Contacts of the strand formed by residues 44 - 49 (chain B) in PDB entry 2OPL
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 HIS 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TRP* 3.5 3.9 - - - -
40B MSE 2.8 47.4 + - + +
41B GLY 3.0 17.7 + - - +
42B GLY 3.1 0.2 - - - -
43B THR* 1.3 77.4 - - - +
45B ASN* 1.3 74.7 + - - +
68B ASP* 2.7 29.6 + - - -
69B LEU 3.3 17.0 - - - -
70B ASP* 3.3 10.0 + - - +
80B ARG* 3.7 43.5 + - + +
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Residues in contact with ASN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLY* 3.2 25.5 + - - -
97A THR* 3.8 13.9 - - + +
98A THR* 3.2 26.1 + - - -
37B ASN* 3.0 34.7 + - - +
38B GLN 3.6 8.7 - - - +
39B TRP* 3.9 8.4 - - + -
40B MSE 3.9 5.4 - - - -
43B THR 3.9 3.8 + - - -
44B HIS* 1.3 80.1 - - - +
46B GLN* 1.3 60.8 + - - +
68B ASP* 3.7 0.5 - - - -
69B LEU* 2.9 39.5 + - - +
84B PRO* 5.5 0.2 - - - +
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Residues in contact with GLN 46 (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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37B ASN* 3.2 5.7 - - - -
38B GLN* 2.9 36.6 + - + +
40B MSE 4.0 27.5 - - + +
45B ASN* 1.3 75.7 - - - +
47B ALA* 1.3 58.5 + - - +
48B THR* 4.3 4.2 + - - +
66B VAL* 3.1 37.4 - - + +
67B PHE 3.2 7.6 - - - +
68B ASP* 3.4 26.1 + - - +
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Residues in contact with ALA 47 (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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90A VAL* 3.8 33.0 - - + -
93A SER* 3.5 24.2 - - - +
35B ALA* 5.3 2.0 - - + -
36B THR 3.2 7.6 - - - +
37B ASN* 3.9 2.7 - - - +
46B GLN* 1.3 74.3 - - - +
48B THR* 1.3 62.4 + - - +
65B MSE 3.8 0.5 - - - +
66B VAL* 3.3 4.0 - - - +
67B PHE* 2.8 34.9 + - + +
69B LEU* 4.1 4.4 - - + +
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Residues in contact with THR 48 (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 ALA* 3.4 6.6 - - - +
36B THR* 2.8 45.5 + - - +
46B GLN* 5.0 4.3 + - - +
47B ALA* 1.3 75.5 + - - +
49B ILE* 1.3 74.8 + - - +
50B LYS* 4.4 4.6 + - + +
64B PRO* 3.9 20.2 - - + -
65B MSE 3.3 9.2 - - - +
66B VAL* 3.8 17.7 - - + +
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Residues in contact with ILE 49 (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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82A ALA* 4.4 2.0 - - + -
86A GLU* 3.5 46.7 - - + +
90A VAL* 3.8 26.9 - - + -
34B ARG 3.3 22.9 - - - +
35B ALA* 3.6 18.2 - - + -
48B THR* 1.3 73.4 - - - +
50B LYS* 1.3 62.4 + - - +
51B ASP 5.4 0.4 - - - +
62B ARG* 3.6 4.9 - - - +
64B PRO* 3.4 3.3 - - - +
65B MSE 2.8 59.2 + - + +
67B PHE* 3.9 11.4 - - + -
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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
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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