Contacts of the strand formed by residues 50 - 59 (chain B) in PDB entry 1R5V
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 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B HIS 3.6 1.0 - - - +
44B PHE* 3.8 0.9 - - - -
45B TYR* 3.2 79.5 + - + +
47B GLY 4.6 0.2 - - - +
48B THR 4.6 0.2 - - - -
49B GLN* 1.3 84.5 - - + +
51B VAL* 1.3 69.4 + - - +
52B ARG* 4.4 9.5 - - - +
70B ASP* 3.4 26.5 + - - -
107B ARG* 4.4 0.4 - - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B HIS 3.4 7.9 - - - +
44B PHE* 3.8 22.9 - - + -
48B THR* 3.9 6.3 - - - +
50B ARG* 1.3 83.6 + - - +
52B ARG* 1.3 69.5 + - - +
69B SER* 4.6 1.0 + - - -
70B ASP* 4.5 5.9 - - - +
102B VAL* 3.8 17.6 - - + +
106B CYS* 3.6 33.0 - - + -
107B ARG* 3.5 49.3 + - + +
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU 3.6 1.6 - - - +
42B CYS* 3.8 0.3 - - - -
43B HIS* 2.9 46.6 + - + +
45B TYR* 4.1 31.3 + - + -
50B ARG* 4.4 7.6 - - - +
51B VAL* 1.3 82.4 - - - +
53B LEU* 1.3 64.4 + - - +
54B LEU* 4.0 27.4 - - - +
66B ARG* 5.5 2.6 - - - +
68B ASP* 2.8 37.1 + - - +
69B SER* 3.6 5.8 - - - +
70B ASP* 3.3 28.6 + - - +
102B VAL* 5.2 0.2 - - - -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B SER* 4.6 6.3 - - - -
41B GLU 3.4 22.9 - - - +
42B CYS* 4.1 3.4 - - - -
52B ARG* 1.3 73.3 - - - +
54B LEU* 1.3 63.2 + - - +
55B VAL* 4.1 22.9 - - + -
67B PHE* 3.5 12.2 - - + +
68B ASP* 3.6 3.1 - - - +
69B SER* 2.8 39.0 + - - -
98B LYS 4.0 8.3 - - - +
101B GLU* 3.7 38.1 - - + +
102B VAL* 3.7 21.8 - - + +
105B VAL* 6.3 0.7 - - + -
106B CYS* 3.9 19.1 - - - -
8E PRO* 6.0 2.9 - - + -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS 3.6 2.1 - - - +
41B GLU* 2.8 58.4 + - - +
43B HIS* 4.5 8.3 - - + +
52B ARG* 4.0 27.1 - - - +
53B LEU* 1.3 74.8 - - - +
55B VAL* 1.3 68.5 + - - +
56B ARG* 3.9 20.3 + - + -
66B ARG* 4.3 25.4 - - + +
67B PHE 3.3 17.0 - - - +
68B ASP* 4.2 13.0 - - + +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B SER* 5.2 3.8 - - - +
39B LYS 3.2 9.2 - - - +
40B SER* 3.6 21.3 - - - +
53B LEU* 4.1 24.5 - - + -
54B LEU* 1.3 74.2 - - - +
56B ARG* 1.3 63.2 + - - +
57B TYR* 3.4 32.8 - - + +
66B ARG* 3.0 8.5 - - - +
67B PHE* 2.9 47.0 + - + +
74B PHE* 5.6 0.2 - - + -
98B LYS* 4.6 17.3 - - + -
101B GLU* 5.2 1.1 - - - +
8E PRO* 5.7 0.4 - - + -
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASP 2.7 30.3 + - - -
142A ASP* 4.1 6.9 - - - +
38B SER* 3.2 6.2 - - - -
39B LYS* 2.8 43.7 + - + +
41B GLU* 3.0 34.9 + - - -
54B LEU* 4.0 20.2 - - + +
55B VAL* 1.3 79.0 - - - +
57B TYR* 1.3 62.4 + - - +
58B PHE* 3.7 31.1 - - + -
63B GLU* 2.9 43.6 + - - +
65B LEU 3.8 3.4 - - - -
66B ARG* 3.6 10.6 - - + +
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Residues in contact with TYR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP* 6.0 2.0 - - - -
69A ASN* 6.1 1.6 - - - -
36B GLU* 4.1 17.3 - - - -
37B TYR 3.7 2.5 - - - -
38B SER* 4.0 19.1 - - - -
55B VAL* 3.4 29.5 - - + +
56B ARG* 1.3 77.2 - - - +
58B PHE* 1.3 61.1 + - - +
63B GLU* 3.3 5.7 - - - +
64B ASN* 2.9 41.3 + - - +
65B LEU* 2.9 33.4 + - + +
66B ARG 4.8 0.2 - - - -
74B PHE* 4.2 12.1 - + - -
88B TRP* 3.8 34.5 - + - -
98B LYS* 4.8 7.3 - - - -
9E LYS 5.5 0.7 + - - -
10E ALA* 5.6 1.2 - - - -
11E ALA* 4.6 14.3 + - - +
13E LYS* 4.3 11.2 - - - +
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ASP 4.2 2.5 - - - -
143A HIS* 3.6 29.2 - - + -
35B LEU 3.6 1.0 - - - +
36B GLU* 3.9 6.6 - - - +
37B TYR* 2.7 65.7 + + + +
39B LYS* 3.7 26.5 - - + -
56B ARG* 3.7 50.3 - - + -
57B TYR* 1.3 75.8 - - - +
59B TYR* 1.3 61.4 + - - +
60B ASN 3.9 10.1 - - - +
62B GLU 3.0 7.4 - - - +
63B GLU* 3.3 38.4 - - + -
64B ASN* 3.9 3.8 - - - +
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Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 4.0 15.9 - - + -
73A MET* 3.7 39.0 - - + -
74A LYS* 3.6 9.1 - - - -
77A SER* 3.5 27.1 + - - -
80A THR* 4.7 14.7 - - - -
34B PHE* 3.4 25.4 - + + -
35B LEU 3.4 12.3 - - - -
36B GLU* 4.6 1.6 - - - +
58B PHE* 1.3 72.7 - - - +
60B ASN* 1.3 89.2 + - + +
61B LEU 3.1 3.3 + - - -
62B GLU* 2.9 21.9 + - + +
64B ASN* 3.7 16.7 - - - +
80B LEU* 3.6 20.6 - - + -
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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