Contacts of the helix formed by residues 659 - 681 (chain A) in PDB entry 2KIS
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 LYS 659 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ASN* 2.6 11.6 + - + -
658A PRO* 1.3 74.3 - - - +
660A GLU* 1.3 78.7 + - + +
661A ARG 3.1 0.9 - - - -
662A LYS* 3.1 12.9 + - - +
663A GLN* 3.0 20.5 + - - +
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Residues in contact with GLU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A LEU* 3.5 26.1 - - + +
622A MET* 4.7 4.6 - - + +
656A LEU* 3.5 33.4 - - + -
657A ASN* 3.1 13.0 + - - +
659A LYS* 1.3 98.1 - - + +
661A ARG* 1.3 58.0 + - - +
663A GLN* 3.1 41.1 + - - +
664A VAL* 2.9 25.3 - - - +
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Residues in contact with ARG 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A PHE* 3.4 28.9 - - + -
640A TRP* 3.4 29.4 - - + -
653A TYR* 3.0 49.0 + - - -
654A LEU* 4.2 8.7 - - - +
656A LEU* 3.6 23.3 + - + +
657A ASN 2.7 15.7 + - - +
658A PRO* 4.1 28.5 - - + +
660A GLU* 1.3 77.9 - - - +
662A LYS* 1.3 63.7 + - - +
664A VAL* 3.4 5.9 + - - +
665A PHE* 3.2 22.7 + - - +
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Residues in contact with LYS 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A TRP* 5.2 7.7 - - - +
658A PRO 3.2 21.6 + - - +
659A LYS* 3.1 8.0 + - - +
661A ARG* 1.3 79.3 - - - +
663A GLN* 1.3 62.3 + - - +
665A PHE* 3.4 31.7 + - - +
666A ASP* 3.2 23.2 + - + +
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Residues in contact with GLN 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A MET* 3.1 30.3 - - + +
659A LYS* 3.0 17.2 - - + +
660A GLU* 3.1 53.1 + - - +
662A LYS* 1.3 73.4 - - - +
664A VAL* 1.3 53.5 + - - -
666A ASP* 4.9 2.9 - - - -
667A GLN* 2.8 49.6 + - + +
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Residues in contact with VAL 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A MET* 3.5 38.8 - - + +
625A PHE* 3.7 20.0 - - + -
626A LYS* 4.1 19.6 - - + +
629A LEU* 3.5 21.9 - - + +
656A LEU* 4.7 4.7 - - + -
660A GLU 2.9 25.7 + - - +
661A ARG* 3.8 7.0 - - - +
662A LYS 3.4 0.4 - - - -
663A GLN* 1.3 77.2 - - - +
665A PHE* 1.3 55.4 + - - +
667A GLN* 4.2 3.5 - - - +
668A TYR* 3.0 30.7 + - - +
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Residues in contact with PHE 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 4.6 3.6 - - + -
634A VAL* 3.6 26.2 - - + -
635A SER 4.8 0.9 - - - -
638A SER 4.3 11.9 - - - -
640A TRP* 3.4 65.5 - + + -
643A GLU* 4.6 2.0 - - + -
661A ARG 3.2 10.8 + - - +
662A LYS* 3.5 28.9 - - - +
663A GLN 3.1 1.0 - - - -
664A VAL* 1.3 74.2 - - - +
666A ASP* 1.3 62.1 + - - +
667A GLN 3.1 1.1 - - - -
668A TYR* 3.1 3.3 + + - +
669A VAL* 2.9 60.2 + - + +
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Residues in contact with ASP 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LYS* 3.2 21.2 + - + +
663A GLN* 4.2 3.4 - - - +
665A PHE* 1.3 82.9 - - + +
667A GLN* 1.3 67.2 + - + +
669A VAL* 3.2 11.6 - - - +
670A LYS* 3.0 33.9 + - - +
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Residues in contact with GLN 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A MET* 6.1 3.6 - - + -
663A GLN* 2.8 32.6 + - + +
664A VAL* 4.2 3.8 - - - +
666A ASP* 1.3 86.0 + - + +
668A TYR* 1.3 59.3 + - - +
670A LYS* 3.5 31.1 + - - +
671A THR* 2.9 29.9 + - - +
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Residues in contact with TYR 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A LYS* 4.1 22.7 - - + -
629A LEU* 3.3 46.3 + - + -
630A LEU* 3.8 21.3 - - + +
633A GLY* 4.4 3.5 - - - -
634A VAL* 3.5 36.4 + - + -
636A ALA 4.7 3.8 - - - -
664A VAL 3.0 22.1 + - - +
665A PHE* 3.1 2.2 + + - +
667A GLN* 1.3 74.9 - - - +
669A VAL* 1.3 67.2 - - + +
671A THR* 3.4 6.0 - - + +
672A ARG* 2.8 71.0 + - + +
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Residues in contact with VAL 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A SER 4.3 0.9 - - - +
636A ALA* 3.7 36.1 - - - +
665A PHE* 2.9 57.5 + - + +
666A ASP* 3.2 19.5 - - - +
668A TYR* 1.3 81.7 - - + +
670A LYS* 1.3 61.7 + - + +
673A ALA* 2.9 31.7 + - - +
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Residues in contact with LYS 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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666A ASP* 3.0 21.3 + - - +
