Contacts of the strand formed by residues 72 - 81 (chain A) in PDB entry 3GG0
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 ARG 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A SER* 3.5 2.6 - - - -
10A GLN* 2.9 45.8 + - + +
11A VAL 4.0 5.9 + - - +
12A HIS* 3.5 37.2 + - + +
13A PRO* 3.5 23.1 - - - +
14A ASP* 5.3 3.8 + - - -
71A HIS* 1.3 77.8 - - - +
73A ASP* 1.3 86.3 + - - +
74A VAL* 3.4 5.7 + - - -
143A GLU* 3.0 36.4 + - - -
146A GLN* 3.8 26.0 + - - +
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Residues in contact with ASP 73 (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 ARG* 3.4 8.3 - - - +
9A SER* 3.7 3.3 - - - -
10A GLN* 2.9 33.9 + - - +
72A ARG* 1.3 86.9 - - - +
74A VAL* 1.3 64.9 + - - +
75A VAL* 3.3 13.0 + - - +
141A LEU* 3.9 6.6 - - - +
146A GLN* 3.4 30.3 + - - +
147A PRO* 5.4 1.9 - - - +
333A HIS 5.4 1.6 - - - -
369A TRP* 3.9 21.8 + - + -
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Residues in contact with VAL 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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7A TYR* 3.9 15.9 - - + -
8A ARG 3.6 4.3 - - - -
9A SER* 4.1 3.1 - - - -
62A PHE* 3.6 36.5 - - + -
65A ILE* 5.1 0.9 - - + -
66A GLN* 4.4 26.2 + - + +
71A HIS* 3.5 37.9 - - + +
72A ARG* 4.5 3.8 - - - -
73A ASP* 1.3 73.6 - - - +
75A VAL* 1.3 61.8 + - - +
76A GLU 4.2 0.3 + - - -
333A HIS 4.2 0.7 - - - +
334A ILE* 3.8 23.4 - - - +
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Residues in contact with VAL 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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7A TYR* 3.3 3.0 - - - -
8A ARG* 2.9 51.9 + - + +
73A ASP 3.4 15.3 - - - +
74A VAL* 1.3 71.8 - - - +
76A GLU* 1.3 61.8 + - - +
77A LEU* 3.4 3.6 - - + +
333A HIS 3.4 20.6 - - - +
334A ILE 3.7 3.8 - - - +
335A SER 3.9 1.6 - - - -
336A GLY* 3.5 29.4 - - - +
339A GLN* 3.5 20.0 - - - +
369A TRP* 3.6 22.4 - - + -
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Residues in contact with GLU 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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5A LEU* 4.5 4.0 - - + +
6A ILE 3.7 11.7 - - - +
7A TYR* 4.1 4.0 - - - +
62A PHE* 4.3 17.3 - - + -
74A VAL 4.1 1.4 + - - -
75A VAL* 1.3 71.8 - - - +
77A LEU* 1.3 59.6 + - - +
78A MET* 4.1 10.1 + - - +
79A ARG* 2.9 56.7 + - - +
334A ILE 2.9 16.3 + - - +
335A SER* 3.7 2.1 - - - -
336A GLY* 2.7 32.2 + - - -
337A THR* 4.3 0.9 + - - -
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Residues in contact with LEU 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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6A ILE* 2.8 20.6 + - + +
7A TYR* 4.2 2.9 - - - -
8A ARG* 3.6 45.8 - - + +
48A PHE* 3.5 34.3 - - + -
75A VAL* 3.4 21.8 - - + +
76A GLU* 1.3 78.6 - - - +
78A MET* 1.3 61.5 + - - +
124A ARG* 3.5 16.6 + - - -
128A LEU* 4.6 21.2 - - + +
336A GLY* 4.2 9.4 - - - -
337A THR* 4.2 12.8 + - - -
318B GLN* 5.2 0.3 - - - +
351B ASP 5.8 1.3 - - - +
352B LEU* 5.4 2.3 - - - +
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Residues in contact with MET 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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4A THR* 3.9 28.3 - - + +
5A LEU* 3.3 6.6 - - - +
6A ILE* 2.9 54.7 + - + +
76A GLU* 3.8 4.0 - - - +
77A LEU* 1.3 82.9 - - - +
79A ARG* 1.3 67.7 + - - +
80A ASP* 4.1 17.0 - - + -
81A TYR 5.5 2.7 - - - +
82A SER* 6.4 0.2 - - - -
86A ARG* 6.1 3.4 - - - +
123A ASP* 6.1 0.4 - - - +
124A ARG* 3.7 45.1 - - + +
125A MET* 4.7 7.6 - - + +
128A LEU* 4.2 11.0 - - + -
318B GLN* 5.5 1.1 - - - -
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Residues in contact with ARG 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 THR* 4.7 11.2 - - + -
4A THR 3.4 6.1 - - - +
5A LEU* 3.5 25.7 - - + +
55A GLU* 5.5 8.4 + - - +
58A LEU* 5.6 1.6 - - - +
59A GLU* 4.5 30.9 + - - +
62A PHE* 3.6 22.4 - - - -
76A GLU* 2.9 39.9 + - - +
78A MET* 1.3 74.0 - - - +
80A ASP* 1.3 64.9 + - - +
124A ARG* 5.3 0.8 - - - +
318B GLN* 5.3 5.8 + - - +
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Residues in contact with ASP 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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3A THR* 3.3 7.4 - - - +
4A THR* 2.7 40.2 + - - +
78A MET* 4.1 22.3 - - + +
79A ARG* 1.3 77.9 - - - +
81A TYR* 1.3 96.2 + - - +
124A ARG* 4.5 10.5 + - - +
293B ARG* 2.8 37.0 + - - +
318B GLN* 4.6 5.4 + - - +
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Residues in contact with TYR 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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1A MET* 3.5 26.5 - - + -
2A LEU 3.5 6.7 - - - +
3A THR* 4.1 15.0 - - + +
55A GLU* 4.0 23.3 + - + -
78A MET* 5.5 2.6 - - - +
80A ASP* 1.3 101.3 + - - +
82A SER* 1.3 60.4 + - - +
286B ARG* 6.1 3.1 - - - -
290B LYS* 3.6 41.7 - - + +
293B ARG* 4.1 19.9 - - + +
294B VAL* 4.2 16.6 - - + -
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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