Contacts of the strand formed by residues 5 - 15 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E GLU* 2.6 39.1 + - - -
4E GLU* 1.3 90.4 + - - +
6E THR* 1.3 65.8 + - - +
26E PHE* 3.5 24.6 - + + -
27E ASP* 2.7 30.9 + - - +
42F HIS* 3.7 0.5 - - - -
43F PHE* 2.8 37.5 + - + +
109F TYR* 3.6 33.0 - + + -
117F VAL* 3.7 13.8 - - + +
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Residues in contact with THR 6 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E HIS* 1.3 79.2 + - - +
7E ILE* 1.3 66.5 + - - +
8E ILE* 3.6 30.7 - - + -
25E ASP* 3.6 0.8 - - - +
26E PHE* 3.5 4.0 - - - -
27E ASP* 2.8 44.5 + - - +
40F GLU* 4.7 1.6 - - + -
41F CYS 3.2 10.5 - - - +
42F HIS* 3.6 27.2 + - + +
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Residues in contact with ILE 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E THR* 1.3 76.6 - - - +
8E ILE* 1.3 65.9 + - - +
24E PHE* 4.0 27.4 - - + -
25E ASP 3.1 7.9 - - - +
26E PHE* 4.1 15.9 - - + -
31E ILE* 4.8 1.3 - - + -
8F PHE* 6.2 2.2 - - + -
39F SER 3.7 0.9 - - - +
40F GLU* 3.5 0.2 - - - -
41F CYS* 2.7 51.3 + - + +
43F PHE* 3.5 29.2 - - + -
105F CYS 4.6 1.1 - - - +
108F ASN* 4.3 3.4 - - + +
109F TYR* 3.9 18.6 - - + +
112F PHE* 3.5 32.3 - - + -
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Residues in contact with ILE 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E THR* 3.6 22.2 - - + -
7E ILE* 1.3 82.7 - - - +
9E GLN* 1.3 73.0 + - - +
10E ALA* 3.9 7.1 + - + +
23E MET 3.6 0.9 - - - +
24E PHE* 3.1 8.1 - - - -
25E ASP* 2.7 62.0 + - + +
139E PRO* 5.0 9.2 - - + -
140E ARG 5.7 3.1 - - - +
38F LYS* 4.2 14.1 - - + -
39F SER 3.2 10.3 - - - +
40F GLU* 3.9 30.5 - - + +
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Residues in contact with GLN 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 1.3 72.7 - - - +
10E ALA* 1.3 60.5 + - - +
11E GLN* 2.7 26.6 + - - +
22E PHE* 3.4 23.5 - - + -
23E MET 3.3 4.5 - - - +
24E PHE* 3.4 25.0 - - + -
62E ASN* 3.6 0.8 - - - +
7F ALA* 3.3 10.2 - - - -
8F PHE* 2.8 67.8 + - + +
10F GLU* 5.5 1.4 + - - -
37F CYS* 3.7 1.6 - - - +
38F LYS* 3.2 3.6 - - - -
39F SER* 2.8 39.2 + - - +
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Residues in contact with ALA 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 3.9 2.9 + - + -
9E GLN* 1.3 74.8 - - - +
11E GLN* 1.3 62.2 + - - +
12E PHE* 5.8 0.8 - - - -
21E GLU 3.9 0.7 - - - +
22E PHE* 3.5 1.4 + - - -
23E MET* 2.8 60.3 + - + +
137E PHE 6.1 0.2 - - - +
139E PRO* 4.3 12.1 - - + -
36F TYR* 4.3 12.3 - - + +
37F CYS 3.6 3.8 - - - -
38F LYS* 4.0 18.4 - - + -
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Residues in contact with GLN 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLN* 2.7 33.7 + - - +
10E ALA* 1.3 74.7 - - - +
12E PHE* 1.3 64.2 + - - +
21E GLU 3.1 13.2 - - - +
22E PHE* 3.5 12.7 - - + -
62E ASN* 3.4 31.6 + - - +
63E ILE* 4.3 2.0 - - + -
66E ASN* 2.6 35.9 + - - +
10F GLU* 3.7 15.6 + - - +
35F GLU 4.0 0.2 - - - +
36F TYR* 3.2 6.6 - - - -
37F CYS* 3.0 44.1 + - + +
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Residues in contact with PHE 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ALA 5.8 0.4 - - - -
11E GLN* 1.3 80.3 - - - +
13E TYR* 1.3 69.2 - - - +
14E LEU* 4.4 4.0 - - + -
19E ARG* 4.0 18.4 - - + -
20E GLY* 3.2 4.2 - - - -
21E GLU* 3.1 72.1 + - + +
63E ILE* 3.9 5.4 - - - +
66E ASN* 4.2 7.8 + - - -
115E PRO* 3.7 26.0 - - + -
137E PHE* 4.4 7.9 - + + -
145E PHE* 3.9 27.8 - + - -
34F LEU* 3.6 19.7 - - + -
35F GLU 3.1 16.2 - - - +
36F TYR* 3.6 13.5 - + + -
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Residues in contact with TYR 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 1.3 77.5 - - - +
14E LEU* 1.3 59.0 + - - +
15E LEU* 3.9 22.9 - - + +
18E LYS* 3.5 40.9 + - - +
19E ARG 3.2 17.9 - - - -
20E GLY* 4.1 6.5 - - - -
36E ILE* 5.6 2.9 - - + -
63E ILE* 4.3 13.9 - - + +
66E ASN* 4.1 21.1 - - + +
67E LYS* 3.5 53.2 - - + +
70E LEU* 3.6 21.2 - - + +
34F LEU* 3.5 4.7 - - - +
35F GLU 3.1 26.9 + - - +
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Residues in contact with LEU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 4.4 3.8 - - + -
13E TYR* 1.3 77.4 - - - +
15E LEU* 1.3 75.0 + - - +
17E ASP* 3.9 20.0 - - + +
18E LYS* 2.6 34.5 + - - -
19E ARG* 2.6 27.3 + - + +
114E PRO* 4.0 21.1 - - + -
115E PRO* 4.2 11.7 - - + +
116E VAL* 3.4 36.6 - - + -
32F TRP* 4.2 6.3 - - + -
33F PHE 3.5 15.7 - - - +
34F LEU* 4.0 12.3 - - + -
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Residues in contact with LEU 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E TYR* 3.9 15.3 - - + +
14E LEU* 1.3 81.4 - - - +
16E PRO* 1.3 68.5 - - + +
17E ASP* 3.3 5.2 - - - -
18E LYS* 3.7 28.9 - - + -
67E LYS 6.1 0.2 - - - +
70E LEU* 3.5 28.3 - - + -
71E ASP* 4.3 11.9 - - - +
74E LYS* 4.2 20.9 - - + +
32F TRP* 3.3 2.8 - - - -
33F PHE* 2.8 46.2 + - + +
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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