Contacts of the helix formed by residues 680 - 697 (chain A) in PDB entry 1OAK
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 VAL 680 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A LEU* 3.9 20.9 - - + -
529A GLU* 3.6 37.6 + - + +
532A VAL* 3.2 38.5 - - + +
533A LEU* 4.7 1.6 - - + +
653A ILE* 3.5 21.2 - - + +
679A SER* 1.3 72.5 - - - +
681A ASP* 1.3 68.5 + - - +
682A GLU 3.2 0.4 - - - -
683A LEU* 3.1 41.3 - - + +
684A GLU* 4.4 0.9 + - - +
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Residues in contact with ASP 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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532A VAL* 4.7 9.5 - - - +
679A SER* 2.9 18.1 + - - +
680A VAL* 1.3 90.7 - - - +
682A GLU* 1.3 61.3 + - + +
683A LEU 3.2 0.6 + - - -
684A GLU* 3.9 10.6 + - - +
685A GLN* 4.3 11.0 + - - +
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Residues in contact with GLU 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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676A VAL 4.8 1.6 - - - +
677A LEU* 3.7 21.3 - - + +
678A SER* 2.8 43.8 + - - -
679A SER* 2.9 15.6 + - - +
681A ASP* 1.3 76.9 - - + +
683A LEU* 1.3 67.1 + - - +
684A GLU 3.2 1.1 - - - -
685A GLN* 3.1 27.3 + - + +
686A GLN* 3.1 30.2 + - + +
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Residues in contact with LEU 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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532A VAL* 4.3 2.2 - - + +
533A LEU* 3.4 39.3 - - + -
536A PHE* 3.4 45.9 - - + -
621A LEU* 4.8 0.2 - - + -
651A VAL* 4.4 8.7 - - + -
653A ILE* 4.3 15.5 - - + -
677A LEU* 3.2 25.5 - - + +
680A VAL* 3.1 31.3 + - + +
681A ASP 3.2 0.6 - - - -
682A GLU* 1.3 78.5 - - - +
684A GLU* 1.3 57.0 + - - +
686A GLN* 3.5 1.2 + - - +
687A ARG* 2.8 29.3 + - - +
690A ILE* 5.1 0.6 - - + +
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Residues in contact with GLU 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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536A PHE* 4.9 2.7 - - - +
539A ASP* 4.3 10.2 - - - +
680A VAL 4.4 1.0 + - - +
681A ASP 3.9 8.3 + - - +
682A GLU 3.2 0.6 - - - -
683A LEU* 1.3 77.8 - - - +
685A GLN* 1.3 66.8 + - + +
687A ARG* 3.2 51.7 + - - +
688A ASP* 4.5 1.2 + - - +
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Residues in contact with GLN 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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681A ASP 4.3 11.3 + - - +
682A GLU* 3.1 31.4 + - - +
684A GLU* 1.3 78.3 - - + +
686A GLN* 1.3 64.5 + - + +
688A ASP* 4.7 2.6 + - - +
689A GLU* 3.6 13.5 - - - +
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Residues in contact with GLN 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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675A PHE* 3.9 19.8 - - - +
676A VAL 5.4 0.2 + - - -
677A LEU* 3.6 27.2 - - + +
682A GLU* 3.1 17.6 + - + +
683A LEU 3.7 1.6 - - - +
685A GLN* 1.3 81.0 - - + +
687A ARG* 1.3 65.9 + - - +
688A ASP 3.1 3.4 - - - -
689A GLU* 2.9 46.1 + - - +
690A ILE* 2.9 24.7 + - + +
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Residues in contact with ARG 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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536A PHE* 3.7 17.7 - - + -
539A ASP* 3.6 25.2 + - + +
540A MET* 3.9 18.8 - - - +
543A ARG* 2.6 64.7 - - - +
683A LEU 2.8 15.0 + - - +
684A GLU* 3.2 50.6 + - - +
686A GLN* 1.3 75.9 - - - +
688A ASP* 1.3 75.6 + - - +
690A ILE* 3.4 2.6 + - - +
691A VAL* 3.0 33.7 + - + +
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Residues in contact with ASP 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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507A MET* 4.8 11.5 - - - +
543A ARG* 3.2 30.1 + - - -
684A GLU 4.5 1.2 + - - -
685A GLN 4.7 2.4 + - - +
686A GLN 3.1 1.2 - - - -
687A ARG* 1.3 91.0 + - - +
689A GLU* 1.3 67.9 + - - +
691A VAL* 3.5 4.7 + - - +
692A SER* 3.0 28.4 + - - -
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Residues in contact with GLU 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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675A PHE* 4.6 8.1 - - + -
