Contacts of the strand formed by residues 35 - 40 (chain B) in PDB entry 2OMZ
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 PHE 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LYS* 2.9 54.7 - - + -
34B VAL* 1.3 75.8 - - - +
36B TYR* 1.3 60.4 + - - +
37B SER* 4.2 1.2 + - - -
55B ARG* 3.1 55.6 - - + +
56B GLU* 4.2 6.5 - - + -
79B HIS 3.8 0.7 - - - +
80B ALA* 3.5 2.8 - - - -
81B VAL* 2.9 45.8 + - + +
82B SER 3.7 10.8 - - - -
83B SER* 3.6 31.6 - - - -
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B TRP* 4.1 16.6 - + - -
24B ILE* 4.4 6.5 - - + -
25B LYS* 3.5 19.8 - - + +
26B SER* 3.0 37.5 + - - -
29B ASP* 4.2 3.6 + - - +
34B VAL* 3.5 39.3 - - + +
35B PHE* 1.3 72.9 - - - +
37B SER* 1.3 60.8 + - - +
53B ILE* 3.7 25.5 - - + +
54B GLU 4.3 0.7 - - - +
55B ARG* 2.9 43.9 + - - +
56B GLU 4.2 6.7 - - - -
57B THR 4.5 1.6 - - - -
58B GLY* 3.6 26.7 - - - -
79B HIS 3.4 12.1 - - - +
80B ALA* 4.2 0.4 - - + -
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Residues in contact with SER 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE 5.2 0.9 + - - -
36B TYR* 1.3 77.0 - - - +
38B ILE* 1.3 72.3 + - - +
39B THR* 5.8 1.1 - - - -
53B ILE* 3.4 7.8 - - - +
55B ARG* 6.3 0.2 - - - -
78B SER* 3.5 1.2 - - - -
79B HIS* 2.9 49.8 + - - +
81B VAL* 5.8 3.1 - - - +
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Residues in contact with ILE 38 (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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24B ILE* 5.3 1.8 - - + -
37B SER* 1.3 81.0 - - - +
39B THR* 1.3 69.2 + - - +
43B ALA* 3.7 18.9 - - + +
44B ASP* 4.4 7.4 - - - +
51B PHE* 3.4 38.1 - - + +
52B ILE* 3.7 11.2 - - - +
53B ILE* 3.7 31.8 - - + +
60B LEU* 3.9 17.7 - - + -
76B LEU* 4.7 7.9 - - + -
77B PHE 3.3 11.9 - - - +
78B SER* 4.2 9.2 - - - -
79B HIS* 4.3 0.2 - - - -
94B ILE* 5.7 1.8 - - + -
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Residues in contact with THR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 5.6 1.3 - - - +
38B ILE* 1.3 79.9 - - - +
40B GLY* 1.3 62.7 + - - +
43B ALA* 3.8 4.7 - - - +
44B ASP* 3.4 24.7 - - - +
76B LEU* 3.3 8.8 - - - +
77B PHE* 3.0 38.5 + - - +
79B HIS* 2.8 35.0 + - + +
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Residues in contact with GLY 40 (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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39B THR* 1.3 77.4 + - - +
41B GLN* 1.3 61.9 + - - -
43B ALA* 3.1 19.6 + - - -
44B ASP* 3.0 16.7 + - - -
45B THR* 3.3 11.6 + - - -
75B THR 3.8 11.9 - - - -
76B LEU* 4.6 0.2 - - - -
77B PHE* 4.6 8.5 - - - -
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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