Contacts of the strand formed by residues 49 - 58 (chain B) in PDB entry 1I3R
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 49 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B HIS 3.7 2.6 - - - +
43B PHE* 3.8 0.2 - - - -
44B TYR* 3.1 75.0 + - + +
46B GLY 3.9 0.3 - - - +
48B GLN* 1.3 88.1 - - - +
50B VAL* 1.3 68.2 + - - +
51B ARG* 4.2 22.0 - - - +
69B ASP* 4.3 15.0 + - - -
106B ARG* 4.8 0.9 - - - +
304B NAG 5.0 5.7 - - + +
67D ASP* 5.1 1.8 + - - -
69D ASP* 3.1 47.7 + - - +
70D VAL* 4.1 3.2 - - - +
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Residues in contact with VAL 50 (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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42B HIS 3.4 9.2 - - - +
43B PHE* 3.9 27.1 - - + -
47B THR* 3.9 9.4 - - - +
49B ARG* 1.3 86.0 + - - +
51B ARG* 1.3 66.4 + - - +
52B LEU 4.3 0.2 - - - -
68B SER* 4.5 1.9 + - - -
69B ASP* 5.2 2.3 - - - +
101B VAL* 4.0 23.7 - - + +
105B CYS* 3.8 32.1 - - + -
106B ARG* 3.6 35.1 + - + +
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Residues in contact with ARG 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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40B GLU 3.6 1.4 - - - +
41B CYS* 3.6 2.1 - - - -
42B HIS* 2.7 60.6 + - + +
44B TYR* 4.6 8.4 + - + -
49B ARG* 4.2 20.6 - - - +
50B VAL* 1.3 79.1 - - - +
52B LEU* 1.3 65.1 + - - +
53B LEU* 4.0 31.8 - - - +
65B ARG* 5.0 4.9 - - - +
67B ASP* 2.7 36.8 + - - +
68B SER* 3.6 9.2 - - - +
69B ASP* 3.3 23.7 + - - +
51D ARG* 3.6 35.5 - - - +
65D ARG* 5.8 1.8 - - - +
67D ASP* 4.5 4.3 + - - -
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Residues in contact with LEU 52 (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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8B PHE* 3.7 38.4 - - + -
39B SER 4.6 0.2 - - - -
40B GLU 3.5 13.7 - - - +
50B VAL 4.3 0.2 - - - -
51B ARG* 1.3 72.8 - - - +
53B LEU* 1.3 68.7 + - - +
54B VAL* 4.0 23.8 - - + -
66B PHE* 3.3 17.1 - - + +
67B ASP* 3.5 3.6 - - - +
68B SER* 2.6 49.0 + - - +
97B LYS* 4.0 20.9 - - - +
100B GLU* 4.4 7.2 - - + +
101B VAL* 3.9 16.2 - - + +
105B CYS* 4.1 9.9 - - - -
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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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38B LYS 3.6 0.9 - - - +
40B GLU* 2.9 59.1 + - - +
42B HIS* 4.1 10.8 - - + +
51B ARG* 3.9 35.2 + - - +
52B LEU* 1.3 74.5 - - - +
54B VAL* 1.3 64.7 + - - +
55B ARG* 3.8 15.4 + - + +
65B ARG* 4.1 36.8 - - - +
66B PHE 4.2 6.1 - - - +
67B ASP* 4.3 7.2 - - + -
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 5.4 0.7 - - + -
10B GLU* 4.7 1.6 - - - +
37B CYS* 3.8 12.3 - - - -
38B LYS 3.4 3.4 - - - +
39B SER* 3.5 25.4 - - - +
52B LEU* 4.0 28.3 - - + -
53B LEU* 1.3 73.8 - - - +
55B ARG* 1.3 62.4 + - - +
56B TYR* 3.6 27.8 - - + +
65B ARG* 3.0 10.4 - - - +
66B PHE* 2.9 44.0 + - + +
73B PHE* 5.5 0.2 - - + -
97B LYS* 4.3 17.3 - - - +
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Residues in contact with ARG 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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141A ASP* 2.9 29.1 + - - +
142A ASP* 4.1 5.1 + - - +
37B CYS* 3.3 2.9 - - - -
38B LYS* 2.7 46.0 + - + +
40B GLU* 2.8 40.4 + - - -
53B LEU* 4.0 18.1 - - + +
54B VAL* 1.3 81.2 - - - +
56B TYR* 1.3 63.4 + - - +
57B PHE* 3.5 32.9 - - + -
62B GLU* 3.0 35.9 + - - +
64B LEU 3.7 3.4 - - - -
65B ARG* 3.7 8.9 - - - +
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Residues in contact with TYR 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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69A ASN* 5.9 0.9 - - - -
10B GLU* 2.9 33.6 + - + -
11B GLY 5.0 1.9 + - - -
13B LYS* 4.4 22.0 - - - +
35B GLU* 4.5 5.4 - - - +
36B TYR 3.5 3.4 - - - +
37B CYS* 3.8 15.5 - - + -
54B VAL* 3.6 24.9 - - + +
55B ARG* 1.3 73.7 - - - +
57B PHE* 1.3 63.4 + - - +
62B GLU* 3.3 4.7 - - - +
63B ASN* 2.9 34.6 + - - +
64B LEU* 2.9 44.9 + - + +
65B ARG* 4.4 1.1 - - - -
73B PHE* 3.8 25.4 - + - -
87B TRP* 3.7 27.5 - + - -
93B PHE* 5.8 0.9 - - - -
97B LYS* 4.9 4.2 + - - -
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Residues in contact with PHE 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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142A ASP 3.7 16.4 - - - -
143A HIS* 3.4 36.3 - - + -
13B LYS* 6.2 0.2 - - - -
34B LEU 3.6 0.5 - - - +
35B GLU* 3.8 8.2 - - - +
36B TYR* 2.6 62.9 + + + +
37B CYS* 4.9 0.2 - - - -
38B LYS* 3.8 15.3 - - + -
55B ARG* 3.5 50.7 - - + -
56B TYR* 1.3 76.5 - - - +
58B TYR* 1.3 59.8 + - - +
59B ASN 3.9 8.7 - - - +
61B GLU 3.3 7.6 - - - +
62B GLU* 3.7 30.1 - - + -
63B ASN* 3.9 3.1 - - - +
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Residues in contact with TYR 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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70A LEU* 3.9 16.8 - - + -
73A MET* 3.4 40.2 - - + -
74A LYS* 3.7 8.7 - - - -
77A SER* 3.3 30.5 + - - -
80A THR 4.1 7.2 + - - -
82A ASP* 4.3 3.8 - - - +
33B PHE* 3.3 25.0 - - + -
34B LEU 3.2 9.9 - - - -
35B GLU* 4.3 3.4 - - - +
57B PHE* 1.3 73.8 - - - +
59B ASN* 1.3 90.8 + - + +
60B LEU 3.3 2.4 + - - -
61B GLU* 3.2 16.5 + - - +
63B ASN* 3.6 17.0 - - - +
79B LEU* 3.8 19.5 - - + -
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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