685A GLN 3.6 20.4 - - - +
686A GLN* 2.9 32.2 + - - +
688A ASP* 1.3 80.2 - - - +
690A ILE* 1.3 65.7 + - - +
692A SER* 3.3 6.8 + - - -
693A TYR* 3.0 24.4 + - - +
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Residues in contact with ILE 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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536A PHE* 3.8 24.2 - - + -
540A MET* 3.5 23.3 - - + -
619A LEU* 4.6 9.0 - - + -
651A VAL* 4.5 17.0 - - + -
675A PHE* 3.9 40.8 - - + -
677A LEU* 5.0 4.5 - - + -
683A LEU 5.1 0.2 - - - +
686A GLN* 2.9 26.3 + - + +
687A ARG 3.6 7.2 - - - +
689A GLU* 1.3 77.8 - - - +
691A VAL* 1.3 62.9 + - - +
692A SER 3.2 0.2 + - - -
693A TYR* 3.3 1.9 + - - +
694A LEU* 3.0 42.8 + - + +
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Residues in contact with VAL 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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507A MET 4.9 5.4 - - - +
508A TYR 5.6 0.4 - - - -
509A CYS* 4.7 6.7 - - + +
540A MET* 3.4 31.4 - - + -
543A ARG* 3.9 37.2 - - + +
544A LEU* 4.1 16.1 - - + +
687A ARG* 3.0 25.1 + - + +
688A ASP* 3.9 5.8 - - - +
690A ILE* 1.3 75.3 - - - +
692A SER* 1.3 62.5 + - - +
694A LEU* 4.1 7.2 - - - +
695A CYS* 3.1 22.4 + - + +
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Residues in contact with SER 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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688A ASP 3.0 19.1 + - - -
689A GLU* 3.5 8.3 - - - -
690A ILE 3.1 0.2 - - - -
691A VAL* 1.3 74.7 - - - +
693A TYR* 1.3 59.7 - - - +
695A CYS* 3.1 6.4 + - - +
696A ASP* 2.8 46.1 + - - -
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Residues in contact with TYR 693 (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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649A ILE* 3.5 17.5 - - + -
670A PRO 4.6 1.6 + - - -
671A GLU* 2.7 25.8 + - - -
673A LYS* 3.4 40.1 - - + +
675A PHE* 4.1 13.9 - + + -
689A GLU 3.0 16.3 + - - +
690A ILE 3.7 3.8 - - - +
692A SER* 1.3 75.0 - - - +
694A LEU* 1.3 72.3 + - + +
696A ASP* 3.1 20.4 + - + +
697A LEU* 3.1 54.7 + - + +
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Residues in contact with LEU 694 (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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513A LEU* 4.3 8.7 - - + +
515A LEU* 3.9 36.3 - - + -
540A MET* 4.6 4.0 - - + -
617A ILE* 3.4 28.7 - - + +
619A LEU* 4.2 17.7 - - + -
649A ILE* 3.8 35.9 - - + -
675A PHE* 5.0 0.4 - - + -
690A ILE* 3.0 28.4 + - + +
691A VAL* 4.1 5.8 - - - +
693A TYR* 1.3 86.4 - - + +
695A CYS* 1.3 62.6 + - - +
697A LEU* 3.3 10.6 + - - +
698A ALA* 3.7 7.3 + - - +
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Residues in contact with CYS 695 (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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508A TYR 4.8 2.7 - - - -
509A CYS* 2.0 56.1 - - + -
510A SER 4.5 0.4 - - - -
511A ARG* 3.5 26.7 - - - -
513A LEU* 5.3 1.1 - - - -
691A VAL* 3.1 19.4 + - + +
692A SER* 3.1 7.5 + - - +
694A LEU* 1.3 76.4 - - - +
696A ASP* 1.3 61.5 + - - +
697A LEU 3.1 0.2 - - - -
698A ALA* 2.9 30.7 + - - +
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Residues in contact with ASP 696 (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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511A ARG* 4.0 20.6 + - - +
692A SER* 2.8 32.4 + - - +
693A TYR* 3.1 11.0 + - + +
695A CYS* 1.3 75.7 - - - +
697A LEU* 1.3 59.9 + - + +
698A ALA 3.1 9.3 + - - +
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Residues in contact with LEU 697 (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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615A SER* 2.6 26.6 + - - -
617A ILE* 3.8 22.4 - - + -
647A ILE* 3.8 32.8 - - + +
649A ILE* 4.2 2.2 - - + -
671A GLU* 4.1 24.0 - - + +
693A TYR* 3.1 61.7 + - + +
694A LEU* 3.6 6.1 - - - +
695A CYS 3.1 1.2 - - - -
696A ASP* 1.3 80.5 - - + +
698A ALA* 1.3 52.7 + - - +
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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