Contacts of the helix formed by residues 75 - 89 (chain B) in PDB entry 2G73
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 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B PRO* 5.0 0.2 - - - -
73B GLY 4.1 1.4 + - - -
74B GLU* 1.3 74.9 - - - +
76B ASN* 1.3 65.4 + - - +
77B GLU* 3.6 17.4 + - - +
78B ASP* 2.9 42.4 + - - -
79B ALA* 3.0 20.8 + - - +
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Residues in contact with ASN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.3 34.6 - - - +
34B ALA 5.3 0.2 + - - -
35B PHE* 4.7 3.3 - - + -
70B PRO* 3.4 14.8 - - + +
74B GLU 4.8 1.8 + - - -
75B SER* 1.3 72.6 - - - +
77B GLU* 1.3 64.8 + - - +
79B ALA* 3.3 8.6 + - - +
80B VAL* 3.0 32.5 + - - +
119B PRO* 3.9 19.6 - - + +
121B PHE* 3.9 21.8 - - + -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B SER* 3.0 19.4 + - - +
76B ASN* 1.3 86.7 + - - +
78B ASP* 1.3 56.2 + - - +
80B VAL* 3.2 7.5 + - - +
81B ILE* 3.0 34.3 + - + +
95B PRO* 3.9 27.3 - - + +
121B PHE* 3.3 31.4 - - + -
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Residues in contact with ASP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY 5.4 0.3 - - - +
74B GLU* 3.7 17.6 - - + +
75B SER* 2.9 37.4 + - - +
77B GLU* 1.3 73.2 - - - +
79B ALA* 1.3 61.4 - - - +
81B ILE* 3.2 15.4 + - - +
82B ARG* 2.8 30.1 + - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 3.4 25.6 - - + -
70B PRO* 3.7 19.1 - - + -
74B GLU* 3.4 26.9 + - - +
75B SER 3.0 9.2 + - - +
76B ASN 3.4 8.5 - - - +
78B ASP* 1.3 75.0 - - - +
80B VAL* 1.3 66.1 + - - +
82B ARG* 3.3 5.5 + - - +
83B ARG* 2.9 23.2 + - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 3.3 30.9 - - + -
37B SER* 3.8 24.5 - - - +
76B ASN 3.0 20.8 + - - +
77B GLU* 3.2 9.4 + - - +
79B ALA* 1.3 76.3 - - - +
81B ILE* 1.3 63.3 + - - +
83B ARG* 4.1 1.0 - - - +
84B CYS* 3.0 28.4 + - - -
92B ILE* 3.9 19.1 - - + -
95B PRO* 4.4 9.2 - - + -
121B PHE* 3.9 24.9 - - + -
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLU* 3.0 21.3 + - + +
78B ASP* 3.2 18.4 + - - +
80B VAL* 1.3 77.1 - - - +
82B ARG* 1.3 63.7 + - - +
84B CYS* 3.3 2.8 + - - +
85B ARG* 3.2 54.7 + - + +
90B VAL 4.9 0.3 - - - +
91B GLU* 5.6 0.4 - - - +
92B ILE* 4.0 30.2 - - + +
93B THR 6.4 0.2 - - - -
94B PRO* 6.1 0.9 - - + -
95B PRO* 4.7 10.1 - - + -
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLU* 3.9 9.9 + - - -
69B HIS 3.1 24.5 + - - -
70B PRO* 4.1 0.2 - - - +
71B GLN* 3.6 13.1 - - - +
74B GLU* 2.6 41.9 + - - +
78B ASP 2.8 19.2 + - - +
79B ALA* 3.3 7.0 + - - +
81B ILE* 1.3 75.1 - - - +
83B ARG* 1.3 89.6 + - - +
85B ARG* 3.1 11.9 + - - +
86B TYR* 2.9 28.4 + - + +
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLU* 3.5 23.4 + - - -
21B LYS* 4.5 4.0 - - - +
35B PHE* 3.5 35.4 - - + -
66B VAL* 3.8 13.0 - - + +
68B GLY* 4.3 6.7 - - - -
69B HIS 5.1 0.4 - - - +
79B ALA 2.9 12.4 + - - +
82B ARG* 1.3 92.6 - - - +
84B CYS* 1.3 61.6 + - - +
86B TYR* 3.3 33.2 - - - +
87B GLU* 2.8 49.5 + - - +
135B GLU* 3.3 25.1 + - - -
186B EIP 3.3 30.7 + - - -
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Residues in contact with CYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.6 28.7 - - - -
66B VAL* 3.6 19.1 - - - -
80B VAL* 3.0 35.0 + - - +
81B ILE* 3.7 5.4 - - - +
82B ARG 3.2 0.2 - - - -
83B ARG* 1.3 79.1 - - - +
85B ARG* 1.3 56.2 + - - +
88B LEU* 3.1 12.8 + - - +
89B GLY 3.0 20.6 + - - -
90B VAL* 3.0 29.4 + - + +
92B ILE* 4.0 13.2 - - + -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ILE* 3.2 36.1 + - - +
82B ARG* 3.1 11.9 + - - +
84B CYS* 1.3 77.8 - - - +
86B TYR* 1.3 60.3 + - - +
89B GLY* 2.9 23.1 + - - -
90B VAL 3.9 13.2 - - - +
91B GLU* 2.7 44.9 + - - +
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Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG* 2.9 19.4 + - + +
83B ARG* 3.3 40.8 - - - +
85B ARG* 1.3 81.4 - - - +
87B GLU* 1.3 59.8 + - + +
89B GLY 4.7 0.3 + - - -
130B GLN 5.5 0.2 - - - +
132B ASN* 2.9 50.8 + - - +
134B ASP* 5.0 7.8 + - - +
135B GLU* 3.5 29.1 + - + +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B SER 4.7 1.9 - - - +
66B VAL* 3.7 25.1 - - + +
67B CYS 3.2 2.4 + - - +
83B ARG* 2.8 46.7 + - - +
86B TYR* 1.3 76.1 - - + +
88B LEU* 1.3 73.8 + - + +
89B GLY 3.7 0.7 - - - -
131B ILE* 3.9 0.2 - - - -
132B ASN* 2.9 31.5 + - - +
135B GLU* 4.1 22.2 - - + -
136B VAL* 4.1 13.7 - - + +
185B MG 2.0 33.0 - - - -
186B EIP 3.2 0.7 + - - -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.0 20.2 - - + -
47B LEU* 3.8 23.1 - - + -
49B THR* 4.0 19.7 - - + -
65B SER 3.9 17.0 - - - +
66B VAL* 4.3 8.3 - - + -
84B CYS* 3.1 12.4 + - - +
87B GLU* 1.3 89.9 - - + +
89B GLY* 1.3 63.5 + - - +
90B VAL* 3.0 9.7 + - + +
129B LEU* 3.5 12.6 - - + +
130B GLN 2.9 28.8 + - - -
131B ILE* 3.7 24.2 - - + +
136B VAL* 4.0 11.0 - - + -
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Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B CYS 3.0 0.6 + - - -
85B ARG* 2.9 28.3 + - - -
86B TYR 4.4 0.2 - - - -
87B GLU 3.7 0.4 - - - -
88B LEU* 1.3 77.4 - - - +
90B VAL* 1.3 57.6 + - - +
91B GLU* 4.1 3.5 + - - +
127B SER* 4.1 2.8 + - - -
128B ALA 4.0 7.1 - - - +
130B GLN* 3.3 25.8 + - - +
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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