Contacts of the strand formed by residues 32 - 44 (chain E) in PDB entry 2I5B
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 VAL 32 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E MET* 4.7 1.3 - - - -
4E HIS* 3.8 10.1 - - + +
5E LYS 3.9 2.2 - - - -
6E ALA* 3.7 37.0 - - + +
27E PHE* 2.8 31.6 + - + +
28E GLN* 4.0 7.4 + - - +
30E LYS 3.6 12.6 - - - +
31E ASN* 1.3 79.5 - - - +
33E TYR* 1.3 65.2 + - - +
34E GLY 3.2 3.8 + - - -
224E ALA* 3.6 35.7 - - + +
227E ALA* 4.1 7.9 - - + -
228E LYS* 3.7 14.8 - - + -
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Residues in contact with TYR 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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3E MET* 3.7 39.4 - - + -
4E HIS 2.9 18.3 + - - +
5E LYS* 3.4 13.4 - - + +
6E ALA 2.9 27.1 + - - +
28E GLN* 5.3 3.4 - - - -
32E VAL* 1.3 68.0 - - - +
34E GLY* 1.3 67.1 + - - +
35E MET* 3.8 36.1 - - + +
73E ILE* 5.9 2.7 - - + -
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Residues in contact with GLY 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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6E ALA 3.6 4.0 - - - -
24E LEU* 3.9 18.7 - - - +
27E PHE* 3.8 22.2 - - - -
28E GLN* 5.3 3.0 + - - -
32E VAL 3.2 5.6 + - - -
33E TYR* 1.3 81.3 - - - +
35E MET* 1.3 68.7 + - - +
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Residues in contact with MET 35 (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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5E LYS* 4.2 14.4 - - + -
6E ALA 3.0 11.5 + - - +
7E LEU* 3.5 3.6 - - - +
8E THR* 2.9 28.5 + - - +
24E LEU* 4.3 0.6 - - - +
27E PHE* 4.9 1.0 - - - -
33E TYR* 3.8 24.0 - - + +
34E GLY* 1.3 78.8 - - - +
36E THR* 1.3 64.4 + - - +
69E ILE* 3.8 28.5 - - + -
73E ILE* 3.8 43.5 - - + -
75E VAL* 3.7 28.9 - - + -
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Residues in contact with THR 36 (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 THR* 3.6 10.1 - - + -
20E ILE* 3.5 33.6 - - + +
24E LEU* 3.8 34.8 - - + -
35E MET* 1.3 77.5 - - - +
37E ALA* 1.3 59.5 + - - +
38E LEU* 3.6 14.8 - - - +
65E GLN* 3.6 10.2 + - - +
69E ILE* 3.4 13.1 - - - +
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Residues in contact with ALA 37 (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 LEU* 4.1 5.3 - - + +
8E THR 2.9 13.0 + - - +
9E ILE* 3.6 8.1 - - + -
10E ALA 3.3 21.4 + - - -
36E THR* 1.3 71.1 - - - +
38E LEU* 1.3 63.9 + - - +
39E THR* 3.4 4.0 + - - +
62E ILE* 4.7 3.8 - - + +
65E GLN* 3.6 17.0 - - + -
66E LEU* 3.7 36.1 - - + -
69E ILE* 4.0 3.2 - - + +
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Residues in contact with LEU 38 (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 3.4 2.0 - - - -
12E SER* 4.3 21.3 - - - +
20E ILE* 3.3 40.4 - - + -
36E THR* 4.1 12.3 - - - +
37E ALA* 1.3 71.0 - - - +
39E THR* 1.3 59.5 + - - +
40E VAL 5.1 0.4 - - - +
41E ILE* 6.0 5.2 - - + -
57E ILE* 3.7 19.9 - - + +
62E ILE* 3.6 10.4 - - - +
65E GLN* 2.7 35.4 + - - +
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Residues in contact with THR 39 (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 ILE* 3.6 31.2 - - + -
10E ALA 2.8 20.9 + - - +
37E ALA 3.7 5.8 - - - +
38E LEU* 1.3 73.7 - - - +
40E VAL* 1.3 65.7 + - - +
57E ILE* 3.2 23.9 + - - +
62E ILE* 3.8 19.6 - - + +
82E MET 2.7 22.7 + - - -
83E LEU* 4.0 4.3 - - + -
84E PRO* 4.0 9.0 - - - -
88E ILE* 3.9 21.0 - - + +
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Residues in contact with VAL 40 (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 GLY* 3.4 11.7 - - - -
12E SER* 2.8 26.0 + - - -
38E LEU* 5.1 0.9 - - - +
39E THR* 1.3 86.3 + - - +
41E ILE* 1.3 68.3 + - - +
42E VAL* 4.1 2.9 - - + -
54E VAL* 4.9 10.1 - - + -
55E PHE 3.6 11.2 - - - +
56E PRO* 3.4 28.3 - - + -
57E ILE* 3.5 6.6 - - - +
82E MET* 3.9 24.0 - - + -
84E PRO* 3.6 29.6 - - + -
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Residues in contact with ILE 41 (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 SER* 4.1 18.2 - - - +
14E SER* 4.8 7.0 - - - +
38E LEU* 6.0 5.4 - - + -
40E VAL* 1.3 76.7 - - - +
42E VAL* 1.3 67.2 + - - +
43E ALA* 5.0 2.0 - - + +
54E VAL* 3.8 0.3 - - - -
55E PHE* 2.8 60.6 + - + +
57E ILE* 4.1 18.6 - - + +
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Residues in contact with VAL 42 (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 SER 3.1 14.2 + - - +
13E ASP* 5.1 1.8 - - + -
14E SER* 2.7 35.9 + - - -
40E VAL* 4.6 6.1 - - + -
41E ILE* 1.3 78.1 - - - +
43E ALA* 1.3 67.0 + - - +
44E MET* 3.9 18.7 - - + +
52E HIS* 4.1 21.1 - - + -
53E GLN 3.4 7.2 - - - +
54E VAL* 4.3 16.6 - - + -
82E MET* 3.8 35.0 - - + -
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Residues in contact with ALA 43 (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 SER* 3.5 15.3 - - - +
41E ILE* 4.2 2.9 - - + -
42E VAL* 1.3 76.2 - - - +
44E MET* 1.3 67.2 + - - +
52E HIS* 3.4 5.7 - - - -
53E GLN* 2.8 44.8 + - - +
55E PHE* 4.4 13.2 - - + -
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Residues in contact with MET 44 (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 ASP* 3.2 31.0 - - + +
14E SER* 4.6 2.7 - - - -
15E SER* 4.2 17.7 - - - +
42E VAL* 3.9 19.1 - - + +
43E ALA* 1.3 82.9 - - - +
45E ASP* 1.3 60.0 + - - +
46E PRO* 3.2 15.1 - - - +
50E TRP* 3.4 56.6 - - + +
51E ASN 3.4 4.5 - - - -
52E HIS* 3.8 30.3 - - + +
53E GLN* 3.6 3.1 - - - +
212E HIS* 5.1 7.0 - - + -
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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