Contacts of the helix formed by residues 655 - 669 (chain A) in PDB entry 3OJX
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 GLU 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A MET* 1.3 81.0 - - - +
656A HIS* 1.3 67.7 + - - +
657A THR* 4.1 11.0 - - - +
658A GLN* 2.8 33.6 + - + +
659A ALA* 2.9 10.3 + - - +
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Residues in contact with HIS 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A ASN* 4.9 5.9 + - - -
645A TYR* 4.0 35.9 - + + +
646A ASP* 4.3 14.6 + - - -
649A ALA* 4.5 8.6 - - + +
654A MET 3.8 1.2 + - - -
655A GLU* 1.3 69.7 - - - +
657A THR* 1.3 67.5 + - - +
659A ALA* 2.9 18.5 + - - +
660A VAL* 2.9 25.6 + - + +
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Residues in contact with THR 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A GLU* 4.1 10.0 - - - +
656A HIS* 1.3 83.8 - - - +
658A GLN* 1.3 66.7 + - + +
660A VAL* 3.5 6.8 + - - +
661A ASP* 3.4 28.5 + - - +
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Residues in contact with GLN 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A MET* 3.5 24.0 - - + +
655A GLU* 2.8 40.9 + - + +
657A THR* 1.3 77.4 - - + +
659A ALA* 1.3 64.5 - - - +
661A ASP* 3.4 9.6 + - - +
662A TYR* 3.2 21.7 + - - +
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Residues in contact with ALA 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A TYR* 3.3 31.2 - - + +
648A VAL* 3.8 7.8 - - + +
649A ALA* 3.8 19.5 - - + +
654A MET* 3.7 10.0 - - + -
655A GLU 2.9 9.6 + - - +
656A HIS* 2.9 9.3 + - - +
658A GLN* 1.3 74.8 - - - +
660A VAL* 1.3 61.1 + - - +
662A TYR* 3.2 2.8 + - - +
663A VAL* 3.0 32.4 + - - +
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Residues in contact with VAL 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A TYR* 3.6 49.6 - - + +
656A HIS* 2.9 31.1 + - + +
657A THR* 3.7 9.6 - - - +
658A GLN 3.2 0.2 - - - -
659A ALA* 1.3 77.4 - - - +
661A ASP* 1.3 62.7 + - - +
663A VAL* 3.3 1.7 + - - +
664A LYS* 2.8 48.7 + - + +
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Residues in contact with ASP 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A THR* 3.4 19.2 + - - +
658A GLN* 3.4 10.4 + - - +
659A ALA 3.4 0.6 - - - -
660A VAL* 1.3 83.4 - - - +
662A TYR* 1.3 53.6 + - - +
664A LYS* 3.6 5.5 - - - +
665A LYS* 2.7 35.6 + - - +
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Residues in contact with TYR 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A TRP* 3.9 5.6 - + - -
620A ILE* 4.0 12.3 + - + +
621A HIS* 3.2 45.9 + + - +
648A VAL* 3.9 32.8 - - + -
654A MET* 4.2 18.6 - - + -
658A GLN 3.2 13.6 + - - +
659A ALA 3.4 9.4 - - - +
660A VAL 3.1 0.2 - - - -
661A ASP* 1.3 75.9 - - - +
663A VAL* 1.3 65.5 + - - +
665A LYS* 3.3 10.2 + - + +
666A LEU* 3.1 41.1 + - + +
671A ARG* 5.5 1.4 + - - -
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Residues in contact with VAL 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A GLN* 4.5 11.2 - - + +
644A PHE* 4.0 25.8 - - + +
645A TYR* 3.5 35.9 - - + -
648A VAL* 4.2 12.3 - - + -
659A ALA 3.0 16.4 + - - +
662A TYR* 1.3 74.9 - - - +
664A LYS* 1.3 63.9 + - - +
666A LEU* 3.1 27.8 + - + +
667A MET* 3.3 9.2 + - - +
672A TYR* 3.9 29.2 - - + -
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Residues in contact with LYS 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLU* 3.8 27.5 + - - -
641A GLN* 4.3 2.5 - - - +
645A TYR* 3.1 26.6 + - - +
660A VAL* 2.8 33.2 + - + +
661A ASP* 4.1 4.7 - - - +
663A VAL* 1.3 74.3 - - - +
665A LYS* 1.3 64.9 + - - +
667A MET* 3.3 21.2 + - - +
668A THR* 3.2 28.2 + - + +
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Residues in contact with LYS 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A ASP 2.7 23.9 + - - +
662A TYR* 3.5 11.9 - - + +
663A VAL 3.2 0.2 - - - -
664A LYS* 1.3 74.0 - - - +
666A LEU* 1.3 53.0 + - - +
668A THR* 3.0 11.9 + - - +
669A LYS* 2.7 61.7 + - + +
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Residues in contact with LEU 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A ILE* 4.3 15.9 - - + -
625A ALA 5.5 0.2 - - - +
627A ILE* 4.8 8.1 - - + -
648A VAL* 5.8 0.9 - - + -
662A TYR* 3.1 33.4 + - + +
663A VAL* 3.1 26.6 + - + +
665A LYS* 1.3 77.2 - - - +
667A MET* 1.3 60.9 + - - +
669A LYS* 3.1 7.0 + - + +
670A GLY 3.0 4.9 + - - -
671A ARG* 2.8 71.6 + - + +
672A TYR* 4.0 22.4 - - + -
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Residues in contact with MET 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU* 4.5 13.5 - - + +
179A GLU* 5.8 2.0 - - - +
180A HIS* 5.6 9.4 - - - +
641A GLN* 3.7 29.4 - - - +
663A VAL* 3.4 13.2 - - - +
664A LYS* 3.6 22.9 - - - +
665A LYS 3.2 0.6 - - - -
666A LEU* 1.3 75.2 - - - +
668A THR* 1.3 60.9 + - + +
670A GLY* 2.7 22.9 + - - -
672A TYR* 3.5 51.5 - - + +
674A LEU* 5.0 12.1 - - + -
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Residues in contact with THR 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A LYS* 3.2 13.4 + - + +
665A LYS* 3.0 21.7 + - - +
667A MET* 1.3 77.4 - - + +
669A LYS* 1.3 59.6 + - - +
670A GLY* 3.0 5.4 + - - -
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Residues in contact with LYS 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A LYS* 2.7 42.8 + - + +
666A LEU* 3.4 10.8 - - + +
667A MET 3.1 0.2 - - - -
668A THR* 1.3 78.7 + - - +
670A GLY* 1.3 59.1 + - - +
671A ARG* 3.4 18.9 + - - +
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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