Contacts of the strand formed by residues 57 - 66 (chain A) in PDB entry 1VFQ
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LYS* 4.9 4.2 - - - +
31A TYR* 3.1 69.9 + - + +
33A GLY 4.8 2.8 + - - -
55A ASP 5.9 0.2 - - - -
56A VAL* 1.3 85.6 - - + +
58A LEU* 1.3 64.3 + - - +
81A TRP 3.2 10.5 - - - +
82A ILE* 4.4 7.2 - - + -
86A VAL* 4.2 22.7 - - + -
90A GLN* 3.3 35.6 + - - +
93A LYS* 4.0 8.1 - - - +
94A THR* 2.7 46.0 + - + +
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Residues in contact with LEU 58 (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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28A THR* 4.3 11.4 - - + -
29A PHE 3.5 14.8 - - - +
30A LYS* 4.9 6.3 - - + +
31A TYR* 5.5 0.2 - - - -
48A PHE* 4.1 20.9 - - + -
51A GLN* 3.9 39.3 - - + +
52A CYS* 4.1 3.1 - - - -
56A VAL* 4.3 12.6 - - + -
57A ARG* 1.3 75.8 - - - +
59A PHE* 1.3 84.0 + - - +
60A ALA* 4.2 1.8 - - + -
79A ILE 5.1 0.2 - - - +
80A THR* 3.7 2.8 - - - +
81A TRP* 2.8 52.3 + - + +
94A THR* 5.3 0.8 - - - +
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Residues in contact with PHE 59 (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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28A THR* 3.1 6.8 - - - -
29A PHE* 2.8 56.8 + - + +
31A TYR* 3.7 34.3 - + - -
36A ILE* 3.9 7.4 - - + -
58A LEU* 1.3 77.0 - - - +
60A ALA* 1.3 62.6 + - - +
78A LEU* 4.8 5.2 - - + -
79A ILE 3.2 7.0 - - - +
80A THR* 3.4 35.0 - - + -
94A THR* 3.7 22.9 - - + -
97A ASP* 3.9 8.5 - - + -
98A LYS* 3.8 22.0 - - + -
101A VAL* 3.9 29.8 - - + -
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Residues in contact with ALA 60 (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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27A VAL 3.3 11.2 - - - +
28A THR* 4.3 0.7 - - + -
29A PHE* 4.5 3.1 - - - -
48A PHE* 3.5 38.8 - - + -
58A LEU* 4.2 1.8 - - + -
59A PHE* 1.3 78.0 - - - +
61A PHE* 1.3 61.6 + - - +
62A VAL* 4.1 8.7 - - + -
77A ALA 3.6 0.9 - - - +
78A LEU* 3.4 10.0 - - - +
79A ILE* 2.7 40.7 + - + +
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Residues in contact with PHE 61 (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 TYR* 3.5 39.3 - + - -
17A VAL* 3.5 38.5 - - + +
18A ARG* 3.5 28.5 - - + -
26A TRP* 3.5 2.9 - - - -
27A VAL* 3.0 39.8 + - + -
29A PHE* 4.1 11.6 - - + -
60A ALA* 1.3 73.4 - - - +
62A VAL* 1.3 61.2 + - - +
76A PHE* 3.6 24.9 - + + -
77A ALA 3.4 11.0 - - - -
105A VAL* 3.4 21.3 - - + -
107A ASN 3.3 19.5 - - - -
108A PHE* 4.2 4.5 - - + -
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Residues in contact with VAL 62 (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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17A VAL* 4.2 4.7 - - - -
25A ILE* 3.2 12.6 - - + +
26A TRP* 4.0 14.6 - - + -
45A TYR* 4.0 18.2 - - + -
48A PHE* 4.8 3.1 - - + -
60A ALA* 4.2 13.2 - - + -
61A PHE* 1.3 86.9 - - - +
63A ARG* 1.3 68.9 + - - +
64A PHE* 3.4 35.8 + - + -
75A LYS 3.7 1.0 - - - +
76A PHE* 3.2 6.4 - - - +
77A ALA 2.8 37.5 + - - +
79A ILE* 4.4 16.2 - - + -
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Residues in contact with ARG 63 (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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17A VAL* 3.2 38.1 + - + +
18A ARG 3.3 19.6 + - - -
19A ASP 3.8 7.1 + - - -
20A ASP* 3.2 23.8 + - - +
22A SER 5.8 0.4 + - - -
24A VAL 5.6 0.2 - - - -
25A ILE* 2.8 47.0 + - + +
62A VAL* 1.3 73.6 - - - +
64A PHE* 1.3 61.7 + - - +
65A THR* 4.2 1.6 + - - +
74A SER* 2.8 33.8 + - - +
75A LYS 3.7 3.4 - - - +
76A PHE* 3.6 22.9 - - + -
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Residues in contact with PHE 64 (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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25A ILE* 6.4 0.7 - - + -
45A TYR* 3.3 52.5 - + + -
62A VAL* 3.4 29.6 - - + -
63A ARG* 1.3 76.0 - - - +
65A THR* 1.3 60.6 + - - +
66A THR* 3.8 1.7 + - + -
74A SER* 3.4 5.2 + - - -
75A LYS 2.7 41.8 + - - +
77A ALA* 3.8 13.7 - - + -
79A ILE* 4.6 4.0 - - + -
122A GLU* 4.6 5.4 - - + -
125A ILE* 3.7 26.9 - - + -
126A LYS* 3.9 25.4 - - + -
129A LEU* 3.9 25.8 - - + -
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Residues in contact with THR 65 (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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63A ARG* 4.2 1.8 + - - +
64A PHE* 1.3 72.7 - - - +
66A THR* 1.3 61.3 + - - +
72A LYS* 4.1 25.4 - - + -
73A ARG 4.2 4.0 - - - +
74A SER* 4.7 6.5 + - - +
126A LYS* 3.0 29.3 + - - +
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Residues in contact with THR 66 (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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64A PHE* 4.2 9.0 - - + +
65A THR* 1.3 78.8 - - - +
67A GLY* 1.3 62.1 + - - +
72A LYS* 3.3 9.3 - - - +
73A ARG* 2.7 48.4 + - - +
75A LYS* 3.7 35.9 - - + +
126A LYS* 4.5 12.3 - - + +
129A LEU* 4.2 17.5 - - + -
130A LYS* 6.2 5.2 - - - -
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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