Contacts of the strand formed by residues 74 - 82 (chain A) in PDB entry 1VRR
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 LYS 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A GLU* 5.7 1.1 - - - -
72A GLY 3.2 7.0 + - - +
73A TRP* 1.3 74.3 - - - +
75A GLU* 1.3 67.3 + - + +
119A ASP 3.3 5.0 - - - +
121A VAL* 2.8 37.2 + - - +
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Residues in contact with GLU 75 (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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65A LYS* 5.9 2.2 + - - +
74A LYS* 1.3 81.8 - - - +
76A SER* 1.3 63.5 + - - +
77A ARG* 6.1 0.4 - - + -
117A GLN* 3.0 27.3 + - - +
118A THR 3.5 4.9 - - - +
119A ASP* 3.4 22.4 + - + +
121A VAL* 5.2 0.2 - - - -
13C A 5.6 7.4 - - - +
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Residues in contact with SER 76 (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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74A LYS 4.0 0.2 + - - -
75A GLU* 1.3 76.6 - - - +
77A ARG* 1.3 65.5 + - - +
78A THR* 5.2 0.3 + - - -
116A ASN 3.9 0.5 - - - +
117A GLN* 3.6 5.2 + - - -
118A THR* 3.1 30.0 + - - -
121A VAL* 3.8 28.7 - - - +
148A PHE* 4.0 21.2 - - - -
153A LYS* 5.7 3.3 + - - +
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Residues in contact with ARG 77 (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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75A GLU* 6.1 1.1 - - + -
76A SER* 1.3 79.4 + - - +
78A THR* 1.3 66.2 + - - +
79A ASN* 3.4 32.7 + - - +
115A TYR* 3.4 47.8 + - + -
116A ASN 3.4 10.3 - - - +
117A GLN* 3.2 29.2 + - - +
153A LYS* 5.7 0.6 + - - -
13C A 4.1 17.4 + - - -
14C A 3.4 43.7 + - - -
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Residues in contact with THR 78 (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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76A SER* 5.2 0.2 + - - -
77A ARG* 1.3 74.0 - - - +
79A ASN* 1.3 68.8 + - - +
80A TYR* 3.6 11.2 - - + -
115A TYR* 3.1 5.4 - - - -
116A ASN* 3.0 40.0 + - - +
148A PHE* 3.8 21.9 - - + -
153A LYS* 3.4 28.3 + - - +
186B ARG* 5.7 3.6 - - - +
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Residues in contact with ASN 79 (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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77A ARG* 3.4 42.6 + - - +
78A THR* 1.3 80.2 - - - +
80A TYR* 1.3 65.8 + - - +
81A TYR* 6.3 1.1 - - + -
97A PRO* 3.5 31.4 - - + +
100A GLN* 4.6 0.5 + - - +
114A SER 3.7 5.8 + - - +
115A TYR* 3.6 11.1 - - - +
14C A 5.5 2.2 + - - -
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Residues in contact with TYR 80 (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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78A THR* 3.6 17.7 - - + -
79A ASN* 1.3 77.6 - - - +
81A TYR* 1.3 69.8 + - - +
82A VAL* 3.7 11.7 - - + -
97A PRO* 5.0 0.4 - - - -
100A GLN* 3.3 16.4 - - - +
113A LYS* 3.8 3.1 - - - +
114A SER* 2.9 57.3 + - - +
115A TYR* 3.7 12.8 + - - -
116A ASN* 2.8 34.8 + - + -
139A TYR* 5.4 0.3 + - - -
182B TYR* 3.4 48.2 - + - +
183B ASN* 4.2 6.1 + - - -
186B ARG* 3.6 16.6 + - - -
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Residues in contact with TYR 81 (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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79A ASN* 6.3 1.3 - - + -
80A TYR* 1.3 80.5 - - - +
82A VAL* 1.3 61.1 + - - +
89A ILE* 5.5 0.5 - - - +
92A THR* 4.8 6.4 + - - -
97A PRO* 3.6 38.8 - - + -
98A GLU* 4.5 2.2 - - - -
100A GLN* 3.2 13.5 + - + +
101A LYS* 3.8 37.4 + - + +
104A ILE* 3.8 24.4 - - + +
111A ALA* 3.9 18.8 - - + -
112A LEU 3.2 6.5 - - - -
113A LYS* 3.8 34.7 - - + +
182B TYR* 3.8 15.6 + - - -
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Residues in contact with VAL 82 (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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80A TYR* 3.7 17.3 - - + -
81A TYR* 1.3 77.2 - - - +
83A THR* 1.3 63.7 + - - +
89A ILE* 5.2 1.1 - - + -
104A ILE* 4.8 1.6 - - - -
110A GLU 3.9 0.7 - - - +
111A ALA* 3.9 1.0 - - - -
112A LEU* 2.8 53.0 + - + +
114A SER* 4.6 3.1 - - - -
176B TYR* 4.2 7.0 - - + +
178B GLU* 4.0 26.9 - - + +
179B GLY* 4.0 12.3 - - - +
182B TYR* 3.4 40.8 - - + -
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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