Contacts of the helix formed by residues 667 - 681 (chain A) in PDB entry 3KAS
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 ASP 667 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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664A GLU* 2.7 37.7 + - + +
665A LYS 3.3 0.2 - - - -
666A THR* 1.3 78.1 + - - +
668A ARG* 1.3 61.9 + - - +
669A PHE* 3.4 15.5 + - - +
670A VAL* 2.9 37.0 + - + +
671A MET* 3.1 9.7 + - - +
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Residues in contact with ARG 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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396A PHE 5.3 2.6 + - - -
397A VAL* 4.2 39.9 + - + +
665A LYS 5.8 0.2 - - - -
666A THR 3.5 6.4 + - - +
667A ASP* 1.3 73.6 + - - +
669A PHE* 1.3 61.2 + - + +
671A MET* 4.2 7.6 - - - +
672A LYS* 3.0 30.0 + - - +
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Residues in contact with PHE 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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667A ASP* 3.0 13.8 + - - +
668A ARG* 1.3 82.7 - - + +
670A VAL* 1.3 64.4 + - - +
672A LYS* 3.5 8.9 + - + +
673A LYS* 3.1 22.2 + - + +
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Residues in contact with VAL 670 (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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663A ALA* 3.8 23.8 - - + -
664A GLU* 3.4 21.1 - - - +
667A ASP* 2.9 49.6 + - + +
669A PHE* 1.3 76.4 - - - +
671A MET* 1.3 62.3 + - + +
673A LYS* 3.3 8.9 + - + +
674A LEU* 3.0 35.5 + - + +
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Residues in contact with MET 671 (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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605A VAL* 3.9 25.4 - - + +
606A GLU* 3.8 28.7 - - + -
660A PHE* 3.9 15.9 - - + -
663A ALA* 4.1 22.4 - - - -
664A GLU 4.2 2.2 - - - +
665A LYS* 4.0 35.4 - - + +
667A ASP 3.1 17.4 + - - +
668A ARG* 4.2 6.5 - - - +
670A VAL* 1.3 74.8 - - - +
672A LYS* 1.3 54.6 + - - +
674A LEU* 3.1 2.3 + - - +
675A ASN* 2.6 48.4 + - - +
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Residues in contact with LYS 672 (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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3A PO4 3.4 19.7 + - - +
398A GLU* 3.6 35.3 + - - +
400A ASP* 4.3 5.7 + - - -
401A HIS* 3.4 19.2 + - + -
668A ARG 3.0 23.1 + - - +
669A PHE* 3.5 10.1 - - + +
670A VAL 3.4 0.2 - - - -
671A MET* 1.3 74.1 - - - +
673A LYS* 1.3 55.9 + - + +
675A ASN* 3.7 5.0 - - - +
676A ASP* 2.8 67.7 + - - +
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Residues in contact with LYS 673 (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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669A PHE* 3.1 11.5 + - + +
670A VAL* 3.5 12.1 - - + +
672A LYS* 1.3 82.6 - - - +
674A LEU* 1.3 69.3 + - + +
676A ASP* 3.6 6.1 + - - +
677A ARG* 3.2 63.0 + - - +
751A GLY* 5.0 2.8 - - - -
752A ASP* 4.4 20.6 + - - -
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Residues in contact with LEU 674 (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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656A LEU* 3.9 19.6 - - + +
659A ASP* 3.7 39.3 - - + +
660A PHE* 3.4 31.5 - - + -
663A ALA* 3.8 17.5 - - + -
670A VAL* 3.0 26.4 + - + +
671A MET* 3.8 2.7 - - - +
673A LYS* 1.3 83.6 - - + +
675A ASN* 1.3 67.6 + - - +
677A ARG* 3.2 24.8 + - - +
678A VAL* 3.2 23.6 + - - +
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Residues in contact with ASN 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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398A GLU* 4.8 9.8 + - - +
