Contacts of the helix formed by residues 75 - 89 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PRO* 5.0 0.2 - - - -
73A GLY 3.9 2.2 + - - -
74A GLU* 1.3 79.0 - - - +
76A ASN* 1.3 59.7 + - - +
77A GLU* 3.6 13.6 + - - +
78A ASP* 3.0 34.2 + - - +
79A ALA* 2.9 27.3 + - - +
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Residues in contact with ASN 76 (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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33A LEU* 4.5 11.3 - - - +
34A ALA 4.7 1.6 + - - -
35A PHE* 4.8 2.0 - - + +
70A PRO* 3.5 23.8 - - - +
74A GLU 3.7 1.0 + - - -
75A SER* 1.3 71.0 - - - +
77A GLU* 1.3 65.5 + - - +
79A ALA* 3.2 8.0 + - - +
80A VAL* 3.0 33.8 + - - +
119A PRO* 3.5 27.6 - - - +
121A PHE* 3.4 28.0 - - + -
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Residues in contact with GLU 77 (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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75A SER* 3.7 12.0 - - - +
76A ASN* 1.3 87.5 + - - +
78A ASP* 1.3 65.2 + - - +
80A VAL* 3.5 4.3 + - - +
81A ILE* 3.1 31.4 + - + +
95A PRO* 3.8 40.2 - - + +
121A PHE* 3.7 18.0 - - + -
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Residues in contact with ASP 78 (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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74A GLU* 3.6 17.1 - - + +
75A SER* 3.0 26.6 + - - +
77A GLU* 1.3 77.8 - - - +
79A ALA* 1.3 58.5 + - - +
81A ILE* 3.4 17.0 + - - +
82A ARG* 2.8 30.3 + - - +
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Residues in contact with ALA 79 (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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35A PHE* 3.4 28.6 - - + -
70A PRO* 3.8 16.4 - - + -
74A GLU* 3.4 26.2 + - - +
75A SER 2.9 10.8 + - - +
76A ASN 3.2 8.3 + - - +
78A ASP* 1.3 72.4 - - - +
80A VAL* 1.3 61.0 + - - +
82A ARG* 3.3 6.6 + - - +
83A ARG* 2.8 28.8 + - - +
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Residues in contact with VAL 80 (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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35A PHE* 3.4 30.2 - - + -
37A SER* 3.4 27.4 - - - +
76A ASN 3.0 21.0 + - - +
77A GLU* 3.7 8.1 - - - +
78A ASP 3.2 0.2 - - - -
79A ALA* 1.3 78.6 - - - +
81A ILE* 1.3 57.3 - - - +
83A ARG* 3.1 1.2 + - - +
84A CYS* 2.8 45.8 + - - -
92A ILE* 4.0 13.5 - - + -
95A PRO* 4.1 9.2 - - + -
121A PHE* 4.0 22.4 - - + -
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Residues in contact with ILE 81 (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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77A GLU* 3.1 25.1 + - + +
78A ASP* 3.6 16.6 - - - +
80A VAL* 1.3 78.1 - - - +
82A ARG* 1.3 63.6 + - - +
84A CYS* 3.3 3.4 + - - +
85A ARG* 3.0 56.2 + - - +
90A VAL 4.8 0.3 - - - +
91A GLU* 5.7 0.4 - - - +
92A ILE* 3.9 31.9 - - + +
93A THR 5.6 0.2 - - - +
94A PRO* 5.5 1.8 - - + -
95A PRO* 4.0 13.9 - - + -
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Residues in contact with ARG 82 (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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4A GLU* 3.7 21.6 + - - -
69A HIS 3.0 24.5 + - - -
70A PRO* 3.8 2.4 - - - +
71A GLN* 3.8 13.3 - - - +
74A GLU* 2.5 43.3 + - - +
78A ASP 2.8 19.3 + - - +
79A ALA* 3.4 9.8 + - - +
81A ILE* 1.3 73.9 - - - +
83A ARG* 1.3 79.9 + - - +
85A ARG* 3.2 10.2 + - - +
86A TYR* 2.8 31.4 + - + +
