Contacts of the strand formed by residues 34 - 39 (chain E) in PDB entry 4XXD
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* 3.8 24.9 - - + -
27E PHE* 4.2 18.4 - - + -
29E PHE* 3.6 25.1 - - + -
32E TYR* 4.6 4.9 - - - +
33E SER* 1.3 81.2 - - - +
35E SER* 1.3 63.1 + - - +
50E GLN* 3.7 2.5 - - - +
51E ILE* 3.0 35.2 + - - +
71E ARG* 3.6 16.2 - - - +
78E LEU* 3.8 21.1 - - + -
92E CYS* 4.2 11.0 - - - -
93E ALA 3.7 15.7 - - - +
94E SER* 3.6 25.1 - - - +
20F PHE* 4.8 1.1 - - - -
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Residues in contact with SER 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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96D TRP* 3.1 30.2 - - - -
34E MET* 1.3 76.2 - - - +
36E TRP* 1.3 63.6 + - - +
37E VAL* 4.0 2.3 - - - +
47E LEU* 3.7 16.2 - - - +
49E ALA 3.2 15.5 - - - -
50E GLN* 4.0 9.9 - - - -
69E ILE* 4.2 2.2 - - - -
78E LEU* 4.3 0.4 - - - -
92E CYS* 3.4 7.6 - - - -
93E ALA* 2.7 42.5 + - - +
20F PHE* 4.2 2.6 - - - -
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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 GLU* 4.0 11.2 - - + -
20E LEU* 3.7 43.3 - - + -
21E SER 4.0 14.8 - - - -
22E CYS* 4.1 14.4 - - + -
35E SER* 1.3 72.6 - - - +
37E VAL* 1.3 57.7 + - - +
47E LEU* 3.8 1.6 - - - +
48E VAL* 2.8 38.7 + - + -
49E ALA 3.1 10.8 + - - +
69E ILE* 3.5 26.7 - - + -
78E LEU* 3.3 24.8 - - + +
79E TYR 3.4 14.8 + - - -
80E LEU* 3.5 38.8 - - + +
90E TYR* 4.2 12.8 - - + -
91E TYR 3.3 21.5 - - - -
92E CYS* 3.8 21.5 - - + -
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Residues in contact with VAL 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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96D TRP* 3.7 30.3 - - + -
98D PHE* 3.7 26.5 - - + -
35E SER* 4.0 2.7 - - - +
36E TRP* 1.3 77.5 - - - +
38E ARG* 1.3 62.3 + - - +
45E LEU* 3.9 8.1 - - + -
46E GLU 3.5 22.2 - - - +
47E LEU* 3.9 11.0 - - + +
48E VAL* 4.6 0.4 - - - -
90E TYR* 3.8 1.2 - - - -
91E TYR* 2.8 38.2 + - - +
93E ALA* 4.5 4.0 - - + -
98E TRP* 3.8 23.1 - - + -
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Residues in contact with ARG 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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37E VAL* 1.3 75.7 - - - +
39E GLN* 1.3 64.7 + - - +
40E ALA* 5.4 1.1 - - - +
44E GLY 3.7 1.6 - - - +
45E LEU* 3.7 1.0 - - - -
46E GLU* 2.7 75.7 + - + +
48E VAL* 3.5 19.4 - - + +
62E THR* 3.8 24.9 + - - +
63E VAL* 3.9 15.3 - - - +
67E PHE* 4.6 0.2 - - - -
85E GLU* 3.9 18.8 + - - +
86E ASP* 2.9 32.5 + - - +
88E ALA* 3.9 11.9 - - + -
89E VAL 3.4 8.3 - - - +
90E TYR* 3.1 34.2 + - + -
91E TYR* 5.0 1.3 - - - -
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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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38D GLN* 2.9 41.3 + - - +
87D TYR* 3.3 15.4 + - - -
38E ARG* 1.3 74.7 - - - +
40E ALA* 1.3 66.1 + - - +
41E PRO* 3.9 0.9 - - - +
43E LYS 2.9 25.2 + - - +
44E GLY 3.3 16.8 - - - +
45E LEU* 4.3 7.0 - - + +
88E ALA* 3.5 3.2 - - - -
89E VAL* 3.0 33.5 + - + +
91E TYR* 3.7 21.2 + - + +
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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