Contacts of the helix formed by residues 82 - 99 (chain A) in PDB entry 2G5W
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 SER 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A TYR* 1.3 90.8 + - - +
83A ASP* 1.3 66.5 + - - +
84A GLU* 3.7 11.4 + - - +
85A GLN* 2.8 37.2 + - - +
86A VAL* 3.1 26.2 + - - +
174A ASN* 4.6 0.7 - - - -
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR 5.1 1.2 - - - +
82A SER* 1.3 72.8 - - - +
84A GLU* 1.3 59.9 + - - +
86A VAL* 3.3 8.8 + - - +
87A GLU* 2.9 37.2 + - + +
174A ASN* 5.3 0.7 + - - -
177A ARG* 3.6 23.3 + - - +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.8 28.8 - - + +
82A SER* 3.3 10.1 + - - +
83A ASP* 1.3 80.1 - - - +
85A GLN* 1.3 55.6 + - - +
87A GLU* 3.5 5.3 + - - +
88A ALA* 3.1 28.7 + - + +
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN 5.7 0.2 + - - -
40A GLY* 3.7 19.3 + - - +
41A VAL* 4.4 10.7 - - + +
42A PRO* 4.0 3.5 - - + +
66A MET* 3.8 4.4 - - - +
79A GLY* 3.2 37.0 - - - +
80A ILE* 3.2 2.0 + - - -
81A TYR* 2.8 56.8 + - - -
82A SER* 2.8 24.8 + - - +
83A ASP 3.2 0.2 - - - -
84A GLU* 1.3 74.7 - - - +
86A VAL* 1.3 66.5 + - - +
88A ALA* 3.2 6.5 + - - +
89A TRP* 2.9 30.2 + - - -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 4.2 7.4 - - + +
82A SER 3.1 15.0 + - - +
83A ASP* 3.5 7.6 - - - +
85A GLN* 1.3 76.3 - - - +
87A GLU* 1.3 70.5 + - - +
89A TRP* 3.3 10.8 + - - +
90A LYS* 3.4 12.0 + - - +
174A ASN* 3.5 28.7 - - + +
177A ARG* 3.4 45.1 - - + +
178A ALA* 3.6 31.4 - - + +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASP* 2.9 23.1 + - + +
84A GLU* 3.8 6.7 - - - +
86A VAL* 1.3 81.2 - - - +
88A ALA* 1.3 61.2 + - - +
90A LYS* 2.7 55.0 + - - +
91A GLN* 4.5 1.2 + - - +
177A ARG* 4.9 5.5 + - - -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.6 28.3 - - + -
42A PRO* 3.7 21.6 - - + +
84A GLU* 3.1 17.1 + - + +
85A GLN 3.2 1.1 + - - +
87A GLU* 1.3 74.1 - - - +
89A TRP* 1.3 64.5 + - - +
91A GLN* 3.3 31.0 + - - +
92A VAL* 4.4 0.2 - - - +
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Residues in contact with TRP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 3.7 13.6 - - + +
46A LEU* 4.2 18.2 - - + -
50A TYR* 4.8 3.6 - + - -
62A SER* 4.4 16.4 - - - -
63A GLU* 4.7 4.3 - - + -
65A THR* 3.7 21.4 - - + +
78A PRO* 3.7 23.6 - - + -
79A GLY 3.0 22.1 + - - -
80A ILE* 3.5 21.4 - - + +
85A GLN 2.9 23.5 + - - +
86A VAL 3.3 6.7 + - - +
88A ALA* 1.3 75.3 - - - +
90A LYS* 1.3 65.3 + - - +
92A VAL* 2.9 50.7 + - + +
93A VAL* 3.2 14.0 + - - +
103A ILE* 5.7 0.7 - - + -
105A CYS* 4.9 0.4 - - - -
178A ALA* 4.1 10.8 - - + -
180A PHE* 3.5 33.2 - + + -
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL* 3.4 10.1 + - - +
87A GLU* 2.7 51.1 + - - +
88A ALA 3.2 1.0 - - - -
89A TRP* 1.3 77.9 - - - +
91A GLN* 1.3 56.8 + - - +
93A VAL* 3.4 1.7 + - - +
94A GLU* 3.0 51.2 + - + +
177A ARG* 3.7 24.1 + - - +
178A ALA* 3.4 23.3 - - - +
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Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO 4.1 2.2 + - - -
