Contacts of the strand formed by residues 88 - 99 (chain W) in PDB entry 1VPP
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 88 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83W ILE* 3.7 3.5 - - - +
84W LYS* 3.0 31.3 + - - +
87W GLN* 1.3 80.2 - - - +
89W GLN* 1.3 67.6 + - - +
90W HIS* 4.7 5.8 - - - -
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Residues in contact with GLN 89 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81W MET* 4.1 17.8 - - - +
82W ARG 3.4 7.0 - - - -
83W ILE* 4.1 22.7 - - + +
88W GLY* 1.3 76.4 - - - +
90W HIS* 1.3 71.8 + - - +
8Y ALA* 3.6 2.6 - - - +
9Y ALA 3.1 40.0 + - - +
10Y ASP* 3.3 14.3 - - - +
11Y ASP* 3.0 28.1 + - - +
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Residues in contact with HIS 90 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81W MET* 3.2 6.4 - - - +
82W ARG* 2.8 40.1 + - - +
88W GLY* 4.7 4.0 - - - -
89W GLN* 1.3 89.8 + - - +
91W ILE* 1.3 59.3 + - - +
3Y TRP* 3.5 22.4 - - + -
5Y GLU* 2.7 30.4 + - + +
7Y CYS 3.2 6.5 - - - +
8Y ALA* 3.6 23.4 + - + +
9Y ALA 4.3 0.4 - - - +
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Residues in contact with ILE 91 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V PHE* 3.6 42.0 - - + -
79W GLN* 3.9 29.2 - - + +
80W ILE 3.8 2.7 - - - -
81W MET* 4.0 15.7 - - + +
90W HIS* 1.3 73.2 - - - +
92W GLY* 1.3 58.6 + - - +
3Y TRP* 3.6 2.5 - - - -
5Y GLU* 3.7 1.2 - - - -
6Y ILE* 2.7 40.7 + - + -
7Y CYS* 2.9 25.1 + - - +
9Y ALA* 3.9 13.8 - - + +
13Y GLY* 3.4 25.4 - - - +
15Y CYS* 5.7 0.4 - - - -
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Residues in contact with GLY 92 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79W GLN* 3.3 6.9 - - - +
80W ILE 2.9 32.1 + - - -
91W ILE* 1.3 73.7 - - - +
93W GLU* 1.3 64.4 + - - -
3Y TRP* 3.3 22.6 - - - -
4Y VAL 3.0 15.3 - - - -
6Y ILE* 3.8 4.3 - - - -
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Residues in contact with GLU 93 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V VAL* 3.6 29.6 - - + +
77W THR* 3.7 26.1 - - + +
78W MET 3.5 2.9 - - - -
79W GLN* 4.6 7.4 + - + +
92W GLY* 1.3 76.7 - - - +
94W MET* 1.4 62.0 + - - +
2Y GLY 3.3 5.2 - - - +
3Y TRP* 3.4 1.6 - - - -
4Y VAL* 2.8 49.8 + - + +
6Y ILE* 4.0 25.4 - - + +
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Residues in contact with MET 94 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35W ILE* 3.5 32.5 - - + -
36W PHE* 4.1 2.9 - - + -
47W PHE* 4.5 7.2 - - - -
77W THR* 3.4 5.3 - - - -
78W MET 2.9 33.7 + - - +
80W ILE* 4.2 15.0 - - + -
92W GLY 4.2 0.2 + - - -
93W GLU* 1.4 77.2 - - - +
95W SER* 1.3 63.3 + - - +
96W PHE* 3.8 28.8 - - + -
1Y ARG 3.4 33.2 - - - +
2Y GLY 4.1 3.8 - - - -
3Y TRP* 3.6 37.9 - - + +
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Residues in contact with SER 95 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75W ASN* 3.4 29.1 + - - +
76W ILE 3.6 5.3 + - - -
77W THR* 4.4 11.4 + - - +
94W MET* 1.3 76.5 - - - +
96W PHE* 1.3 65.9 + - - +
1Y ARG* 5.4 3.5 + - - +
2Y GLY 4.8 3.4 + - - -
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Residues in contact with PHE 96 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35W ILE* 4.0 41.1 - - + -
52W VAL* 4.0 20.4 - - + -
54W LEU* 3.5 28.3 - - + -
75W ASN* 3.2 9.0 - - - -
76W ILE* 2.9 36.0 + - - +
78W MET* 4.0 33.2 - - + -
80W ILE* 4.3 3.8 - - + -
94W MET* 3.8 44.6 - - + -
95W SER* 1.3 78.6 + - - +
97W LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 97 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54W LEU* 3.8 7.8 - - - +
56W ARG* 2.5 47.6 + - - +
73W GLU* 3.7 39.5 - - + +
74W SER 3.7 15.7 - - - +
75W ASN* 4.0 12.2 + - - +
96W PHE* 1.3 73.6 - - - +
98W GLN* 1.3 60.5 + - - +
99W HIS* 4.4 11.2 - - - +
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Residues in contact with GLN 98 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53W PRO 5.0 2.0 + - - -
54W LEU* 3.4 13.3 - - - +
55W MET* 2.8 41.8 + - + +
56W ARG* 3.8 0.7 - - - +
73W GLU* 3.2 10.9 - - - +
74W SER* 2.9 41.5 + - - +
75W ASN 4.6 0.2 - - - -
76W ILE* 3.5 52.2 - - + +
97W LEU* 1.3 72.1 - - - +
99W HIS* 1.3 65.1 + - - +
100W ASN* 3.9 15.3 - - - +
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Residues in contact with HIS 99 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28W PRO* 3.6 7.8 - - - +
55W MET* 3.0 34.9 + - - +
56W ARG* 3.5 27.9 + - + -
57W CYS* 2.8 48.3 + - + +
70W PRO* 3.8 27.3 - - + +
72W GLU 3.8 4.5 - - - +
73W GLU* 3.8 20.5 + - + -
97W LEU* 4.4 9.5 - - + +
98W GLN* 1.3 75.9 - - - +
100W ASN* 1.3 63.2 + - - +
101W LYS 4.9 0.2 - - - +
102W CYS* 4.8 0.7 - - - -
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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