Contacts of the strand formed by residues 744 - 748 (chain N) in PDB entry 2O5J
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 GLN 744 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002M GLU* 3.3 45.0 + - - +
1003M ASP* 4.7 0.3 + - - -
628N ARG* 3.9 23.3 - - + +
629N SER* 3.3 20.0 + - - +
630N VAL* 3.8 20.5 - - + +
631N ILE* 4.3 2.5 - - - -
704N ARG* 5.0 1.1 - - - -
705N ALA* 4.5 16.3 + - - +
742N GLY 4.1 9.3 - - - +
743N ASP* 1.3 82.7 - - - +
745N MET* 1.3 66.4 + - - +
746N ALA 4.3 0.5 + - - -
16X G 6.0 2.1 + - - +
17X C 5.8 3.6 + - - -
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Residues in contact with MET 745 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628N ARG* 3.7 3.0 - - - -
629N SER 3.5 21.9 + - - +
631N ILE* 3.4 30.8 - - + +
702N LEU* 4.3 23.3 - - + -
703N ASN 3.0 18.2 - - - +
704N ARG* 4.1 8.3 - - + -
726N ILE* 4.3 9.2 - - + +
728N LEU* 4.1 19.3 - - + -
736N PHE* 3.4 39.3 - - + -
738N ALA* 3.4 30.3 - - + -
744N GLN* 1.3 77.3 - - - +
746N ALA* 1.3 65.1 + - - +
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Residues in contact with ALA 746 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030M GLN* 4.2 20.6 - - + -
627N GLY 3.1 13.0 - - - +
628N ARG* 3.9 6.3 - - + -
702N LEU* 3.5 8.8 - - - +
703N ASN* 2.9 45.0 + - + +
726N ILE* 5.5 0.7 - - - +
744N GLN 4.3 0.4 + - - -
745N MET* 1.3 76.1 - - - +
747N VAL* 1.3 64.8 + - - +
748N HIS* 4.7 7.2 - - + +
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Residues in contact with VAL 747 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626N SER* 3.2 1.9 - - - -
627N GLY* 2.6 51.4 + - - +
628N ARG 4.2 0.7 - - - +
644N LEU* 5.4 9.2 - - + -
648N MET* 5.3 4.7 - - - -
652N LEU* 4.1 19.5 - - + +
700N VAL* 3.9 25.4 - - + -
701N LEU 3.1 13.0 - - - +
702N LEU* 4.4 8.3 - - + -
726N ILE* 4.7 16.6 - - + -
746N ALA* 1.3 77.8 - - - +
748N HIS* 1.3 80.0 + - - +
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Residues in contact with HIS 748 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030M GLN* 3.9 14.4 - - + -
1031M ARG 4.6 4.2 + - - -
1032M PHE* 3.5 32.9 - + - -
1052M MET* 3.7 13.2 - - + -
1056M LYS* 4.3 4.9 - - - +
623N VAL* 3.4 15.6 - - + +
625N TYR 3.5 7.2 - - - +
626N SER* 3.2 28.8 - - - -
700N VAL* 3.3 5.5 - - - +
701N LEU* 2.8 46.3 + - + +
703N ASN* 5.9 4.9 - - + +
713N ILE* 5.7 4.0 - - + -
746N ALA* 4.7 4.6 - - + +
747N VAL* 1.3 95.4 + - - +
749N VAL* 1.3 72.0 + - - +
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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