Contacts of the strand formed by residues 1 - 15 (chain A) in PDB entry 5GV2
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 MET 1 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A HIS* 1.3 78.0 - - - +
2A GLU* 1.3 62.5 + - - +
81A VAL* 4.0 10.5 - - + -
82A SER 3.4 22.9 - - - +
83A SER* 3.9 11.7 - - - -
84A HIS 4.3 4.5 - - - +
89A VAL* 3.7 30.5 - - + -
97A ILE* 6.1 2.7 - - - -
140A GLU 4.1 3.4 + - - +
141A PHE* 3.5 27.0 - - + -
142A ASP* 3.0 21.1 + - - +
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Residues in contact with GLU 2 (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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0A HIS 4.6 0.2 - - - +
1A MET* 1.3 77.4 - - - +
3A LEU* 1.3 60.1 + - - +
4A HIS* 3.0 31.6 + - - +
81A VAL* 3.3 7.6 - - - +
82A SER* 2.8 35.5 + - - +
83A SER 3.5 9.2 - - - +
84A HIS* 2.5 41.4 + - - +
85A SER 4.2 1.2 - - - +
86A GLY* 3.3 15.1 + - - -
141A PHE* 4.1 2.9 - - - -
142A ASP* 3.3 11.4 - - + +
144A TYR* 3.6 27.3 + - + -
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Residues in contact with LEU 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU* 1.3 71.9 - - - +
4A HIS* 1.3 64.9 + - - +
5A ILE* 5.0 0.9 - - + -
79A LEU* 4.4 24.7 - - + -
80A ASN 3.6 6.7 - - - +
81A VAL* 3.8 24.2 - - + -
101A VAL* 5.2 7.0 - - + -
123A ILE* 5.8 0.7 - - + -
133A VAL* 4.6 9.9 - - + -
137A LEU* 3.4 33.9 - - + -
141A PHE* 3.8 21.6 - - + +
142A ASP 3.1 6.1 + - - +
143A ILE* 3.2 27.6 - - + +
144A TYR 2.8 27.2 + - - +
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Residues in contact with HIS 4 (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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2A GLU* 3.0 32.5 + - + +
3A LEU* 1.3 76.9 - - - +
5A ILE* 1.3 63.0 + - - +
6A LEU* 3.6 19.3 + - + +
78A VAL 3.6 0.2 - - - +
79A LEU* 3.4 4.6 - - - -
80A ASN* 2.8 49.0 + - + +
82A SER* 3.2 22.7 + - - -
86A GLY* 4.5 4.4 - - - -
144A TYR* 3.3 31.7 - + + +
151A PRO* 4.1 17.5 - - + +
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Residues in contact with ILE 5 (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 LEU* 5.0 3.6 - - + -
4A HIS* 1.3 68.8 - - - +
6A LEU* 1.3 65.6 + - - +
77A LEU* 4.5 11.7 - - + -
78A VAL 3.6 5.2 - - - +
79A LEU* 3.5 26.0 - - + -
130A LEU* 3.8 27.8 - - + -
133A VAL* 5.6 2.0 - - + -
134A ILE* 4.4 9.9 - - + -
143A ILE* 3.6 28.7 - - + -
144A TYR 2.8 13.4 + - - +
145A ARG* 3.5 39.4 - - + +
146A GLU* 2.8 29.5 + - - +
154A VAL* 4.6 2.7 - - + -
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Residues in contact with LEU 6 (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 HIS* 4.2 22.7 - - + +
5A ILE* 1.3 84.2 - - - +
7A GLU* 1.3 66.2 + - - +
8A HIS* 3.3 21.0 + - + +
77A LEU* 5.3 2.3 - - - +
78A VAL* 2.8 32.8 + - + +
80A ASN* 4.4 8.7 - - + +
122A PHE* 3.7 31.0 - - + -
145A ARG* 4.2 6.6 + - - -
146A GLU* 3.6 19.7 - - + +
234A GLU* 4.1 17.9 - - - +
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Residues in contact with GLU 7 (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 LEU* 1.3 72.6 - - - +
8A HIS* 1.3 66.8 + - + +
9A ARG* 3.5 13.0 + - - +
40A LYS* 3.8 25.8 + - - +
77A LEU* 5.6 0.3 - - - +
145A ARG* 5.6 1.7 + - - +
146A GLU* 2.9 37.9 + - - +
147A VAL* 4.0 0.2 - - - -
148A GLY* 3.1 29.7 + - - -
149A GLY* 3.1 20.3 + - - -
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Residues in contact with HIS 8 (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 LEU* 3.3 27.1 - - + +
7A GLU* 1.3 81.4 + - + +
9A ARG* 1.3 62.3 + - - +
10A VAL* 4.0 9.9 - - + -
40A LYS* 4.0 39.2 + - + +
