Contacts of the strand formed by residues 22 - 30 (chain E) in PDB entry 4P5K
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 GLN 22 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D SER* 6.1 0.3 - - - -
15E CYS* 4.1 11.5 - - + +
16E TYR 3.4 6.0 - - - +
17E ALA* 3.5 24.4 + - - +
21E THR* 1.3 94.0 + - - +
23E ARG* 1.3 62.4 + - - +
40E SER* 4.5 1.4 + - - -
73E PRO* 3.3 26.2 - - - +
77E CYS* 2.9 40.0 + - + +
78E ARG* 3.2 34.4 - - - +
81E TYR* 3.9 26.0 - - - +
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Residues in contact with ARG 23 (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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1D ILE* 3.8 45.2 + - - +
15E CYS* 3.5 2.4 - - - -
16E TYR* 2.7 49.9 + - + +
18E PHE* 6.3 2.2 - - + -
21E THR* 6.0 2.2 - - + -
22E GLN* 1.3 75.3 - - - +
24E PHE* 1.3 61.0 + - - +
25E LEU* 4.2 9.9 - - + +
39E ASP* 2.6 38.7 + - - +
40E SER* 4.0 7.2 - - - +
41E ASP* 3.5 40.6 + - - +
77E CYS* 5.0 1.3 - - - -
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Residues in contact with PHE 24 (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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-20E GLN* 3.6 23.6 - - - -
13E GLN* 4.0 4.9 - - + -
14E GLU 3.3 19.5 - - - -
23E ARG* 1.3 75.7 - - - +
25E LEU* 1.3 74.5 + - - +
26E GLU* 3.8 32.8 - - + -
38E PHE* 3.6 15.4 - + - +
39E ASP* 3.6 3.5 - - - +
40E SER* 3.0 34.5 + - - -
69E GLU* 4.0 13.7 - - - -
72E VAL* 3.6 25.8 - - + -
73E PRO* 3.7 20.4 - - + +
76E MET* 3.7 19.1 - - + -
77E CYS* 3.9 12.8 - - - -
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Residues in contact with LEU 25 (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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1D ILE* 4.7 9.4 - - + -
12E ARG 3.5 1.6 - - - +
13E GLN* 3.4 1.9 - - - -
14E GLU* 2.5 56.5 + - - +
16E TYR* 3.3 33.2 - - + -
23E ARG* 4.2 19.5 - - + +
24E PHE* 1.3 84.0 - - - +
26E GLU* 1.3 58.0 + - - +
27E ARG* 3.9 31.9 - - + +
37E ARG* 4.1 14.6 - - - -
38E PHE 3.2 6.5 - - - +
39E ASP* 3.8 20.4 - - - +
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Residues in contact with GLU 26 (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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-20E GLN* 3.5 16.1 + - - +
-18E PHE* 4.0 6.3 - - + -
12E ARG 3.0 12.6 - - - +
13E GLN* 3.0 31.5 + - + +
24E PHE* 3.8 15.7 - - + -
25E LEU* 1.3 74.1 - - - +
27E ARG* 1.3 62.8 + - - +
28E TYR* 2.5 40.9 + - + -
37E ARG* 3.4 5.4 - - - +
38E PHE* 2.9 36.6 + - + +
69E GLU* 3.1 29.8 - - - +
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Residues in contact with ARG 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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1D ILE* 5.4 5.3 - - - +
143D TYR* 3.3 21.4 + - - -
-18E PHE* 4.2 2.3 - - - -
11E GLY* 3.1 9.0 - - - -
12E ARG* 2.9 39.0 + - + +
14E GLU* 2.7 53.2 + - - +
16E TYR* 4.0 5.5 + - - -
25E LEU* 3.9 19.8 - - + +
26E GLU* 1.3 80.8 - - - +
28E TYR* 1.3 65.9 + - - +
29E ILE* 4.0 13.5 - - + -
34E GLU* 2.7 26.5 + - + +
36E VAL 3.9 3.1 - - - -
37E ARG* 3.6 27.3 - - + +
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Residues in contact with TYR 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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69D ASN* 4.0 11.9 - - - -
-18E PHE* 3.6 21.8 - + + -
-17E HIS* 2.8 61.4 + + + -
-15E ILE* 4.1 10.8 - - + -
9E PHE* 4.1 10.1 - + + -
10E GLN 4.2 1.6 - - - -
11E GLY* 5.9 0.2 - - - -
26E GLU* 2.5 42.5 + - + -
27E ARG* 1.3 75.1 - - - +
29E ILE* 1.3 60.1 + - - +
34E GLU* 3.6 2.3 - - - -
35E PHE* 3.0 39.2 + - + -
36E VAL* 3.0 40.2 + - + +
37E ARG 5.2 0.7 - - - -
45E PHE* 4.7 8.7 - + - -
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Residues in contact with ILE 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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143D TYR* 3.8 31.2 - - + -
9E PHE* 3.4 10.3 - - - -
10E GLN* 2.9 75.8 + - + +
12E ARG* 4.2 10.8 - - + +
27E ARG* 4.0 17.7 - - + +
28E TYR* 1.3 78.8 - - - +
30E TYR* 1.3 62.4 + - - +
32E ARG 3.9 4.3 - - - +
33E GLU 3.5 26.7 - - - +
34E GLU* 3.7 18.6 - - + +
35E PHE* 3.8 4.1 - - - -
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Residues in contact with TYR 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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70D LEU* 4.9 2.5 - - + -
73D LEU* 3.6 49.1 + - + -
74D ILE* 4.2 6.9 - - + -
77D SER* 2.9 37.0 + - - -
80D THR* 2.5 30.7 + - + -
7E TYR* 3.8 13.2 - - + +
8E LEU 3.5 20.4 - - - -
9E PHE* 4.4 5.2 - + + -
29E ILE* 1.3 72.4 - - - +
31E ASN* 1.3 91.3 + - - +
33E GLU* 2.8 30.3 + - + +
35E PHE* 3.8 7.7 - - + -
51E LEU* 4.9 6.5 - - + -
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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