Contacts of the helix formed by residues 674 - 692 (chain A) in PDB entry 2O8F
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 GLY 674 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672A MET 3.4 1.2 + - - -
673A GLY* 1.3 80.4 - - - +
675A LYS* 1.3 67.1 + - - +
677A THR* 4.2 0.9 - - - -
678A TYR* 3.5 22.2 + - - +
802A VAL* 4.6 5.5 - - - +
815A TYR* 4.5 1.1 - - - -
936A ADP 2.9 41.0 + - - -
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Residues in contact with LYS 675 (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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667A ILE* 4.0 25.0 - - + +
668A THR 3.9 24.7 - - - +
669A GLY 3.7 9.8 + - - +
670A PRO 3.3 16.1 + - - +
671A ASN* 4.5 4.8 - - - +
674A GLY* 1.3 75.8 - - - +
676A SER* 1.3 67.2 + - - +
678A TYR* 3.3 5.9 + - - +
679A ILE* 3.3 27.5 + - - +
748A ASP* 5.8 2.2 - - - +
749A GLU* 4.8 15.5 + - - -
781A ALA* 4.3 13.7 - - + -
782A THR 4.7 11.2 - - - -
783A HIS* 6.0 1.1 - - - +
802A VAL* 3.8 19.7 - - + -
936A ADP 2.8 34.8 + - - +
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Residues in contact with SER 676 (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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675A LYS* 1.3 72.4 - - - +
677A THR* 1.3 61.8 + - - +
679A ILE* 3.1 16.1 - - - +
680A ARG* 3.0 41.9 + - - +
748A ASP* 3.0 22.0 + - - -
935A MG 2.2 31.8 - - - -
936A ADP 2.9 17.5 + - - -
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Residues in contact with THR 677 (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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639A HIS* 3.6 30.8 - - + -
642A VAL* 4.2 10.4 - - + +
650A PHE* 4.1 13.0 - - + -
674A GLY 4.3 0.4 - - - -
675A LYS 3.3 0.2 - - - -
676A SER* 1.3 73.4 - - - +
678A TYR* 1.3 57.1 + - - +
680A ARG* 3.5 6.0 + - - +
681A GLN* 2.9 29.8 + - - +
936A ADP 2.8 60.3 + - + +
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Residues in contact with TYR 678 (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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653A ASN* 3.7 19.3 - - + +
654A ASP 2.6 23.0 + - - -
655A VAL* 3.5 29.5 - - + +
656A TYR 4.9 0.2 + - - -
665A HIS* 6.1 0.5 - - - -
667A ILE* 3.7 19.7 - - + -
674A GLY 3.5 16.2 + - - +
675A LYS* 3.3 4.2 + - - +
676A SER 3.3 0.6 - - - -
677A THR* 1.3 79.4 - - - +
679A ILE* 1.3 57.1 + - - +
681A GLN* 3.4 30.2 - - - +
682A THR* 2.8 21.3 + - - -
779A MET* 3.5 22.6 - - + +
800A LEU* 4.2 15.4 - - + +
817A VAL* 3.6 36.1 - - + +
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Residues in contact with ILE 679 (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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667A ILE* 3.6 30.1 - - + -
675A LYS 3.3 6.7 + - - +
676A SER* 3.1 17.9 - - - +
678A TYR* 1.3 76.4 - - - +
680A ARG* 1.3 64.6 + - + +
682A THR* 3.7 11.4 - - - -
746A ILE* 3.7 40.1 - - + +
747A ILE 4.0 4.9 - - - +
748A ASP* 3.8 37.7 - - + +
779A MET* 3.7 26.1 - - + +
781A ALA* 4.0 18.8 - - + +
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Residues in contact with ARG 680 (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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308A ARG 4.1 4.9 + - - -
309A ALA* 3.3 52.3 + - + +
310A LEU* 3.5 9.4 - - - +
639A HIS* 4.2 12.3 - - + +
676A SER* 3.0 35.9 + - - +
677A THR* 4.0 5.2 - - - +
679A ILE* 1.3 79.8 - - + +
681A GLN* 1.3 58.1 + - - +
