Contacts of the strand formed by residues 11 - 16 (chain E) in PDB entry 3Q2K
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 ILE 11 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E ARG* 5.6 1.6 - - - +
10E LYS* 1.3 74.8 - - - +
12E ARG* 1.3 63.8 + - - +
13E PHE* 3.5 19.7 + - + -
35E ARG 3.1 12.0 + - - +
36E ALA* 2.8 30.8 - - + +
37E GLU* 3.3 11.5 + - - +
74E ASP* 3.9 19.1 - - + +
75E ALA* 5.1 0.2 - - + -
309E ILE* 5.1 9.4 - - + -
312E LEU* 3.8 50.0 - - + +
313E ARG* 4.8 15.9 - - + +
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Residues in contact with ARG 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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9E ARG* 3.3 24.7 - - - +
10E LYS 3.6 2.2 + - - +
11E ILE* 1.3 70.1 - - - +
13E PHE* 1.3 60.0 + - - +
37E GLU* 4.5 11.4 + - - +
39E VAL* 3.2 50.2 - - + +
40E GLU* 4.7 0.6 + - - -
72E ASN* 1.9 68.5 + - - +
73E ALA* 3.7 3.5 - - - +
74E ASP* 2.4 84.0 + - - +
75E ALA 3.4 1.2 + - - -
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Residues in contact with PHE 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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11E ILE* 3.5 25.1 + - + -
12E ARG* 1.3 75.0 - - - +
14E GLY* 1.3 60.1 + - - +
29E ILE* 3.8 28.0 - - + -
36E ALA* 4.2 13.7 - - + -
37E GLU 3.3 13.4 + - - +
38E LEU* 3.4 5.6 - - + +
39E VAL* 3.0 26.3 + - - +
40E GLU 3.5 2.4 + - - -
73E ALA* 3.8 3.4 - - - -
75E ALA* 3.4 32.5 - - + -
77E VAL* 4.4 12.3 - - + -
100E VAL* 4.4 13.9 - - + -
305E TYR* 4.1 27.6 - + - -
308E VAL* 4.4 9.9 - - + -
309E ILE* 4.4 16.6 - - + -
312E LEU* 4.4 7.2 - - + -
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Residues in contact with GLY 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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13E PHE* 1.3 74.8 - - - +
15E LEU* 1.3 57.4 + - - -
38E LEU* 3.5 3.8 - - - -
40E GLU 3.3 13.2 - - - -
67E MET* 4.0 9.2 - - - -
73E ALA* 3.5 11.4 - - - +
75E ALA 3.0 11.0 + - - -
76E LEU* 3.6 4.2 - - - -
77E VAL* 2.7 38.0 + - - +
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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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14E GLY* 1.3 73.0 - - - -
16E VAL* 1.3 86.4 + - - +
17E GLY 2.6 29.4 - - - +
18E CYS* 4.6 3.6 - - - -
22E SER* 3.4 35.4 - - - +
25E HIS* 4.2 13.5 - - + -
26E ILE* 4.2 14.4 - - + +
38E LEU* 3.1 15.4 - - + +
40E GLU 3.0 6.5 + - - -
41E ILE* 3.2 13.5 - - + -
42E CYS 3.1 23.0 + - - -
67E MET* 3.2 8.5 - - - +
77E VAL* 3.9 12.3 - - + +
79E ALA* 4.0 9.6 - - + -
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Residues in contact with VAL 16 (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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15E LEU* 1.3 96.9 - - - +
17E GLY* 1.3 59.0 + - - +
42E CYS* 4.1 14.1 - - - -
64E LEU* 4.3 14.8 - - + -
67E MET* 4.5 2.0 - - - -
76E LEU* 4.1 26.5 - - + -
77E VAL 2.7 19.5 + - - +
78E LEU* 3.5 22.0 - - + -
79E ALA 3.1 18.0 + - - -
80E THR* 4.1 2.2 - - + -
88E GLN* 4.1 21.8 - - - +
500E NAI 4.1 15.3 - - + +
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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