41A PHE* 3.9 27.9 - + + +
56A ASP* 4.6 7.7 + - + -
76A TRP 3.7 8.5 - - - +
77A LEU* 3.9 15.1 - - - +
78A VAL* 3.9 17.9 + - + -
146A GLU* 5.1 1.1 + - - -
233A ILE* 4.7 1.4 - - + +
234A GLU* 2.7 43.1 + - + +
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Residues in contact with ARG 9 (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 GLU 3.5 11.0 + - - +
8A HIS* 1.3 77.8 - - - +
10A VAL* 1.3 60.4 + - - +
56A ASP* 3.2 5.0 - - - +
57A GLU* 3.0 67.9 + - + +
75A THR* 3.8 15.4 + - + +
76A TRP 3.6 4.0 - - - -
77A LEU* 4.2 16.6 - - + +
127A GLU* 3.1 36.8 + - - +
145A ARG* 5.3 6.9 - - - +
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Residues in contact with VAL 10 (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 HIS* 4.0 10.3 - - + -
9A ARG* 1.3 78.4 - - - +
11A ARG* 1.3 79.7 + - - +
12A VAL* 4.4 2.5 - - + -
41A PHE* 4.0 16.2 - - + -
54A MET* 4.0 14.1 - - + -
55A VAL 3.3 16.6 - - - +
56A ASP* 4.5 1.8 - - - -
75A THR* 3.7 4.2 - - - +
76A TRP* 2.8 41.6 + - + +
78A VAL* 3.8 28.7 - - + -
124A LEU* 4.0 17.0 - - + -
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Residues in contact with ARG 11 (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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10A VAL* 1.3 81.5 - - - +
12A VAL* 1.3 65.0 + - - +
13A LEU* 4.1 3.8 - - + -
53A LEU 3.8 1.2 - - - +
54A MET* 3.4 4.5 - - - -
55A VAL* 2.7 35.6 + - + +
57A GLU* 4.8 14.1 - - + -
60A PHE* 3.8 51.1 - - + -
71A VAL* 3.4 17.4 - - - +
72A ALA 2.8 30.3 + - - -
73A GLU* 3.7 11.2 + - - +
74A ALA 2.8 21.3 + - - -
75A THR* 3.8 20.8 + - - -
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.4 5.4 - - + -
11A ARG* 1.3 81.4 - - - +
13A LEU* 1.3 67.0 + - - +
52A THR* 6.0 1.3 - - - -
53A LEU 3.5 6.7 - - - +
54A MET* 4.2 23.1 - - + -
71A VAL* 4.4 0.3 - - - +
72A ALA* 2.9 37.0 + - + +
76A TRP* 3.6 26.2 - - + +
113A LEU* 3.8 17.3 - - + -
124A LEU* 4.8 1.3 - - + -
275A PHE* 4.1 16.8 - - + -
300A THR 6.0 0.2 - - - -
301A PHE* 3.8 21.0 - - + +
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Residues in contact with LEU 13 (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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11A ARG* 4.1 8.3 - - + +
12A VAL* 1.3 88.2 - - - +
14A SER* 1.3 58.5 + - - +
52A THR* 3.4 5.7 - - - -
53A LEU* 2.8 50.3 + - + +
55A VAL* 4.4 4.3 - - + -
60A PHE* 3.5 31.4 - - + -
63A LEU* 3.3 34.5 - - + -
69A LEU* 4.4 16.2 - - + -
70A GLN 3.2 8.7 - - - +
71A VAL* 3.6 20.2 - - + -
301A PHE* 3.4 11.7 - - - -
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Residues in contact with SER 14 (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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13A LEU* 1.3 75.1 - - - +
15A VAL* 1.3 59.8 + - - +
16A ALA 4.0 0.8 + - - -
50A ASP* 2.4 35.3 + - - +
51A TYR 3.5 4.7 - - - -
68A PHE 3.4 1.2 - - - +
69A LEU* 3.3 9.1 - - - +
70A GLN* 2.9 43.7 + - - +
301A PHE* 3.5 26.4 - - - -
302A ASN* 4.7 1.7 + - - -
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Residues in contact with VAL 15 (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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14A SER* 1.3 73.0 - - - +
16A ALA* 1.3 78.1 + - - +
17A ARG 3.4 0.7 + - - -
19A GLY* 4.0 4.9 - - - -
20A LEU* 3.7 31.0 - - + +
23A TYR* 4.0 16.6 - - + -
27A LEU* 5.6 2.5 - - + -
44A LEU* 5.4 2.0 - - + -
50A ASP* 3.5 4.2 - - - +
51A TYR* 2.9 51.7 + - + +
53A LEU* 4.9 16.4 - - + -
68A PHE 3.3 7.9 - - - +
69A LEU* 4.1 14.1 - - + -
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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