Contacts of the strand formed by residues 73 - 84 (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 GLU 73 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70W PRO* 3.6 28.2 - - + +
71W THR 5.4 0.4 - - - -
72W GLU* 1.3 81.1 - - - +
74W SER* 1.3 64.1 + - - +
97W LEU* 3.7 27.2 - - + +
98W GLN 3.2 14.6 - - - +
99W HIS* 3.8 13.8 + - + -
100W ASN* 3.6 5.4 + - - +
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Residues in contact with SER 74 (chain W).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73W GLU* 1.3 73.6 - - - +
75W ASN* 1.3 74.1 + - - +
97W LEU* 3.7 7.2 - - - +
98W GLN* 2.9 33.7 + - - +
100W ASN* 2.8 32.9 + - - -
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Residues in contact with ASN 75 (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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74W SER* 1.3 88.5 + - - +
76W ILE* 1.3 62.8 + - - +
77W THR* 5.6 0.4 - - - -
95W SER* 3.4 21.4 + - - +
96W PHE 3.2 16.4 - - - +
97W LEU* 4.0 13.1 + - - +
98W GLN* 4.6 1.7 - - - +
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Residues in contact with ILE 76 (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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13V GLU* 5.0 9.4 - - - +
15V VAL* 3.8 22.7 - - + -
23V ARG* 6.0 1.6 - - - +
54W LEU* 3.9 16.2 - - + -
75W ASN* 1.3 76.0 - - - +
77W THR* 1.3 71.6 + - - +
78W MET* 3.8 14.0 + - + -
94W MET 3.8 0.7 - - - +
95W SER* 3.6 1.5 - - - -
96W PHE* 2.9 37.6 + - + +
98W GLN* 3.5 41.5 - - + +
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Residues in contact with THR 77 (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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13V GLU 5.3 1.8 + - - -
14V VAL* 3.5 18.1 - - + -
15V VAL* 2.9 24.5 + - - +
75W ASN* 5.6 0.3 - - - +
76W ILE* 1.3 76.8 - - - +
78W MET* 1.3 67.2 + - - +
93W GLU* 3.7 40.2 - - + +
94W MET 3.4 13.2 - - - +
95W SER* 4.4 10.5 + - - +
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Residues in contact with MET 78 (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* 4.4 2.2 - - - -
15V VAL* 3.5 18.6 - - + +
20V VAL* 3.8 21.1 - - + -
23V ARG* 5.0 4.7 - - - +
52W VAL* 3.9 27.8 - - - -
53W PRO* 3.3 32.1 - - + +
54W LEU* 3.9 10.1 - - + -
76W ILE* 3.8 26.9 - - + +
77W THR* 1.3 80.8 - - - +
79W GLN* 1.3 64.9 + - - +
80W ILE* 3.6 5.5 + - + +
93W GLU* 3.5 2.5 - - - -
94W MET* 2.9 31.4 + - - +
96W PHE* 4.0 20.6 - - + -
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Residues in contact with GLN 79 (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* 3.9 15.5 - - + +
15V VAL 2.9 14.9 + - - +
16V LYS* 3.5 29.7 - - - +
17V PHE* 3.0 43.9 + - + +
20V VAL* 3.6 14.4 - - - +
78W MET* 1.3 72.3 - - - +
80W ILE* 1.3 67.7 + - - +
91W ILE* 3.9 25.1 - - + +
92W GLY 3.3 8.5 - - - +
93W GLU* 4.6 7.6 + - + +
6Y ILE* 5.0 10.9 - - - +
13Y GLY 4.9 4.2 - - - +
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Residues in contact with ILE 80 (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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20V VAL* 4.1 3.8 - - + -
35W ILE* 4.0 12.8 - - + -
47W PHE* 3.8 30.1 - - + -
48W LYS 4.0 6.1 - - - +
49W PRO* 4.1 14.6 - - + +
52W VAL* 3.7 30.1 - - + -
78W MET* 4.0 9.9 - - + +
79W GLN* 1.3 83.4 - - - +
81W MET* 1.3 73.2 + - - +
91W ILE* 4.1 3.6 - - - -
92W GLY 2.9 18.6 + - - +
94W MET* 4.2 15.7 - - + -
96W PHE* 4.3 7.4 - - + -
3Y TRP* 2.9 31.4 + - + -
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Residues in contact with MET 81 (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* 3.9 14.8 - - + -
46W ILE 3.6 0.9 - - - +
47W PHE* 3.3 5.2 - - - -
48W LYS* 2.8 62.4 + - + +
80W ILE* 1.3 75.6 - - - +
82W ARG* 1.3 68.9 + - - +
83W ILE* 3.9 25.8 - - + -
89W GLN* 4.1 21.1 - - - +
90W HIS 3.2 12.3 - - - +
91W ILE* 4.0 11.2 - - + +
9Y ALA* 4.1 15.0 - - - -
10Y ASP 4.0 19.3 - - - +
11Y ASP* 4.7 7.9 - - - +
13Y GLY* 4.7 3.1 - - - -
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Residues in contact with ARG 82 (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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45W TYR* 3.5 64.8 + - + -
46W ILE 3.6 2.0 - - - +
47W PHE* 3.6 27.3 - - + -
80W ILE 3.7 1.0 + - - -
81W MET* 1.3 72.1 - - - +
83W ILE* 1.3 64.3 + - - +
84W LYS 4.2 0.3 + - - -
89W GLN* 3.4 1.9 - - - -
90W HIS* 2.8 37.7 + - - +
3Y TRP* 3.4 53.7 - - + +
5Y GLU* 5.4 2.6 - - - +
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Residues in contact with ILE 83 (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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45W TYR* 3.3 6.9 - - - -
46W ILE* 2.8 50.1 + - + +
48W LYS* 4.0 26.9 - - + +
81W MET* 3.9 29.4 - - + -
82W ARG* 1.3 77.8 - - - +
84W LYS* 1.3 61.1 + - - +
85W PRO* 3.3 28.8 - - + +
86W HIS 5.3 0.4 - - - +
88W GLY 3.7 8.1 - - - +
89W GLN* 4.1 12.8 - - + +
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Residues in contact with LYS 84 (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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44W GLU* 3.4 48.5 + - - +
45W TYR* 4.1 19.4 - - + +
82W ARG 4.2 0.6 + - - -
83W ILE* 1.3 71.9 - - - +
85W PRO* 1.3 69.9 - - + +
86W HIS 3.3 0.3 + - - -
87W GLN* 2.6 58.1 + - + +
88W GLY* 3.0 20.7 + - - +
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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