Contacts of the strand formed by residues 5 - 15 (chain A) 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 HIS 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLU* 3.4 32.2 + - - -
4A GLU* 1.3 85.5 + - - +
6A THR* 1.3 65.8 + - - +
26A PHE* 3.8 23.4 - + + -
27A ASP* 2.8 30.7 + - - +
43B PHE* 2.9 38.0 + - + +
109B TYR* 3.6 34.5 - + + -
117B VAL* 3.5 16.3 - - + +
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Residues in contact with THR 6 (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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5A HIS* 1.3 77.4 + - - +
7A ILE* 1.3 68.0 + - - +
8A ILE* 3.7 30.1 - - + -
25A ASP* 3.7 1.1 - - - +
26A PHE* 3.4 5.2 - - - -
27A ASP* 2.8 41.4 + - - +
28A GLY 5.9 0.2 - - - -
40B GLU* 4.6 1.1 - - + -
41B CYS 3.4 10.8 - - - +
42B HIS* 3.9 27.2 + - + -
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Residues in contact with ILE 7 (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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6A THR* 1.3 78.8 - - - +
8A ILE* 1.3 66.1 + - - +
24A PHE* 4.0 28.0 - - + -
25A ASP 3.1 7.9 - - - +
26A PHE* 3.8 17.7 - - + -
31A ILE* 5.3 0.4 - - + -
8B PHE* 6.0 1.8 - - + -
39B SER 3.8 1.2 - - - +
40B GLU* 3.5 0.3 - - - -
41B CYS* 2.8 40.8 + - + +
43B PHE* 3.6 32.5 - - + -
105B CYS 4.7 1.3 - - - +
108B ASN* 4.7 3.8 - - + +
109B TYR* 4.1 17.5 - - + +
112B PHE* 3.5 29.4 - - + -
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Residues in contact with ILE 8 (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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6A THR* 3.7 22.7 - - + -
7A ILE* 1.3 84.8 - - - +
9A GLN* 1.3 75.6 + - - +
10A ALA* 3.9 7.4 + - + +
23A MET* 3.6 1.0 - - - +
24A PHE* 3.2 6.0 - - - +
25A ASP* 2.7 60.2 + - + +
139A PRO* 4.9 10.3 - - + -
140A ARG 5.7 3.6 - - - +
38B LYS* 4.2 20.0 - - + -
39B SER 3.4 10.5 - - - +
40B GLU* 3.8 23.1 - - + +
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Residues in contact with GLN 9 (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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8A ILE* 1.3 72.3 - - - +
10A ALA* 1.3 60.7 + - - +
11A GLN* 2.7 26.0 + - - +
22A PHE* 3.3 29.4 - - + -
23A MET 3.3 5.4 - - - +
24A PHE* 3.5 15.4 - - + -
62A ASN* 3.6 0.6 - - - +
7B ALA* 3.3 11.8 - - - +
8B PHE* 2.8 66.8 + - + +
10B GLU* 5.5 1.2 + - - -
37B CYS 3.7 2.1 - - - +
38B LYS* 3.4 3.5 - - - -
39B SER* 3.0 33.6 + - - +
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Residues in contact with ALA 10 (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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8A ILE* 3.9 2.6 - - + -
9A GLN* 1.3 74.8 - - - +
11A GLN* 1.3 61.1 + - - +
12A PHE* 5.8 0.4 - - - -
21A GLU 4.0 0.5 - - - +
22A PHE* 3.4 1.7 - - - -
23A MET* 2.9 61.4 + - + +
137A PHE 5.9 0.7 - - - +
139A PRO* 4.2 16.6 - - + -
36B TYR* 4.3 7.9 - - + +
37B CYS 3.6 3.6 - - - -
38B LYS* 4.0 18.2 - - + -
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Residues in contact with GLN 11 (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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9A GLN* 2.7 33.4 + - - +
10A ALA* 1.3 75.6 - - - +
12A PHE* 1.3 66.3 + - - +
21A GLU 3.1 13.5 - - - +
22A PHE* 3.5 15.7 - - + -
62A ASN* 3.4 28.1 + - - +
63A ILE* 4.2 1.8 - - + -
66A ASN* 2.6 36.7 + - - +
10B GLU* 3.7 17.0 + - - +
35B GLU 4.0 0.2 - - - +
36B TYR* 3.2 5.3 - - - -
37B CYS* 3.0 37.7 + - + +
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Residues in contact with PHE 12 (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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10A ALA 5.8 0.4 - - - -
11A GLN* 1.3 80.0 - - - +
13A TYR* 1.3 68.7 + - - +
14A LEU* 4.3 4.5 - - + -
19A ARG* 4.0 17.9 - - + -
20A GLY* 3.3 3.5 - - - -
21A GLU* 3.1 72.2 + - + +
63A ILE* 3.8 5.0 - - - +
66A ASN* 4.1 7.8 + - - -
115A PRO* 3.7 26.5 - - + -
137A PHE* 4.4 8.3 - + + -
145A PHE* 3.8 28.5 - + - -
34B LEU* 3.7 20.0 - - + -
35B GLU 3.0 15.9 - - - +
36B TYR* 3.6 12.6 - + + -
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Residues in contact with TYR 13 (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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12A PHE* 1.3 76.4 - - - +
14A LEU* 1.3 63.7 + - - +
15A LEU* 4.0 24.3 - - + +
18A LYS* 3.1 40.9 + - - +
19A ARG 3.3 12.8 - - - -
20A GLY* 4.3 1.8 - - - -
36A ILE* 6.2 1.6 - - + -
63A ILE* 4.0 20.6 - - + +
66A ASN* 4.1 20.4 - - + +
67A LYS* 3.4 54.4 - - + +
70A LEU* 3.6 19.5 - - + +
33B PHE 3.9 1.2 - - - +
34B LEU* 3.8 2.3 - - - +
35B GLU* 3.2 26.0 + - - +
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Residues in contact with LEU 14 (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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12A PHE* 4.3 5.4 - - + -
13A TYR* 1.3 76.2 - - - +
15A LEU* 1.3 72.0 + - - +
17A ASP* 3.8 20.0 - - + +
18A LYS* 2.7 32.4 + - - -
19A ARG* 2.8 23.4 + - + +
114A PRO* 3.7 24.5 - - + -
115A PRO* 4.2 15.3 - - + +
116A VAL* 3.6 34.3 - - + -
30B ARG* 5.5 0.2 - - - +
32B TRP* 4.2 11.0 - - + -
33B PHE 3.5 9.9 - - - +
34B LEU* 4.0 10.8 - - + -
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Residues in contact with LEU 15 (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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13A TYR* 4.0 11.7 - - + +
14A LEU* 1.3 82.8 - - - +
16A PRO* 1.3 73.9 - - + +
17A ASP* 3.3 5.4 - - - -
18A LYS* 3.9 28.3 - - + -
70A LEU* 3.5 28.9 - - + +
71A ASP* 4.2 12.1 - - - +
74A LYS* 4.0 26.2 - - + +
32B TRP* 3.5 1.7 - - - +
33B PHE* 3.0 39.2 + - + +
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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