446A ARG* 3.5 9.3 - - - +
605A VAL 2.8 26.2 + - - -
606A GLU* 3.7 1.9 - - - +
607A LEU* 3.1 39.0 + - + +
660A PHE* 3.6 15.8 - - - -
671A MET* 2.6 31.4 + - - +
672A LYS* 3.8 5.1 - - - +
674A LEU* 1.3 74.7 - - - +
676A ASP* 1.3 57.8 + - - +
678A VAL* 3.0 6.9 + - - +
679A MET* 2.9 35.0 + - + +
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Residues in contact with ASP 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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3A PO4 3.2 23.3 + - - -
398A GLU* 5.4 0.2 - - - +
401A HIS* 3.2 27.5 - - - -
672A LYS* 2.8 39.2 + - - +
673A LYS* 3.8 6.6 - - - +
675A ASN* 1.3 73.2 - - - +
677A ARG* 1.3 62.9 + - - +
679A MET* 3.3 14.0 + - - +
680A ARG* 3.2 46.3 + - - +
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Residues in contact with ARG 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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655A ARG* 4.9 3.8 - - - +
656A LEU* 3.6 30.3 - - + +
659A ASP* 3.4 24.2 + - - -
673A LYS* 3.2 53.4 + - - +
674A LEU* 3.2 13.9 + - - +
675A ASN 3.2 0.4 - - - -
676A ASP* 1.3 78.3 - - - +
678A VAL* 1.3 63.2 + - - +
680A ARG* 3.3 27.7 + - - +
681A VAL* 3.6 12.6 + - - +
748A ALA 4.7 10.1 - - - +
749A LEU* 3.5 33.9 + - + +
750A SER 4.8 3.0 + - - -
751A GLY* 3.6 25.7 - - - -
752A ASP* 5.0 0.6 - - - +
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Residues in contact with VAL 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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501A LEU* 5.0 3.4 - - + +
607A LEU* 4.6 11.0 - - + +
609A LEU* 3.6 45.5 - - + +
611A TYR* 3.8 22.7 - - + -
656A LEU* 3.8 5.8 - - + -
660A PHE* 3.6 26.2 - - + -
674A LEU 3.2 13.4 + - - +
675A ASN* 3.0 10.4 + - - +
677A ARG* 1.3 76.3 - - - +
679A MET* 1.3 59.0 + - - +
680A ARG 3.1 4.7 + - - -
681A VAL* 3.3 22.2 + - + +
682A GLU 4.6 0.7 + - - -
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Residues in contact with MET 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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398A GLU* 5.1 0.4 - - - +
401A HIS* 3.1 45.8 - - + +
475A HIS* 3.6 24.1 + - - +
476A LEU* 4.2 19.3 - - - +
477A LYS 4.7 1.6 - - - +
479A PHE* 3.5 35.6 - - + -
549A GLY 5.0 2.8 - - - +
551A PRO* 5.8 2.9 - - - +
607A LEU* 3.9 15.9 - - + +
609A LEU* 4.8 5.4 - - - -
675A ASN* 2.9 18.0 + - + +
676A ASP* 3.4 21.3 - - - +
677A ARG 3.2 0.4 - - - -
678A VAL* 1.3 76.3 - - - +
680A ARG* 1.3 61.0 + - + +
681A VAL 3.5 0.2 - - - -
682A GLU* 4.8 4.6 + - - +
683A TYR 5.0 1.6 + - - -
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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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3A PO4 4.6 6.7 + - - -
475A HIS* 4.5 11.2 - - + +
476A LEU* 4.0 29.5 - - + +
676A ASP* 3.2 46.9 + - - +
677A ARG* 3.8 17.9 - - - +
678A VAL 3.1 1.2 - - - -
679A MET* 1.3 80.3 - - + +
681A VAL* 1.3 70.1 + - - +
682A GLU 3.3 2.0 - - - -
683A TYR* 3.4 3.7 + - - +
684A HIS* 3.1 44.7 + - + +
748A ALA 6.0 2.0 - - - +
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Residues in contact with VAL 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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501A LEU* 4.2 13.2 - - + -
611A TYR* 4.0 21.8 - - + -
614A TYR* 4.2 25.4 - - + -
649A PHE* 4.6 9.9 - - + -
677A ARG 3.6 3.0 + - - +
678A VAL* 3.3 18.3 + - - +
680A ARG* 1.3 80.2 - - - +
682A GLU* 1.3 67.7 + - - +
684A HIS* 3.0 16.6 + - - +
685A PHE* 3.7 15.2 + - + -
745A ALA* 5.5 0.5 - - - +
749A LEU* 3.5 32.5 - - + +
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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