682A THR 3.1 2.0 - - - -
683A GLY 3.2 2.6 + - - -
684A VAL* 3.0 31.8 + - - +
712A VAL* 3.4 29.7 - - + +
746A ILE* 4.9 5.2 - - + -
748A ASP* 3.1 24.2 + - - -
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Residues in contact with GLN 681 (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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637A SER* 3.2 33.7 + - - +
638A ARG 3.4 5.6 - - - +
639A HIS* 2.9 47.3 + - + +
650A PHE* 3.2 18.3 - - - -
653A ASN* 4.6 4.9 - - - +
655A VAL* 5.2 0.2 - - - +
677A THR 2.9 20.5 + - - +
678A TYR* 3.4 32.0 - - - +
680A ARG* 1.3 72.9 - - - +
682A THR* 1.3 64.6 + - - +
684A VAL* 3.7 6.6 - - - +
685A ILE* 3.0 34.6 + - - +
936A ADP 5.9 0.8 + - - -
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Residues in contact with THR 682 (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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632A ILE* 5.6 2.5 - - + -
634A LEU* 4.7 9.1 - - + +
655A VAL* 3.8 35.8 - - + +
657A PHE* 4.5 5.6 - - + -
678A TYR 2.8 17.2 + - - -
679A ILE 3.7 8.7 - - - -
680A ARG 3.1 0.4 - - - -
681A GLN* 1.3 78.7 - - - +
683A GLY* 1.3 59.0 + - - +
685A ILE* 3.2 7.0 + - - +
686A VAL* 3.0 41.6 + - + +
744A LEU* 4.9 8.3 - - + -
746A ILE* 5.9 0.4 - - - -
779A MET* 3.6 21.4 - - - +
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Residues in contact with GLY 683 (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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310A LEU* 3.7 18.0 - - - +
679A ILE 3.8 4.0 + - - -
680A ARG 3.2 7.1 + - - -
682A THR* 1.3 78.9 - - - +
684A VAL* 1.3 61.4 + - - +
686A VAL 3.6 0.3 + - - -
687A LEU* 3.2 19.2 + - - +
708A ILE* 3.4 13.4 - - - +
744A LEU* 3.8 20.2 - - - -
746A ILE* 4.0 7.1 - - - +
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Residues in contact with VAL 684 (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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310A LEU* 3.8 36.8 - - + +
326A LEU* 3.9 23.8 - - + -
639A HIS* 4.4 14.4 - - + +
640A ALA* 4.9 9.6 - - + +
641A CYS* 5.5 2.7 - - - -
680A ARG 3.0 23.0 + - - +
681A GLN* 3.7 8.7 - - - +
682A THR 3.2 0.2 - - - -
683A GLY* 1.3 72.4 - - - +
685A ILE* 1.3 56.0 + - + +
687A LEU* 3.1 5.9 + - - +
688A MET* 2.7 59.1 + - - +
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Residues in contact with ILE 685 (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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634A LEU* 3.7 27.1 - - + -
637A SER* 3.8 28.3 - - - -
638A ARG 3.9 16.6 - - - +
640A ALA 6.1 0.4 - - - +
681A GLN* 3.0 22.8 + - + +
682A THR* 3.6 4.0 - - - +
684A VAL* 1.3 76.3 - - + +
686A VAL* 1.3 54.2 + - + +
688A MET* 3.1 9.5 + - - +
689A ALA* 2.8 32.9 + - - +
695A VAL* 3.4 23.9 - - + +
696A PRO* 3.9 20.2 - - + +
697A CYS* 4.1 11.4 - - - -
702A VAL* 4.7 3.4 - - + -
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Residues in contact with VAL 686 (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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300A MET* 4.8 0.2 - - + -
632A ILE* 4.4 19.3 - - + -
634A LEU* 5.8 0.7 - - + -
682A THR* 3.0 25.9 + - + +
683A GLY 3.8 5.2 - - - +
685A ILE* 1.3 74.4 - - + +
687A LEU* 1.3 63.1 + - - +
689A ALA* 3.3 4.6 + - - +
690A GLN* 3.2 33.7 + - - +
702A VAL* 4.0 23.7 - - + +
705A VAL* 3.8 28.5 - - + -
708A ILE* 4.1 11.2 - - + -
744A LEU* 3.9 17.5 - - + -