43A ASN* 3.4 25.7 - - - +
44A ALA* 3.6 22.3 + - - +
47A ALA* 4.0 9.1 - - + +
87A GLU 4.5 1.2 + - - +
88A ALA* 3.3 23.7 + - - +
90A LYS* 1.3 78.4 - - - +
92A VAL* 1.3 67.2 + - + +
94A GLU* 3.9 9.7 - - - +
95A ALA* 3.0 31.2 + - - +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 4.3 8.3 - - + -
43A ASN 4.0 7.2 - - - +
46A LEU* 4.0 11.0 - - + -
47A ALA* 3.6 30.4 - - + +
50A TYR* 3.6 33.4 - - + -
88A ALA 4.4 0.2 - - - +
89A TRP* 2.9 36.1 + - + +
91A GLN* 1.3 79.5 - - + +
93A VAL* 1.3 64.1 + - + +
95A ALA* 3.4 4.9 - - - +
96A VAL* 3.1 22.0 + - - +
103A ILE* 4.9 6.5 - - + -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TRP* 3.2 14.1 + - + +
90A LYS 3.8 4.5 - - - +
92A VAL* 1.3 75.5 - - + +
94A GLU* 1.3 56.6 + - + +
96A VAL* 2.9 8.5 + - - +
97A HIS* 2.7 66.0 + - + +
103A ILE* 4.0 9.9 - - + -
178A ALA 4.0 14.6 - - - +
179A GLY* 3.4 19.3 - - - +
180A PHE* 3.9 36.6 - - + +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS* 3.0 40.6 + - + +
91A GLN* 3.9 7.5 - - - +
93A VAL* 1.3 77.5 - - + +
95A ALA* 1.3 57.5 + - - +
97A HIS* 3.8 9.2 - - + +
98A ALA* 2.8 31.4 + - - +
178A ALA 6.1 0.2 - - - +
207B GLN* 5.4 6.4 + - + +
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA* 4.2 24.7 - - + +
51A ALA* 4.3 10.2 - - + +
91A GLN 3.0 19.5 + - - +
92A VAL 3.4 6.3 - - - +
94A GLU* 1.3 78.8 - - - +
96A VAL* 1.3 63.1 + - - +
98A ALA* 3.5 7.6 + - - +
99A LYS* 3.5 23.4 + - - +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TYR* 3.9 18.8 - - + -
51A ALA 4.5 0.2 - - - +
54A THR* 3.4 27.9 - - + +
60A LEU* 3.9 20.2 - - + -
92A VAL 3.1 17.1 + - - +
93A VAL 2.9 9.6 + - - +
95A ALA* 1.3 75.4 - - - +
97A HIS* 1.3 63.9 + - - +
99A LYS 3.2 8.1 + - - -
100A GLY 3.2 0.2 + - - -
101A GLY* 3.1 43.6 + - - +
103A ILE* 4.0 28.5 - - + -
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Residues in contact with HIS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 2.7 38.0 + - + +
94A GLU* 3.9 8.1 - - + +
96A VAL* 1.3 70.9 - - - +
98A ALA* 1.3 60.3 + - - +
100A GLY* 2.8 21.0 + - - -
101A GLY 3.3 15.7 + - - -
102A PHE* 5.6 0.7 - + - -
103A ILE* 4.2 5.6 - - + -
179A GLY* 3.3 23.1 + - - -
181A ASP* 3.0 37.2 + - - -
158B ALA* 4.7 8.7 - - - +
159B SER* 5.2 1.7 - - - -
207B GLN* 5.0 11.2 + - - +
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLU 2.8 22.3 + - - +
95A ALA* 3.6 9.2 - - - +
97A HIS* 1.3 73.6 - - - +
99A LYS* 1.3 61.6 + - + +
100A GLY 3.3 0.3 + - - -
162B PRO* 3.3 22.2 - - - +
207B GLN* 5.1 7.1 - - + +
208B TYR* 4.0 10.7 + - - +
217B ARG* 5.8 6.3 - - - +
221B GLN* 3.7 29.1 - - - +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 3.7 39.4 + - + +
52A GLN* 5.7 2.1 + - - +
54A THR* 3.8 22.7 + - + +
55A THR 3.8 1.7 - - - -
56A PRO* 3.6 21.9 - - + +
95A ALA 3.5 5.7 + - - +
96A VAL 3.2 2.9 + - - +
97A HIS 3.2 0.8 - - - -
98A ALA* 1.3 80.0 - - + +
100A GLY* 1.3 59.4 + - - +
101A GLY 3.4 4.0 + - - -
162B PRO* 3.6 14.6 - - + +
221B GLN* 6.1 0.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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