Contacts of the strand formed by residues 34 - 39 (chain E) in PDB entry 4WFH
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 MET 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E LEU* 4.1 12.3 - - + -
22E CYS* 3.9 8.1 - - - -
24E VAL* 4.4 8.1 - - - -
27E TYR* 3.8 21.5 - - - +
29E PHE* 4.2 21.3 - - + -
32E TYR 3.7 1.9 + - - +
33E ILE* 1.3 73.7 - - - +
35E ASN* 1.3 64.9 + - - +
36E TRP* 5.0 3.4 - - - +
50E LEU* 3.1 3.8 - - - +
51E ILE* 2.8 51.7 + - + +
53E PRO* 4.3 6.5 - - + +
79E ALA* 4.5 10.5 - - + -
96E CYS* 3.4 33.4 - - + -
97E THR 3.7 19.7 - - - +
98E ARG* 4.4 3.6 - - - -
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Residues in contact with ASN 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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90D TRP* 3.4 17.2 - - - -
33E ILE* 4.2 0.2 - - - +
34E MET* 1.3 79.8 - - - +
36E TRP* 1.3 74.4 + - - +
47E TRP* 2.9 26.3 + - + +
49E GLY 3.2 9.0 - - - +
50E LEU* 3.5 8.3 - - - +
96E CYS* 3.4 2.3 - - - -
97E THR* 2.8 43.7 + - + +
99E GLY 2.9 28.3 + - - +
103E PHE* 3.3 23.2 - - + -
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Residues in contact with TRP 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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6E GLN* 3.8 21.1 - - - -
20E THR* 3.9 31.9 - - + -
21E SER 4.2 3.1 - - - -
22E CYS* 3.8 29.4 - - + -
34E MET* 5.0 5.3 - - + +
35E ASN* 1.3 82.4 + - - +
37E VAL* 1.3 67.0 + - - +
47E TRP* 3.8 2.3 - - - -
48E ILE* 2.8 44.2 + - + +
49E GLY 3.1 8.8 + - - +
51E ILE* 5.5 2.2 - - + +
70E LEU* 3.4 32.0 - - + +
79E ALA* 4.0 14.9 - - + +
80E TYR 3.9 7.4 + - - -
81E MET* 3.7 40.4 - - + -
94E TYR* 5.0 1.3 - - + -
95E TYR 3.2 22.0 - - - -
96E CYS* 3.9 7.4 - - + +
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Residues in contact with VAL 37 (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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97D PHE* 4.4 9.0 - - + -
36E TRP* 1.3 81.4 - - - +
38E LYS* 1.3 71.3 + - - +
45E LEU* 4.0 23.3 - - + -
46E GLU 3.2 20.2 - - - +
47E TRP* 4.5 13.2 - - + -
48E ILE* 3.8 4.0 - - - -
93E ILE 3.9 0.3 - - - +
94E TYR* 3.3 5.2 - - - +
95E TYR* 2.8 37.2 + - + +
97E THR* 3.9 24.2 - - + -
103E PHE* 5.2 1.8 - - + -
106E TRP* 4.0 19.7 - - + -
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Residues in contact with LYS 38 (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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37E VAL* 1.3 75.1 - - - +
39E GLN* 1.3 64.9 + - - +
40E ARG* 4.4 12.9 + - - +
44E ASN 3.8 1.0 - - - +
45E LEU* 3.6 3.8 - - - -
46E GLU* 2.8 60.6 + - + +
48E ILE* 3.9 8.0 - - + +
64E PHE* 4.0 18.8 - - + -
89E GLU* 2.9 28.2 + - - +
90E ASP* 3.9 13.3 + - - +
92E ALA* 4.0 15.7 - - + -
93E ILE 3.6 3.1 - - - -
94E TYR* 3.7 35.5 + - + +
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Residues in contact with GLN 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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37D GLN* 3.0 41.2 + - - -
86D TYR* 3.1 18.0 + - - -
37E VAL 4.2 0.2 + - - -
38E LYS* 1.3 74.7 - - - +
40E ARG* 1.3 61.8 + - - +
41E HIS* 3.8 2.1 + - - -
42E GLY* 4.3 10.4 - - - +
43E LYS 3.3 25.5 + - - +
44E ASN 4.1 4.0 - - - +
45E LEU* 3.7 20.0 - - + +
92E ALA* 3.9 1.8 - - - -
93E ILE* 2.8 44.0 + - + +
95E TYR* 3.2 19.6 + - + -
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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