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Residues in contact with LEU 687 (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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300A MET* 4.1 12.1 - - - -
302A LEU* 4.3 23.8 - - + -
310A LEU* 3.8 23.3 - - + -
312A LEU* 3.9 20.2 - - + -
326A LEU* 5.0 4.0 - - + -
346A ILE* 4.2 21.3 - - + +
349A PRO* 4.1 13.1 - - + +
683A GLY 3.2 12.6 + - - +
684A VAL* 3.1 5.9 + - - +
686A VAL* 1.3 76.0 - - - +
688A MET* 1.3 66.1 + - - +
690A GLN* 3.0 11.6 + - - +
691A ILE* 3.1 43.2 + - + +
708A ILE* 4.0 6.1 - - + -
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Residues in contact with MET 688 (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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326A LEU* 4.4 15.5 - - + -
330A LEU* 4.0 28.5 - - + -
619A TYR* 4.2 9.2 - - + -
640A ALA* 4.0 12.8 - - + -
684A VAL* 2.7 44.3 + - + +
685A ILE* 3.5 7.0 - - - +
687A LEU* 1.3 72.5 - - - +
689A ALA* 1.3 60.9 + - - +
690A GLN 3.5 0.2 + - - -
691A ILE* 3.5 12.7 + - + +
693A CYS* 3.2 34.6 + - + +
694A PHE 3.4 21.8 - - - +
695A VAL* 4.5 4.5 - - + -
696A PRO* 3.8 24.5 - - + -
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Residues in contact with ALA 689 (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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356A ILE* 3.3 18.0 - - - +
360A LEU* 4.6 4.2 - - - +
622A PRO* 3.8 21.0 - - + +
624A ILE* 4.1 10.7 - - + +
685A ILE 2.8 16.6 + - - +
686A VAL 3.4 7.2 - - - +
687A LEU 3.1 0.2 - - - -
688A MET* 1.3 76.5 - - - +
690A GLN* 1.3 59.7 + - + +
691A ILE 3.5 0.2 - - - -
692A GLY* 3.9 3.8 + - - -
693A CYS 4.1 4.0 - - - -
695A VAL* 3.9 9.8 - - + +
702A VAL* 4.1 22.7 - - + -
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Residues in contact with GLN 690 (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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300A MET* 3.4 29.0 - - + +
349A PRO* 4.2 3.6 - - + -
350A LEU* 2.9 53.0 + - - +
351A MET* 4.5 1.8 - - - -
356A ILE* 4.0 14.8 - - + +
624A ILE* 6.3 0.7 - - + -
686A VAL* 3.2 17.3 + - - +
687A LEU 3.0 6.8 + - - +
689A ALA* 1.3 79.7 - - + +
691A ILE* 1.3 61.4 + - - +
692A GLY 3.2 1.6 - - - -
702A VAL* 4.9 3.3 - - + +
703A SER 4.3 0.5 - - - +
704A ILE* 3.4 24.9 - - + +
705A VAL* 2.7 35.3 + - - +
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Residues in contact with ILE 691 (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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326A LEU* 5.5 0.9 - - + -
330A LEU* 4.1 16.8 - - + -
345A TRP* 3.8 31.9 - - + +
346A ILE* 3.8 22.0 - - + +
349A PRO* 4.9 2.2 - - + -
350A LEU* 5.4 0.2 - - - -
356A ILE* 4.8 0.7 - - - -
359A ARG* 2.3 36.8 + - - +
608A PHE* 3.7 30.5 - - + -
687A LEU* 3.1 37.7 - - + +
688A MET* 3.9 15.0 - - + +
689A ALA 3.5 0.8 - - - -
690A GLN* 1.3 78.8 - - - +
692A GLY* 1.3 59.1 + - - +
693A CYS* 4.6 3.8 - - + +
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Residues in contact with GLY 692 (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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356A ILE* 4.1 19.7 - - - -
359A ARG* 3.6 25.5 - - - +
360A LEU* 3.7 18.7 - - - +
363A VAL* 3.7 11.3 - - - +
608A PHE* 4.4 5.2 - - - -
688A MET 3.8 0.4 + - - -
689A ALA 3.9 0.8 + - - -
690A GLN 3.2 3.2 - - - -
691A ILE* 1.3 81.9 - - - +
693A CYS* 1.3 60.4 + - - +
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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