Contacts of the strand formed by residues 32 - 37 (chain E) in PDB entry 5U2V
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 LEU 32 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 6.0 3.4 - - + -
22E CYS* 4.3 15.7 - - - -
24E TYR* 3.8 31.4 - - + -
29E PHE* 4.0 11.4 - - + -
31E GLY* 1.3 74.3 - - - +
33E PHE* 1.3 70.5 + - - +
34E TRP* 3.6 23.5 - - + +
47E SER 4.5 0.2 - - - -
48E TYR* 3.4 5.3 - - - -
49E ASN* 2.9 38.5 + - + +
64E LEU* 4.4 5.8 - - + -
71E SER* 3.5 37.9 - - - +
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Residues in contact with PHE 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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30E ASN 5.2 1.8 - - - -
31E GLY* 4.3 10.1 - - - -
32E LEU* 1.3 88.0 - - - +
34E TRP* 1.3 64.3 + - - +
35E TYR* 3.6 34.3 + + + -
45E PHE* 3.7 30.3 - + - -
47E SER 3.3 4.3 - - - +
48E TYR* 3.4 34.1 - + + -
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Residues in contact with TRP 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLN* 3.7 22.4 - - - -
20E ILE* 3.6 43.1 - - + -
21E ASN 4.1 0.9 - - - -
22E CYS* 3.5 32.8 - - + -
32E LEU* 3.6 16.3 - - + +
33E PHE* 1.3 74.2 - - - +
35E TYR* 1.3 61.4 + - - +
45E PHE* 4.1 1.4 - - - -
46E LEU* 2.8 37.6 + - + -
47E SER* 2.9 34.7 + - - +
49E ASN* 5.3 0.9 - - - -
62E SER* 4.3 6.7 - - - -
71E SER* 3.0 19.9 + - - -
72E TYR* 4.0 2.6 - - - -
73E LEU* 3.6 38.7 - - + +
86E TYR* 4.7 14.1 - - - -
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Residues in contact with TYR 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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33E PHE* 3.6 38.6 - + + -
34E TRP* 1.3 81.1 - - - +
36E GLN* 1.3 58.6 + - - +
37E GLN* 4.1 0.6 + - - +
43E PRO* 4.2 21.5 - - + -
44E THR* 3.3 12.3 - - - +
45E PHE* 3.4 40.5 - + + +
46E LEU* 4.1 5.6 - - - +
86E TYR* 3.4 23.2 - - - -
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Residues in contact with GLN 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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35E TYR* 1.3 71.7 - - - +
37E GLN* 1.3 64.1 + - - +
38E HIS* 3.4 33.0 + - + +
42E ALA 3.8 1.6 - - - +
43E PRO* 3.3 0.9 - - - +
44E THR* 2.7 52.4 + - - +
46E LEU* 3.8 24.9 - - + +
60E PHE* 4.4 22.2 - - - -
75E LEU* 6.0 1.0 - - - +
81E LYS 4.6 5.3 + - - -
82E ASP* 4.7 7.7 + - - +
84E ALA* 3.9 19.0 - - + +
85E SER 3.7 3.8 - - - +
86E TYR* 4.8 1.1 - - - +
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Residues in contact with GLN 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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35E TYR* 5.5 0.4 - - + +
36E GLN* 1.3 77.7 - - - +
38E HIS* 1.3 66.3 + - - +
39E ALA* 3.7 1.3 + - - -
40E GLY 5.8 1.0 - - - +
41E GLU 3.1 28.4 + - - +
42E ALA 4.1 1.3 - - - -
43E PRO* 3.9 31.7 - - + +
84E ALA* 4.0 2.0 - - - -
85E SER* 2.8 48.7 + - - +
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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