Contacts of the strand formed by residues 71 - 79 (chain A) in PDB entry 2GW5
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 GLY 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ARG* 4.6 2.2 - - - -
40A GLU 3.7 8.3 - - - -
41A LYS* 4.7 0.9 - - - -
69A HIS 3.8 0.6 + - - -
70A THR* 1.3 75.5 - - - +
72A ARG* 1.4 63.6 - - - -
73A TYR* 3.6 9.1 - - - -
91A LEU 3.6 1.6 - - - +
92A VAL* 3.7 1.0 - - - -
93A LEU 2.9 31.9 + - - -
183A TYR* 3.4 24.7 - - - +
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Residues in contact with ARG 72 (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 ARG* 3.3 3.1 - - - -
40A GLU* 2.8 74.5 + - + +
71A GLY* 1.4 70.6 - - - -
73A TYR* 1.3 60.8 + - - +
90A PRO* 3.2 39.0 - - + +
91A LEU 3.7 5.2 - - - -
92A VAL* 4.4 12.7 - - + +
183A TYR* 3.2 31.4 - - + +
501A IPA 3.6 10.4 + - - +
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.6 18.6 - - + +
24A LEU* 3.5 29.6 - - + -
37A LEU* 3.7 10.3 - - + -
38A TYR 3.1 19.1 - - - -
39A ARG* 2.7 41.3 + - + -
50A ILE* 3.9 17.0 - - + -
60A PHE* 4.2 8.6 - + - -
62A ILE* 4.8 0.2 - - - +
69A HIS* 2.5 33.7 + - - +
71A GLY 3.6 12.8 - - - -
72A ARG* 1.3 73.8 - - - +
74A GLY* 1.3 58.0 + - - +
90A PRO* 3.1 8.8 - - - +
91A LEU* 2.9 37.4 + - + +
93A LEU* 3.8 19.7 - - + +
501A IPA 3.6 3.5 + - - -
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Residues in contact with GLY 74 (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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8A LEU* 3.9 1.3 - - - -
37A LEU* 3.4 4.8 - - - +
38A TYR* 2.9 33.2 + - - -
73A TYR* 1.3 75.0 - - - +
75A CYS* 1.3 59.9 + - - -
87A LEU* 3.7 7.6 - - - -
88A SER* 3.5 14.6 - - - -
501A IPA 3.3 21.2 - - - -
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Residues in contact with CYS 75 (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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6A PRO* 3.5 7.3 - - - +
8A LEU* 3.9 10.3 - - - -
26A CYS* 2.1 55.4 - - + -
35A TYR* 5.4 0.7 - - + -
36A ARG 3.2 13.2 - - - +
37A LEU* 4.1 12.3 - - + -
74A GLY* 1.3 74.3 - - - +
76A GLN* 1.3 62.3 + - - +
87A LEU* 3.5 5.2 - - - +
88A SER* 2.8 47.1 + - - -
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Residues in contact with GLN 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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6A PRO* 4.1 2.5 - - - -
35A TYR* 3.4 6.9 - - - -
36A ARG* 2.9 36.6 + - + +
38A TYR* 3.4 32.4 + - + -
75A CYS* 1.3 76.9 - - - +
77A TYR* 1.3 61.7 + - - +
84A TRP* 3.5 34.1 - - + +
85A SER* 3.1 33.1 - - - +
86A GLU 3.9 2.9 - - - +
87A LEU* 4.2 15.2 + - + +
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Residues in contact with TYR 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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3A ILE 3.8 5.9 + - - -
4A PRO* 2.5 51.9 + - - +
6A PRO* 3.8 13.7 - - + -
28A GLY* 3.7 22.2 - - - -
29A SER* 3.5 28.2 + - - -
32A ALA* 3.6 22.0 - - + -
34A GLU 3.1 14.6 - - - +
35A TYR* 3.7 17.5 - + + -
76A GLN* 1.3 74.5 - - - +
78A TYR* 1.3 58.9 + - - +
79A SER* 3.8 17.0 + - - -
82A ARG 4.0 0.2 - - - +
84A TRP* 3.4 7.7 - - - -
85A SER* 2.7 47.4 + - - -
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Residues in contact with TYR 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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32A ALA* 3.5 1.4 - - - -
33A GLN* 2.8 62.8 + - + +
34A GLU* 2.9 17.3 + - + +
77A TYR* 1.3 74.4 - - - +
79A SER* 1.3 59.7 + - - +
81A ALA* 3.2 33.4 - - - +
82A ARG* 3.3 26.7 - - - -
84A TRP* 3.6 42.6 - + + -
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Residues in contact with SER 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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3A ILE 5.0 6.9 + - - -
29A SER* 4.2 4.7 + - - -
31A GLU* 3.4 31.9 + - - +
33A GLN* 3.9 10.9 + - - +
77A TYR* 3.8 24.1 + - - -
78A TYR* 1.3 76.3 - - - +
80A ARG* 1.3 84.0 + - - +
81A ALA 3.2 2.9 - - - -
82A ARG* 3.0 22.0 + - - +
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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