP* 1.3 80.0 + - + +
88G SER* 1.3 56.9 + - - +
90G LEU* 3.8 5.8 + - - +
91G PHE* 3.3 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ASP* 3.1 13.4 + - - -
87G ARG* 1.3 80.7 - - - +
89G ASP* 1.3 59.3 + - - +
90G LEU 3.3 0.4 - - - -
91G PHE* 3.9 6.1 - - - +
92G ASN* 2.8 51.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G GLY 3.8 5.4 - - - +
85G MET* 3.5 25.0 - - + +
86G ASP* 3.3 37.7 + - - +
88G SER* 1.3 79.9 - - - +
90G LEU* 1.3 56.0 + - - +
92G ASN* 3.5 5.0 + - - +
93G VAL* 3.2 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G VAL* 3.8 28.3 - - + +
80G ALA 4.0 10.5 - - - +
81G ARG* 4.0 16.8 - - - +
85G MET* 3.7 28.0 - - + +
86G ASP 3.1 13.3 + - - +
87G ARG* 4.0 7.0 - - - +
89G ASP* 1.3 76.3 - - - +
91G PHE* 1.3 60.9 + - - +
93G VAL* 3.7 2.3 + - - +
94G ASN* 3.0 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G ARG 3.3 16.3 + - - +
88G SER* 3.9 7.0 - - - +
90G LEU* 1.3 77.7 - - - +
92G ASN* 1.3 73.8 + - - +
94G ASN* 4.2 3.3 - - - +
95G ALA* 2.8 48.6 + - + +
120G PRO* 4.1 29.6 - - + -
123G THR* 3.7 25.8 - - + -
124G THR* 5.6 2.0 - - + -
127G ILE* 4.7 4.0 - - + -
305G LEU* 3.6 41.3 - - + -
309G PHE* 4.4 13.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G SER* 2.8 41.5 + - - +
89G ASP* 3.5 6.5 + - - +
91G PHE* 1.3 87.3 - - - +
93G VAL* 1.3 63.2 + - + +
95G ALA* 4.2 3.1 - - - +
96G GLY* 3.3 18.4 + - - -
309G PHE* 4.0 21.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G VAL* 3.6 33.0 - - + -
85G MET* 4.1 18.8 - - + -
89G ASP* 3.2 18.4 + - + +
90G LEU* 4.1 3.4 - - - +
91G PHE 3.2 0.2 - - - -
92G ASN* 1.3 78.8 - - + +
94G ASN* 1.3 67.0 + - - +
96G GLY* 3.3 2.6 + - - -
97G ILE* 3.1 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G GLY* 3.1 12.3 - - - -
79G VAL* 2.8 36.3 + - - +
90G LEU* 3.0 45.4 + - - +
91G PHE* 4.2 3.1 - - - +
93G VAL* 1.3 78.8 - - - +
95G ALA* 1.3 62.0 + - - +
97G ILE* 3.4 8.1 + - - +
98G VAL* 3.1 30.5 + - - +
118G THR* 4.1 8.4 - - + +
119G ASN 4.0 22.8 + - - +
120G PRO* 5.6 1.1 - - + -
124G THR* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G PHE* 2.8 29.5 + - + +
92G ASN 4.2 0.4 - - - +
94G ASN* 1.3 75.6 - - - +
96G GLY* 1.3 57.5 - - - +
98G VAL* 3.6 5.6 + - - +
99G LYS* 3.1 28.4 + - - +
124G THR* 5.1 3.7 - - - +
127G ILE* 3.6 30.1 - - + +
309G PHE* 3.6 27.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ASN 3.3 11.2 + - - -
93G VAL 3.3 6.5 + - - -
95G ALA* 1.3 76.3 - - - +
97G ILE* 1.3 57.9 + - - +
99G LYS* 3.4 4.9 - - - +
100G ASN* 2.8 31.2 + - - +
309G PHE* 3.8 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G ILE* 6.5 0.9 - - + -
75G ILE* 5.9 0.2 - - + -
77G ALA* 3.6 32.1 - - + +
78G GLY* 4.1 12.3 - - - +
79G VAL* 4.5 7.0 - - + -
93G VAL* 3.1 32.6 + - + +
94G ASN* 3.6 18.2 - - - +
96G GLY* 1.3 71.8 - - - +
98G VAL* 1.3 58.8 + - + +
99G LYS 3.1 0.3 + - - -
100G ASN* 3.2 7.4 + - - +
101G LEU* 2.8 46.5 + - + +
118G THR* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G ILE* 5.2 6.7 - - + -
94G ASN 3.1 18.4 + - - +
95G ALA* 3.8 4.9 - - - +
97G ILE* 1.3 74.6 - - + +
99G LYS* 1.3 57.5 + - - +
101G LEU* 4.6 5.6 - - - +
102G VAL* 2.8 51.2 + - + +
116G ILE* 5.0 8.7 - - + -
118G THR* 3.4 34.3 - - + +
124G THR* 3.8 38.8 - - + +
127G ILE* 4.3 8.7 - - + -
128G ALA* 4.7 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ALA 3.1 18.3 + - - +
96G GLY* 3.4 8.5 - - - +
98G VAL* 1.3 75.6 - - - +
