Contacts of the strand formed by residues 26 - 34 (chain E) in PDB entry 1I5L
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 GLU 26 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E ILE* 3.8 21.3 - - + +
19E VAL 3.3 12.6 - - - +
20E ARG* 2.4 46.6 + - - +
21E LEU* 4.9 0.4 - - - -
24E GLY 4.6 1.3 - - - +
25E ARG* 1.3 78.2 - - - +
27E PHE* 1.3 67.7 + - - +
28E ARG* 5.1 3.0 - - + -
47E GLU* 3.4 5.7 - - - +
48E ILE* 2.6 59.3 + - + +
55F ARG* 4.4 9.6 + - - -
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Residues in contact with PHE 27 (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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69D PHE* 3.9 37.0 - + - -
17E VAL 3.8 0.7 - - - +
18E ILE* 3.5 5.2 - - - +
19E VAL* 2.9 39.8 + - + +
21E LEU* 4.1 22.7 - - + -
26E GLU* 1.3 78.7 - - - +
28E ARG* 1.3 63.5 + - - +
29E GLY 4.3 0.2 + - - -
42E LEU* 3.7 21.1 - - + -
45E ALA* 4.0 14.8 - - + -
46E GLU 3.4 11.4 - - - -
47E GLU* 4.0 28.3 - - + -
55E ARG* 5.9 0.9 - - - -
57E VAL* 4.2 11.9 - - + -
60E VAL* 4.0 24.9 - - + -
62E ILE* 4.2 12.3 - - + -
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Residues in contact with ARG 28 (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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17E VAL 3.5 7.9 + - - +
18E ILE* 3.8 36.3 - - + +
26E GLU* 5.1 4.3 - - - +
27E PHE* 1.3 80.9 - - - +
29E GLY* 1.3 57.6 + - - +
42E LEU* 5.1 0.7 - - - -
44E ASP 3.8 1.0 - - - +
45E ALA* 3.0 26.4 - - - -
46E GLU* 3.1 32.3 + - - +
48E ILE* 3.2 29.5 - - + +
73E ALA* 4.4 12.1 - - - +
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Residues in contact with GLY 29 (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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16E PRO* 4.1 6.3 - - - +
17E VAL* 2.7 44.3 + - - +
28E ARG* 1.3 75.2 - - - +
30E THR* 1.3 62.0 + - - -
42E LEU* 4.5 6.3 - - - +
43E LEU 4.0 1.3 - - - -
44E ASP 3.7 12.1 - - - -
45E ALA* 4.5 3.6 - - - -
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Residues in contact with THR 30 (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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14E LYS* 3.7 34.9 + - + +
15E SER 3.7 7.0 + - - -
16E PRO* 4.4 4.3 - - - +
29E GLY* 1.3 70.4 - - - -
31E LEU* 1.3 67.4 + - - +
32E ASP* 3.4 2.7 + - - +
42E LEU* 3.3 6.4 - - - -
43E LEU* 2.9 55.2 + - + +
44E ASP* 5.5 1.9 - - - +
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Residues in contact with LEU 31 (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 LEU* 3.4 42.0 - - + +
12E SER* 3.9 22.7 - - - +
13E LEU* 3.6 12.4 - - + -
14E LYS* 2.9 30.8 + - - -
15E SER 3.3 8.1 + - - -
17E VAL* 4.2 18.6 - - + -
29E GLY 3.7 2.6 + - - -
30E THR* 1.3 69.2 - - - +
32E ASP* 1.3 61.2 + - - +
33E GLY 3.3 27.4 - - - +
34E TYR* 4.7 4.3 - - + -
40E LEU* 4.6 15.0 - - + -
41E VAL 3.8 9.6 - - - +
42E LEU* 4.0 7.2 - - + -
70E VAL* 5.6 2.7 - - + -
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Residues in contact with ASP 32 (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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2D PRO* 4.8 1.0 - - - +
3D PRO* 3.2 39.7 - - - +
8D VAL* 4.9 0.9 - - - +
11D ARG* 4.9 6.2 + - - -
13E LEU* 3.3 19.2 - - - +
14E LYS* 5.2 5.5 - - - +
30E THR* 3.4 2.5 + - + +
31E LEU* 1.3 73.1 - - - +
33E GLY* 1.3 56.1 + - - +
41E VAL* 2.8 33.7 + - + +
43E LEU* 3.9 32.7 - - + +
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Residues in contact with GLY 33 (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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2D PRO* 5.1 1.1 - - - -
3D PRO 3.1 21.1 - - - -
5D PRO* 4.5 1.8 - - - -
13E LEU* 4.2 5.8 - - - -
31E LEU* 3.3 9.2 - - - +
32E ASP* 1.3 80.0 - - - +
34E TYR* 1.3 67.8 + - - +
41E VAL* 3.1 30.5 + - - +
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Residues in contact with TYR 34 (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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2D PRO* 5.6 0.7 - - + +
3D PRO 4.1 1.1 + - - +
4D ARG* 3.8 14.9 + - - +
5D PRO* 3.9 8.8 - - - +
6E LEU* 3.6 32.6 + - + +
9E LEU* 3.7 32.3 - - + -
10E ASN* 3.2 50.5 + - + +
13E LEU* 4.1 17.7 - - + -
31E LEU* 4.7 2.7 - - + -
33E GLY* 1.3 77.9 - - - +
35E ASP* 1.3 75.4 + - - +
38E MET 5.4 0.2 - - - -
39E ASN 3.2 16.4 - - - +
40E LEU* 4.1 6.7 - - + -
49J GLN* 4.7 0.7 + - - -
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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