Contacts of the strand formed by residues 5 - 15 (chain E) in PDB entry 1R5I
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* 4.3 1.6 - - - +
4E GLU* 1.3 105.3 + - + +
6E VAL* 1.3 71.8 + - - +
26E PHE* 3.5 23.3 - + + -
27E ASP* 2.6 30.3 + - - +
15F CYS 4.3 0.2 - - - -
16F HIS* 3.6 0.5 - - - -
17F PHE* 2.9 42.8 + - + +
20F GLY 5.7 0.2 - - - -
83F TYR* 4.4 14.8 - + + -
91F VAL* 3.9 31.3 - - + +
124F PRO* 6.6 0.4 - - + -
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Residues in contact with VAL 6 (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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3E GLU* 3.5 26.0 - - + +
5E HIS* 1.3 82.2 - - - +
7E ILE* 1.3 64.5 + - - +
8E ILE* 3.8 27.4 - - + -
25E ASP* 3.7 3.3 - - - +
26E PHE* 3.5 3.2 - - - -
27E ASP* 2.7 41.0 + - - +
15F CYS 3.2 11.2 - - - +
16F HIS* 3.6 28.3 - - + +
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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 VAL* 1.3 74.5 - - - +
8E ILE* 1.3 63.2 + - - +
24E PHE* 4.1 27.6 - - + -
25E ASP 3.2 9.0 - - - +
26E PHE* 3.8 27.6 - - + -
31E ILE* 4.7 9.6 - - + -
13F PHE 3.6 2.6 - - - +
15F CYS* 2.8 47.0 + - + +
17F PHE* 4.0 16.4 - - + -
78F TYR* 5.6 1.9 + - + +
79F CYS* 6.4 0.2 - - - -
82F ASN* 4.3 13.9 - - + +
83F TYR* 3.9 32.5 - - + +
308G TYR* 5.4 1.3 - - + +
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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 VAL* 3.8 22.4 - - + -
7E ILE* 1.3 81.0 - - - +
9E GLN* 1.3 73.9 + - - +
10E ALA* 3.8 13.8 + - + +
23E MSE 3.8 0.2 - - - +
24E PHE* 3.3 4.0 - - - +
25E ASP* 2.8 60.0 + - - +
139E PRO* 5.1 10.3 - - + -
141E GLU* 6.5 1.1 - - + -
12F LYS* 4.5 15.9 - - + +
13F PHE 3.3 9.9 - - - +
14F GLU* 4.1 20.6 - - + +
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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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7E ILE 4.3 0.2 + - - -
8E ILE* 1.3 71.6 - - - +
10E ALA* 1.3 61.3 + - - +
11E GLU* 2.6 29.8 + - - +
22E PHE* 3.5 10.9 - - + -
23E MSE 3.5 3.8 - - - +
24E PHE* 3.3 24.5 - - + -
62E ASN* 3.4 2.8 - - - +
11F LEU 3.8 0.7 - - - +
12F LYS* 3.4 4.9 - - - -
13F PHE* 2.8 47.8 + - + -
78F TYR* 2.7 34.6 + - - +
310G LYS* 3.7 7.2 - - - +
311G GLN 2.8 37.6 + - - -
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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* 3.8 15.4 + - + -
9E GLN* 1.3 74.5 - - - +
11E GLU* 1.3 62.1 + - - +
12E PHE* 6.3 0.2 - - - -
21E GLU* 4.0 3.0 - - - +
22E PHE* 3.6 0.9 - - - -
23E MSE 2.7 51.5 + - + +
139E PRO* 4.3 25.4 - - + -
11F LEU 3.6 5.2 - - - +
12F LYS* 4.5 7.0 - - + -
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Residues in contact with GLU 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* 2.6 32.8 + - - +
10E ALA* 1.3 77.6 - - - +
12E PHE* 1.3 67.4 + - - +
21E GLU* 3.1 13.2 - - - +
22E PHE* 3.1 12.8 - - - -
62E ASN* 2.8 29.9 + - - +
63E ILE* 4.1 3.6 - - + -
66E ASP* 2.6 31.9 - - - +
10F GLN* 3.4 2.8 - - - +
11F LEU* 2.9 55.1 + - + +
13F PHE* 5.0 0.7 - - + -
313G THR* 3.9 1.4 - - - -
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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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11E GLU* 1.3 77.9 - - - +
13E TYR* 1.3 71.7 + - - +
14E LEU* 4.6 4.7 - - + -
19E SER* 3.8 19.7 - - - -
20E GLY* 3.1 5.4 - - - -
21E GLU* 2.9 74.3 + - + +
63E ILE* 3.9 5.8 - - - +
66E ASP* 5.2 3.8 - - - -
115E PRO* 3.4 40.8 - - + -
137E PHE* 3.9 7.4 - + + -
145E PHE* 3.7 20.2 - + - -
8F LEU* 4.1 5.2 - - + -
9F TRP 3.1 13.9 - - - +
10F GLN* 3.8 15.5 - - + +
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Residues in contact with TYR 13 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E PHE* 1.3 77.5 - - - +
14E LEU* 1.3 64.1 + - - +
15E ASN* 3.6 22.2 - - - -
18E GLN* 3.4 25.7 - - - +
19E SER 3.4 9.9 - - - -
20E GLY* 4.0 2.9 - - - -
63E ILE* 3.9 24.5 - - + -
66E ASP* 4.2 20.2 - - + +
67E LYS* 3.1 49.8 - - + +
70E LEU* 3.5 20.2 - - + +
8F LEU* 3.7 1.6 - - - +
9F TRP* 3.0 30.9 + - + +
85H VAL* 5.3 2.5 - - + -
88H ASP* 2.5 30.1 + - - -
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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* 4.6 5.4 - - + -
13E TYR* 1.3 78.2 - - - +
15E ASN* 1.3 64.1 + - - +
17E ASP* 2.9 31.6 - - + +
18E GLN* 2.6 36.6 + - - -
19E SER* 2.8 20.2 + - - +
70E LEU* 4.0 0.2 - - - -
82E ILE* 5.7 0.2 - - + -
114E PRO* 3.9 24.5 - - + -
115E PRO* 4.9 4.9 - - + +
116E VAL* 3.3 28.0 - - + -
6F ARG* 4.0 9.0 - - + -
7F PHE 3.6 17.0 - - - +
8F LEU* 3.9 16.4 - - + -
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Residues in contact with ASN 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* 3.6 19.6 + - - -
14E LEU* 1.3 74.9 - - - +
16E PRO* 1.3 67.4 - - + +
17E ASP* 3.2 5.4 - - - -
18E GLN* 4.0 13.0 + - - +
67E LYS* 5.3 2.8 + - - +
70E LEU* 3.1 33.5 - - + +
71E GLU* 4.9 9.1 - - - +
74E THR* 5.1 2.2 + - - -
5F PRO 4.7 0.2 - - - -
6F ARG* 3.1 9.5 - - - +
7F PHE* 3.0 42.3 + - + +
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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