Contacts of the strand formed by residues 35 - 38 (chain B) in PDB entry 2OME
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 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 3.0 6.0 + - - +
34B PRO* 1.3 73.1 - - - +
36B VAL* 1.3 68.1 + - - +
37B ALA* 4.2 1.6 - - + +
56B THR* 3.5 28.5 - - + +
58B ALA* 4.6 14.4 - - + -
71B LYS* 4.4 25.6 - - + +
72B VAL* 4.1 23.3 - - + -
75B GLU* 4.2 13.4 + - + +
76B ALA* 3.6 31.0 - - + +
77B VAL* 2.9 32.5 + - - +
78B GLY 3.4 4.2 + - - -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PRO* 5.0 1.1 - - + -
35B LEU* 1.3 79.7 - - - +
37B ALA* 1.3 61.9 + - - +
51B LEU* 4.5 8.1 - - + -
55B ALA* 3.6 24.9 - - + -
56B THR 2.9 10.4 + - - +
57B VAL* 3.5 6.1 - - + +
58B ALA* 2.9 26.0 + - - +
77B VAL* 6.0 0.9 - - + -
78B GLY* 3.3 22.0 - - - +
80B MET* 4.4 19.1 - - + -
341B ILE* 4.0 37.9 - - + -
345B ILE* 4.7 4.7 - - + -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 4.2 2.2 - - + -
36B VAL* 1.3 76.0 - - - +
38B LEU* 1.3 61.0 + - - +
39B LEU* 3.6 6.6 + - + +
58B ALA* 3.3 9.2 - - + +
60B CYS* 4.4 10.5 - - - -
72B VAL* 3.4 37.0 - - + -
76B ALA* 4.5 4.2 - - + +
78B GLY 3.0 10.7 + - - +
79B ALA* 3.2 5.9 - - + +
80B MET* 2.9 26.5 + - - +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL 4.1 0.2 + - - -
37B ALA* 1.3 68.6 - - - +
39B LEU* 1.3 63.7 + - - +
40B ASP* 3.8 4.5 - - - +
41B GLY* 3.4 34.2 - - - +
43B ASP 2.8 32.3 - - - +
44B CYS* 4.5 10.8 - - - -
47B GLU* 4.9 7.4 - - - +
58B ALA 2.7 15.8 + - - +
59B PHE* 3.5 4.9 - - + -
60B CYS 2.9 25.1 + - - -
80B MET* 3.4 35.1 - - + +
82B TYR* 3.9 24.2 - - + +
104B ILE* 5.2 3.4 - - + -
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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
------------------------------------------------------------
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