Contacts of the strand formed by residues 626 - 633 (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 SER 626 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006M HIS 4.4 0.2 - - - +
1008M ARG* 3.3 15.9 + - - +
1028M GLY 4.9 1.6 + - - -
1029M GLY* 3.9 4.0 - - - -
1030M GLN* 2.9 36.4 + - - +
623N VAL* 4.0 9.0 - - - -
624N ASP 3.6 3.4 + - - -
625N TYR* 1.3 74.6 - - - +
627N GLY* 1.3 59.6 + - - +
652N LEU* 3.3 20.1 - - - +
747N VAL 3.2 7.4 - - - -
748N HIS* 3.2 27.1 - - - -
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Residues in contact with GLY 627 (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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1006M HIS 3.4 11.7 - - - -
1007M ALA* 4.4 3.8 - - - -
1030M GLN* 3.3 8.2 - - - +
626N SER* 1.3 77.9 - - - +
628N ARG* 1.3 60.4 + - - +
648N MET* 4.5 2.5 - - - -
652N LEU* 4.5 2.7 - - - -
746N ALA* 3.1 5.2 - - - +
747N VAL* 2.6 50.0 + - - +
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Residues in contact with ARG 628 (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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1001M VAL 5.1 3.2 + - - -
1002M GLU* 3.9 14.5 + - - +
1005M MET* 3.7 3.4 - - - +
1006M HIS* 3.4 40.4 + - + +
1030M GLN* 2.9 39.0 + - - +
627N GLY* 1.3 72.3 - - - +
629N SER* 1.3 61.5 + - - +
648N MET* 3.0 15.6 - - - +
744N GLN* 3.9 23.5 - - + +
745N MET 3.7 7.6 - - - +
746N ALA* 3.9 11.2 - - + +
747N VAL* 4.8 1.3 - - - -
17X C 2.5 30.6 + - - -
18X G 2.8 42.9 + - - -
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Residues in contact with SER 629 (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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1002M GLU 5.4 0.7 - - - -
1003M ASP 5.2 2.0 + - - -
1005M MET* 3.7 9.8 - - - +
628N ARG* 1.3 78.5 - - - +
630N VAL* 1.3 81.4 + - - +
631N ILE* 4.1 1.2 - - - +
648N MET* 3.6 19.5 - - - -
724N GLN* 2.7 29.5 + - - +
725N SER* 3.7 0.7 - - - -
726N ILE* 3.8 11.4 - - - +
744N GLN* 3.3 24.5 - - - +
745N MET 3.5 14.3 + - - +
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Residues in contact with VAL 630 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836M GLY 4.7 13.9 - - - +
838M LYS* 6.5 0.9 - - - -
848M VAL* 4.7 15.7 - - + -
1003M ASP* 4.1 26.2 - - + +
629N SER* 1.3 81.2 + - - +
631N ILE* 1.3 71.2 + - - +
632N VAL* 5.2 0.2 - - + -
724N GLN* 4.4 12.1 - - - +
725N SER* 3.2 14.1 - - - -
726N ILE* 2.9 24.8 + - - -
742N GLY* 5.3 6.3 - - - +
743N ASP 4.1 11.4 - - - +
744N GLN* 3.8 22.7 - - + +
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Residues in contact with ILE 631 (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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848M VAL* 5.1 1.9 - - - +
629N SER 4.1 1.6 - - - +
630N VAL* 1.3 81.4 - - - +
632N VAL* 1.3 71.9 + - - +
726N ILE* 3.5 16.4 - - + +
728N LEU* 4.7 7.4 - - + -
738N ALA* 4.0 20.6 - - + -
739N ASP 4.7 0.9 - - - +
740N PHE* 3.6 26.6 - - + +
743N ASP* 3.2 41.3 - - + +
745N MET* 3.4 55.0 - - + +
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Residues in contact with VAL 632 (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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687M ALA* 5.5 0.7 - - + -
835M VAL* 4.7 3.1 - - + +
848M VAL* 4.2 21.8 - - + -
849M VAL 3.8 5.2 - - - +
850M ALA* 3.5 39.9 - - + +
630N VAL* 4.6 1.6 - - + +
631N ILE* 1.3 81.8 - - - +
633N VAL* 1.3 72.3 + - + +
725N SER* 3.3 31.6 - - - +
726N ILE 2.9 7.4 + - - +
727N GLN* 3.1 10.6 - - + +
728N LEU 3.1 19.6 + - - +
740N PHE* 3.3 14.1 - - + -
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Residues in contact with VAL 633 (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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681M GLY* 3.3 25.1 - - - +
682M TYR* 3.4 19.7 - - + +
684M PHE* 4.6 3.8 - - + -
687M ALA* 4.4 3.4 - - + -
850M ALA* 3.8 15.8 - - + +
632N VAL* 1.3 78.3 - - + +
634N GLY* 1.3 62.7 + - - +
635N PRO* 3.2 22.0 - - + +
727N GLN* 4.0 7.3 + - - +
728N LEU 4.0 1.3 - - - -
730N PRO* 4.6 17.3 - - + -
740N PHE* 3.0 37.8 - - + -
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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