667A GLN* 3.5 31.8 + - - +
668A TYR 3.1 0.6 - - - -
669A VAL* 1.3 82.1 - - + +
671A THR* 1.3 79.4 + - - +
673A ALA* 4.0 1.0 - - - +
674A GLU* 3.3 32.3 + - + +
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Residues in contact with THR 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A GLN 2.9 19.5 + - - +
668A TYR* 3.4 10.5 - - + +
670A LYS* 1.3 89.8 - - - +
672A ARG* 1.3 78.3 + - + +
674A GLU* 3.4 6.7 + - - +
675A GLU* 3.3 28.6 + - - +
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Residues in contact with ARG 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A LEU* 4.3 26.9 - - - +
636A ALA* 4.0 5.8 - - + -
668A TYR* 2.8 59.0 + - + +
671A THR* 1.3 76.0 - - + +
673A ALA* 1.3 61.3 + - - +
675A GLU* 3.2 31.1 + - - +
676A GLU* 2.9 49.9 + - - +
679A GLU* 5.1 3.8 + - - -
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Residues in contact with ALA 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ALA* 3.7 16.5 - - + +
637A PHE* 4.9 6.1 - - + -
669A VAL 2.9 22.9 + - - +
670A LYS* 4.0 1.6 - - - +
672A ARG* 1.3 79.7 - - - +
674A GLU* 1.3 65.8 + - - +
675A GLU 2.9 0.3 + - - -
676A GLU* 3.7 11.9 - - - -
677A ARG* 2.8 33.1 + - + +
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Residues in contact with GLU 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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670A LYS* 3.3 24.7 + - + +
671A THR* 3.6 7.4 - - - +
673A ALA* 1.3 77.4 - - - +
675A GLU* 1.3 65.9 + - - +
677A ARG* 4.0 5.3 - - - +
678A ARG* 3.2 30.7 + - - +
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Residues in contact with GLU 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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671A THR* 3.3 20.2 - - - +
672A ARG* 3.2 28.0 + - - +
673A ALA 2.9 1.2 + - - -
674A GLU* 1.3 81.0 - - - +
676A GLU* 1.3 60.1 + - - +
677A ARG 2.8 10.3 + - - -
678A ARG* 2.8 63.5 + - - +
679A GLU* 3.2 17.6 + - - +
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Residues in contact with GLU 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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636A ALA* 3.3 17.2 + - - +
637A PHE* 3.1 34.3 - - + -
672A ARG* 2.9 48.7 + - - +
673A ALA* 3.5 9.4 - - - +
675A GLU* 1.3 72.8 - - - +
677A ARG* 1.3 56.4 + - - +
679A GLU* 3.4 15.1 - - - +
680A LYS 3.8 2.4 + - - -
681A LYS* 2.9 5.0 + - - -
682A ASN* 2.9 61.9 + - + +
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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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637A PHE* 4.5 24.3 - - - +
673A ALA* 2.8 22.3 + - - +
674A GLU* 4.0 7.9 - - - +
675A GLU 2.8 1.4 + - - -
676A GLU* 1.3 77.9 - - - +
678A ARG* 1.3 64.7 + - - +
679A GLU 3.0 3.0 + - - -
680A LYS 3.5 0.7 + - - -
681A LYS* 3.2 79.3 + - + +
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Residues in contact with ARG 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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674A GLU* 3.2 14.4 + - - +
675A GLU* 2.8 52.8 + - - +
677A ARG* 1.3 79.0 - - - +
679A GLU* 1.3 71.6 + - + +
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Residues in contact with GLU 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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672A ARG* 5.1 3.8 + - - -
675A GLU* 3.2 25.0 - - - +
676A GLU* 3.4 16.7 + - - +
677A ARG 3.0 1.8 - - - -
678A ARG* 1.3 91.4 - - + +
680A LYS* 1.3 76.1 + - + +
682A ASN 5.7 0.4 - - - +
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Residues in contact with LYS 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A GLU 3.8 0.8 + - - -
677A ARG 4.1 0.9 - - - -
679A GLU* 1.3 86.9 - - + +
681A LYS* 1.3 75.8 + - + +
682A ASN* 2.9 19.9 + - - +
683A LYS* 4.7 3.5 - - - +
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Residues in contact with LYS 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A PHE* 4.6 5.7 - - - -
676A GLU* 2.9 13.6 + - - -
677A ARG* 3.2 68.6 + - - +
680A LYS* 1.3 83.5 - - + +
682A ASN* 1.3 56.3 + - - +
683A LYS* 2.6 28.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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