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Residues in contact with ARG 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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4A GLU* 3.9 18.1 + - - -
21A LYS* 3.8 11.1 - - - +
35A PHE* 3.5 35.2 - - + -
66A VAL* 3.8 13.1 - - + +
67A CYS 4.6 0.2 - - - +
68A GLY* 4.3 6.7 - - - -
69A HIS 5.6 0.7 - - - +
79A ALA 2.8 13.5 + - - +
82A ARG* 1.3 98.9 - - - +
84A CYS* 1.3 58.0 + - - +
86A TYR* 3.3 31.1 - - - -
87A GLU* 2.8 48.0 + - - +
135A GLU* 3.4 30.7 + - - -
186A EIP 3.3 27.6 + - - -
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Residues in contact with CYS 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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39A LEU* 3.8 17.9 - - - -
66A VAL* 3.5 30.3 - - - -
80A VAL* 2.8 34.3 + - - +
81A ILE* 3.7 6.3 - - - +
82A ARG 3.2 0.2 - - - -
83A ARG* 1.3 77.1 - - - +
85A ARG* 1.3 63.4 + - - +
88A LEU* 3.0 24.7 + - - +
89A GLY 3.0 5.9 + - - -
90A VAL* 3.2 25.4 + - + +
92A ILE* 4.0 14.1 - - + -
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Residues in contact with ARG 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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81A ILE* 3.0 39.8 + - - +
82A ARG* 3.5 10.0 - - - +
84A CYS* 1.3 78.7 - - - +
86A TYR* 1.3 59.3 + - - +
89A GLY* 2.8 26.2 + - - -
90A VAL 3.8 14.8 - - - +
91A GLU* 2.7 44.4 + - - +
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Residues in contact with TYR 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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82A ARG* 2.8 20.8 + - + +
83A ARG* 3.3 37.7 - - - +
85A ARG* 1.3 81.0 - - - +
87A GLU* 1.3 62.3 + - + +
89A GLY 4.7 0.3 + - - -
132A ASN* 2.9 47.9 + - - +
134A ASP* 5.5 4.3 + - - +
135A GLU* 3.5 21.0 + - - -
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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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65A SER 4.7 2.4 - - - +
66A VAL* 3.6 25.4 - - + +
67A CYS 3.1 3.3 - - - +
83A ARG* 2.8 44.3 + - - +
86A TYR* 1.3 76.8 - - + +
88A LEU* 1.3 71.4 + - + +
131A ILE* 4.3 0.2 - - - -
132A ASN* 3.2 32.4 + - - +
135A GLU* 4.0 18.0 - - + +
136A VAL* 4.2 12.0 - - + +
185A MG 1.9 34.2 - - - -
186A EIP 2.8 6.9 + - - -
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Residues in contact with LEU 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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39A LEU* 3.9 20.6 - - + -
47A LEU* 3.8 26.9 - - + -
49A THR* 4.4 10.8 - - + -
65A SER 4.0 15.0 - - - +
66A VAL* 4.5 7.0 - - + -
84A CYS* 3.0 12.4 + - - +
87A GLU* 1.3 93.9 - - + +
89A GLY* 1.3 63.6 + - - +
90A VAL* 2.9 11.9 + - + +
129A LEU* 3.5 9.7 - - + +
130A GLN 2.9 28.1 + - - -
131A ILE* 4.0 18.6 - - + +
136A VAL* 4.0 19.5 - - + -
139A TYR* 6.1 0.2 - - + -
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Residues in contact with GLY 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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84A CYS 3.0 0.4 + - - -
85A ARG* 2.8 27.8 + - - -
86A TYR 4.5 0.4 + - - -
87A GLU 3.8 0.6 - - - -
88A LEU* 1.3 74.2 - - - +
90A VAL* 1.3 55.8 + - - +
91A GLU* 5.6 1.3 - - - +
127A SER* 4.2 3.3 + - - -
128A ALA 3.8 9.7 - - - +
130A GLN* 3.2 25.5 + - - +
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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