100G ASN* 1.3 68.7 + - - +
102G VAL* 4.0 1.0 - - - +
103G GLN* 2.9 61.7 + - - +
127G ILE* 4.1 14.6 - - + -
131G VAL* 3.8 17.9 - - + +
134G LYS* 5.7 4.8 - - - +
309G PHE* 4.2 14.8 - - + -
310G VAL* 4.6 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G TYR* 5.7 0.5 + - - -
61G GLU 5.2 0.9 + - - +
96G GLY 2.8 17.3 + - - +
97G ILE* 3.4 7.0 - - - +
99G LYS* 1.3 80.6 - - - +
101G LEU* 1.3 73.9 + - - +
103G GLN* 3.2 14.9 + - - +
104G GLN* 3.1 47.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
6G LEU* 4.1 26.6 - - + +
33G TYR* 4.0 27.6 - - + +
63G ALA* 4.7 3.8 - - + -
75G ILE* 3.9 20.9 - - + -
77G ALA* 3.6 31.0 - - + -
97G ILE* 2.8 30.4 + - + +
98G VAL 4.0 2.5 - - - +
100G ASN* 1.3 85.9 - - - +
102G VAL* 1.3 57.3 + - - +
104G GLN* 2.9 28.9 + - - +
105G VAL* 3.0 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G ILE* 4.0 20.4 - - + -
98G VAL* 2.8 31.8 + - + +
99G LYS 4.2 2.2 - - - +
101G LEU* 1.3 71.8 - - - +
103G GLN* 1.3 56.0 + - - +
105G VAL* 3.4 11.7 + - + +
106G ALA* 3.0 26.5 + - - +
114G ILE* 5.1 4.9 - - + -
116G ILE* 5.0 2.7 - - + -
128G ALA* 3.8 40.4 - - + +
131G VAL* 3.7 20.4 - - + -
132G LEU* 3.8 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G LYS* 2.9 52.2 + - - +
100G ASN* 3.3 17.6 + - - +
102G VAL* 1.3 76.4 - - - +
104G GLN* 1.3 62.8 + - + +
105G VAL 3.4 0.2 - - - -
106G ALA* 3.6 5.0 + - - +
107G LYS* 3.5 20.8 + - - +
131G VAL* 3.5 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G TYR* 5.0 0.8 + - - -
61G GLU 3.1 22.0 + - - -
62G ASP* 3.6 9.1 - - - +
63G ALA* 2.8 33.8 + - + +
64G THR* 4.1 2.6 + - - +
67G LEU* 3.9 13.9 - - + -
100G ASN* 3.1 42.0 + - - +
101G LEU* 2.9 15.4 + - - +
103G GLN* 1.3 73.5 - - + +
105G VAL* 1.3 65.2 + - - +
107G LYS* 3.4 7.8 + - - +
108G THR* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LEU* 4.1 6.1 - - + -
67G LEU* 3.9 15.9 - - + -
73G VAL* 3.9 27.8 - - + -
75G ILE* 4.6 5.2 - - + -
101G LEU 3.0 17.9 + - - +
102G VAL* 3.5 12.8 - - - +
104G GLN* 1.3 77.0 - - - +
106G ALA* 1.3 58.6 + - - +
109G CYS* 2.8 52.5 + - - +
110G PRO* 5.2 1.1 - - + -
112G ALA* 5.1 0.2 - - + -
114G ILE* 4.0 30.5 - - + -
132G LEU* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G VAL 3.0 17.2 + - - +
103G GLN* 4.0 7.9 - - - +
104G GLN 3.3 0.4 - - - -
105G VAL* 1.3 77.3 - - - +
107G LYS* 1.3 62.1 + - - +
110G PRO* 3.6 23.9 - - - +
131G VAL 5.1 2.5 - - - +
132G LEU* 4.0 10.3 - - + -
135G ALA* 3.8 18.9 - - + +
137G VAL* 3.8 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ASP* 4.9 3.8 + - - -
64G THR* 3.9 18.2 + - - +
103G GLN 3.5 10.7 + - - +
104G GLN* 3.4 10.5 + - - +
105G VAL 3.2 0.6 - - - -
106G ALA* 1.3 81.8 - - - +
108G THR* 1.3 73.6 + - - +
110G PRO* 4.3 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G THR* 3.7 25.3 + - + +
67G LEU* 3.6 16.3 - - + +
68G GLU* 3.6 48.8 - - - +
69G GLY 5.2 1.0 + - - -
104G GLN* 3.1 16.9 + - - +
107G LYS* 1.3 94.7 - - - +
109G CYS* 1.3 59.3 + - - +
110G PRO* 3.5 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G LEU* 3.5 37.7 - - - +
69G GLY* 5.1 1.8 - - - +
70G ALA* 3.8 19.7 - - - +
73G VAL* 3.7 29.4 - - - -
105G VAL* 2.8 27.9 + - - +
108G THR* 1.3 75.3 - - - +
110G PRO* 1.4 64.3 - - - +
111G LYS 3.3 2.9 - - - -
112G ALA* 3.1 15.3 + - - +
----------------------------------------------------------
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