Contacts of the strand formed by residues 73 - 83 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70V PRO* 3.5 26.2 - - + +
72V GLU* 1.3 89.6 + - - +
74V SER* 1.3 66.8 + - - +
97V LEU* 3.6 26.9 - - + +
98V GLN 3.3 8.1 - - - +
99V HIS* 3.7 19.9 + - + -
100V ASN* 3.3 4.2 - - - +
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Residues in contact with SER 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73V GLU* 1.3 79.7 - - - +
75V ASN* 1.3 73.1 - - - +
97V LEU* 3.4 3.4 - - - +
98V GLN* 2.8 45.4 + - - +
100V ASN* 2.7 21.9 + - - -
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Residues in contact with ASN 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74V SER* 1.3 86.2 + - - +
76V ILE* 1.3 61.1 + - - +
77V THR* 5.5 0.4 - - - -
95V SER* 3.3 23.7 + - - +
96V PHE 3.1 6.5 - - - +
97V LEU* 3.5 22.2 + - - +
98V GLN* 3.8 9.3 + - - -
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Residues in contact with ILE 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53V PRO 5.5 0.9 - - - +
54V LEU* 3.7 27.4 - - + -
75V ASN* 1.3 74.9 - - - +
77V THR* 1.3 71.5 + - - +
78V MET* 4.0 20.2 - - + -
94V MET 3.9 0.7 - - - +
95V SER* 3.5 3.2 - - - -
96V PHE* 2.8 41.5 + - + +
98V GLN* 3.7 30.3 - - + +
13W GLU 6.5 0.2 - - - -
15W VAL* 4.3 12.8 - - + -
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Residues in contact with THR 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75V ASN* 5.5 0.7 - - - +
76V ILE* 1.3 75.8 - - - +
78V MET* 1.4 69.1 + - - +
93V GLU* 3.8 39.3 - - + +
94V MET 3.5 11.4 - - - +
95V SER* 4.7 8.3 + - - -
13W GLU 3.5 18.6 + - - -
14W VAL* 3.4 8.8 - - + -
15W VAL* 3.0 23.8 + - - +
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Residues in contact with MET 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52V VAL* 3.9 21.3 - - - -
53V PRO* 3.2 35.2 - - + +
54V LEU* 3.7 17.7 - - + -
76V ILE* 4.0 20.2 - - + -
77V THR* 1.4 81.9 - - - +
79V GLN* 1.3 62.9 + - - +
80V ILE* 3.6 7.4 + - + +
93V GLU* 3.5 1.9 - - - -
94V MET 2.9 31.2 + - - +
96V PHE* 4.2 17.3 - - + -
14W VAL* 4.1 4.5 - - - -
15W VAL* 3.6 20.9 - - + -
20W VAL* 4.0 24.0 - - + -
23W ARG* 5.5 1.6 - - - +
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Residues in contact with GLN 79 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78V MET* 1.3 72.7 - - - +
80V ILE* 1.3 66.7 + - - +
91V ILE* 4.1 9.3 - - + +
92V GLY 3.3 7.0 - - - +
93V GLU* 4.8 1.0 + - + -
14W VAL* 3.7 15.0 - - + +
15W VAL 2.9 15.1 + - - +
16W LYS* 3.4 25.5 - - - +
17W PHE* 2.9 46.4 + - + +
20W VAL* 3.7 12.3 - - - +
6X ILE* 3.7 29.3 - - + +
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Residues in contact with ILE 80 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35V ILE* 4.0 13.0 - - + -
47V PHE* 3.9 11.4 - - + -
48V LYS 3.8 7.9 - - - +
49V PRO* 4.2 5.6 - - + +
52V VAL* 3.7 29.2 - - + -
78V MET* 3.9 14.4 - - + +
79V GLN* 1.3 83.9 - - - +
81V MET* 1.3 75.7 + - - +
91V ILE* 3.4 5.9 - - - -
92V GLY 2.9 31.7 + - - +
94V MET* 3.7 37.5 - - + -
96V PHE* 4.4 4.9 - - + -
17W PHE* 4.5 0.7 - - - -
20W VAL* 4.1 11.7 - - + -
3X TRP* 3.7 3.3 - - - -
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Residues in contact with MET 81 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46V ILE 3.8 0.3 - - - +
47V PHE* 3.3 4.7 - - - -
48V LYS* 2.8 53.6 + - + +
80V ILE* 1.3 76.5 - - - +
82V ARG* 1.3 62.4 + - - +
83V ILE* 4.2 17.3 - - + -
89V GLN* 3.8 33.4 - - + -
90V HIS 3.3 10.8 - - - +
91V ILE* 3.6 10.5 - - + -
17W PHE* 3.4 19.1 - - + -
9X ALA* 5.4 0.2 - - - -
10X ASP 4.0 4.5 - - - +
11X ASP* 4.0 11.0 - - - +
12X TYR 4.0 2.2 - - - -
13X GLY* 3.3 33.9 - - - +
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Residues in contact with ARG 82 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V GLU* 4.9 6.3 + - - -
45V TYR* 3.4 55.6 + - + -
46V ILE 3.5 2.5 - - - -
47V PHE* 3.4 30.0 - - + -
80V ILE 3.9 0.2 + - - -
81V MET* 1.3 72.2 - - - +
83V ILE* 1.3 60.3 + - - +
84V LYS 4.1 0.5 + - - -
89V GLN* 3.4 2.5 - - - -
90V HIS* 2.7 36.9 + - + +
3X TRP* 3.4 72.3 - - + +
5X GLU* 5.3 0.6 + - - -
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Residues in contact with ILE 83 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45V TYR* 3.5 8.8 - - - -
46V ILE* 2.6 62.3 + - + +
48V LYS* 4.5 20.4 - - + -
81V MET* 4.2 15.5 - - + +
82V ARG* 1.3 74.1 - - - +
84V LYS* 1.3 71.2 + - - +
85V PRO* 3.5 11.2 - - + +
86V HIS 5.5 0.2 - - - +
88V GLY 3.7 12.3 - - - +
89V GLN* 4.0 20.0 - - + +
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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