Contacts of the strand formed by residues 72 - 81 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B SER* 3.4 2.9 - - - -
10B GLN* 2.7 55.3 + - - +
11B VAL 4.1 3.2 + - - +
12B HIS* 3.5 37.2 + - + +
13B PRO* 3.5 13.8 - - - +
71B HIS* 1.3 75.9 - - - +
73B ASP* 1.3 82.1 + - - +
74B VAL* 3.3 6.8 + - - -
143B GLU* 2.8 31.5 + - - -
146B GLN* 3.3 33.8 + - - +
148B SER* 5.1 5.5 + - - -
149B ARG* 5.8 1.2 - - - +
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Residues in contact with ASP 73 (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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8B ARG 3.6 5.5 - - - +
9B SER* 3.6 4.3 - - - -
10B GLN* 3.9 16.4 + - + +
72B ARG* 1.3 92.8 + - + +
74B VAL* 1.3 65.1 + - - +
75B VAL* 3.3 14.1 + - - +
141B LEU* 4.4 6.6 - - + +
146B GLN* 3.3 30.3 + - - +
147B PRO* 5.4 3.1 - - - +
333B HIS 5.3 1.6 - - - -
369B TRP* 3.8 34.6 + - + -
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Residues in contact with VAL 74 (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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7B TYR* 4.0 15.5 - - + -
8B ARG 3.5 4.5 - - - -
9B SER* 4.0 4.0 - - - -
62B PHE* 3.7 35.7 - - + -
65B ILE* 5.2 0.4 - - + -
66B GLN* 4.0 29.4 - - + +
71B HIS* 3.8 33.4 - - + +
72B ARG* 4.5 4.7 - - - -
73B ASP* 1.3 74.4 - - - +
75B VAL* 1.3 61.7 + - - +
76B GLU 4.1 0.7 + - - -
333B HIS 4.1 1.6 - - - +
334B ILE* 3.9 21.8 - - - +
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Residues in contact with VAL 75 (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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7B TYR* 3.2 5.0 - - - -
8B ARG* 2.7 52.8 + - + +
73B ASP 3.3 15.7 - - - +
74B VAL* 1.3 74.3 - - - +
76B GLU* 1.3 61.0 + - - +
77B LEU* 3.5 9.6 + - + +
333B HIS 3.8 5.4 - - - +
334B ILE 3.7 3.6 - - - +
335B SER 4.0 0.9 - - - -
336B GLY* 3.4 30.7 - - - +
339B GLN* 3.5 23.1 - - - +
369B TRP* 3.7 26.9 - - + -
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Residues in contact with GLU 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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5B LEU* 4.2 10.3 - - + -
6B ILE 3.9 9.6 - - - +
7B TYR* 4.2 3.8 - - - +
62B PHE* 3.7 15.9 - - + -
74B VAL* 4.1 2.8 + - - +
75B VAL* 1.3 70.1 - - - +
77B LEU* 1.3 62.7 + - - +
78B MET 4.5 5.4 - - - +
79B ARG* 2.7 54.2 + - - +
334B ILE* 2.9 20.6 + - + +
335B SER* 4.0 2.1 - - - -
336B GLY* 2.9 23.7 + - - -
337B THR* 4.3 2.8 + - - -
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Residues in contact with LEU 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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318A GLN* 5.1 1.2 - - - +
351A ASP 5.8 2.2 - - - +
352A LEU* 5.2 3.3 - - - +
6B ILE* 2.9 18.0 + - + +
7B TYR* 4.2 2.2 - - - -
8B ARG* 3.5 57.9 - - + +
48B PHE* 3.7 29.6 - - + -
75B VAL* 3.6 21.1 - - + +
76B GLU* 1.3 79.0 - - - +
78B MET* 1.3 62.8 + - + +
124B ARG* 4.0 14.7 + - - -
128B LEU* 4.8 17.5 - - + +
336B GLY* 3.9 10.8 - - - -
337B THR* 4.0 13.1 + - - +
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Residues in contact with MET 78 (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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293A ARG* 6.3 0.9 - - - +
318A GLN* 5.5 1.3 - - - -
4B THR* 4.4 22.2 - - + +
5B LEU* 3.4 3.8 - - - +
6B ILE* 2.8 59.3 + - + +
76B GLU* 3.9 2.8 - - - +
77B LEU* 1.3 83.3 - - - +
79B ARG* 1.3 69.5 + - - +
80B ASP* 4.5 15.3 - - + +
86B ARG* 6.3 0.9 - - - +
123B ASP* 5.9 0.7 - - - +
124B ARG* 3.4 44.9 - - + +
125B MET* 4.6 7.2 - - + +
128B LEU* 3.9 19.7 - - + -
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Residues in contact with ARG 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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318A GLN* 5.5 5.2 + - - +
3B THR* 4.5 11.2 - - + +
4B THR 3.3 11.7 - - - +
5B LEU* 3.7 18.4 - - + +
55B GLU* 5.6 4.3 + - - +
58B LEU* 5.3 2.6 - - - +
59B GLU* 4.2 27.1 - - - +
62B PHE* 3.6 22.8 - - - +
76B GLU* 2.7 45.5 + - - +
78B MET* 1.3 77.1 - - - +
80B ASP* 1.3 66.9 + - - +
124B ARG* 5.3 0.2 - - - +
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Residues in contact with ASP 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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289A LEU* 4.7 11.5 - - - +
293A ARG* 3.3 35.4 + - - +
318A GLN* 4.8 10.4 + - - +
3B THR* 3.4 6.4 - - - +
4B THR* 2.7 37.0 + - - -
78B MET* 4.5 19.8 - - + +
79B ARG* 1.3 79.2 - - - +
81B TYR* 1.3 80.6 + - - +
124B ARG* 5.5 3.8 + - - +
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Residues in contact with TYR 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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289A LEU* 6.2 0.9 - - + -
290A LYS* 3.6 42.8 - - + +
293A ARG* 3.7 29.4 - - + +
294A VAL* 4.0 20.4 - - + -
1B MET* 3.7 32.1 - - + -
2B LEU 3.4 13.5 - - - +
3B THR* 4.2 11.2 - - + +
4B THR* 4.9 0.4 + - - -
55B GLU* 3.1 29.5 + - + -
80B ASP* 1.3 90.3 + - - +
82B SER* 1.3 60.2 + - - +
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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