Contacts of the helix formed by residues 651 - 668 (chain A) in PDB entry 4KXA
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 SER 651 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A LYS* 5.4 1.0 - - - +
622A ASP* 3.6 11.2 + - - -
649A THR 4.3 0.4 + - - -
650A PHE* 1.3 75.7 - - - +
652A SER* 1.3 65.5 + - - +
653A ALA* 3.7 3.2 + - - +
654A ASP* 3.0 35.9 + - - +
655A ARG* 3.0 22.4 + - - +
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Residues in contact with SER 652 (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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435A GLN* 6.2 0.7 - - - -
438A ASP* 6.0 2.0 - - - -
648A LYS* 4.8 1.2 + - - -
651A SER* 1.3 73.0 - - - +
653A ALA* 1.3 64.1 + - - +
655A ARG* 3.4 18.9 + - - +
656A ALA* 3.1 18.0 + - - +
688A ASN* 3.1 42.1 + - - -
690A LEU* 4.5 7.2 - - - -
691A PRO* 3.4 16.5 - - - +
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Residues in contact with ALA 653 (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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438A ASP* 4.4 12.7 + - - +
441A LEU* 4.1 14.9 - - + +
622A ASP* 3.9 33.7 - - + +
651A SER* 3.2 2.8 + - - +
652A SER* 1.3 79.3 - - - +
654A ASP* 1.3 56.6 + - - +
656A ALA* 3.3 4.7 + - - +
657A SER* 2.9 29.0 + - - -
690A LEU* 3.9 18.8 - - + +
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Residues in contact with ASP 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A LYS* 4.2 21.0 + - + +
620A ASN 4.4 2.3 - - - +
621A PRO* 3.7 10.8 - - - +
622A ASP* 2.9 30.2 + - - +
623A HIS 4.6 0.3 + - - -
650A PHE* 4.2 13.0 - - + -
651A SER* 3.0 32.8 + - - +
653A ALA* 1.3 75.4 - - - +
655A ARG* 1.3 60.2 + - - +
657A SER* 3.3 5.6 + - - -
658A LEU* 2.9 40.3 + - + +
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Residues in contact with ARG 655 (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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643A LEU* 3.9 22.0 - - + -
647A HIS* 3.5 25.1 + - - -
648A LYS* 3.7 18.4 - - - +
650A PHE* 3.3 30.1 + - + +
651A SER* 3.0 8.0 + - - +
652A SER* 3.4 31.3 + - - +
654A ASP* 1.3 72.8 - - - +
656A ALA* 1.3 66.9 + - - +
657A SER 3.2 0.2 + - - -
658A LEU* 3.3 8.6 + - - +
659A ILE* 2.9 32.6 + - + +
682A TYR* 3.7 9.4 - - - +
686A GLU* 2.7 44.8 + - - -
688A ASN* 3.2 16.4 + - - +
691A PRO* 3.5 15.8 - - + +
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Residues in contact with ALA 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A LEU* 5.4 1.8 - - + -
442A LEU* 5.4 0.4 - - + -
446A LEU* 4.9 4.0 - - + -
652A SER 3.1 7.2 + - - +
653A ALA* 3.5 9.0 - - - +
655A ARG* 1.3 79.4 - - - +
657A SER* 1.3 57.6 + - - +
659A ILE* 3.4 3.9 + - - +
660A ASP* 2.8 31.1 + - - +
690A LEU* 3.5 39.5 - - + +
691A PRO* 4.0 8.4 - - - +
694A ARG* 3.9 15.7 - - + +
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Residues in contact with SER 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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441A LEU* 5.3 0.7 - - - -
446A LEU* 4.9 4.0 - - - +
620A ASN* 4.7 3.9 + - - +
623A HIS* 2.8 46.0 + - - +
653A ALA 2.9 17.1 + - - -
654A ASP* 3.6 9.9 - - - -
655A ARG 3.2 0.2 - - - -
656A ALA* 1.3 75.1 - - - +
658A LEU* 1.3 65.0 + - - +
660A ASP* 3.3 4.8 + - - +
661A ASP* 2.9 36.6 + - - +
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Residues in contact with LEU 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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616A PHE* 6.1 0.7 - - + -
618A LYS* 6.0 2.9 - - + -
619A ILE 5.5 3.6 - - - +
631A TYR* 4.2 25.8 - - + +
636A TRP* 3.7 23.0 - - + -
639A ILE* 4.4 21.1 - - + -
643A LEU* 5.9 4.5 - - + -
650A PHE* 4.0 35.2 - - + -
654A ASP* 2.9 26.2 + - + +
655A ARG* 3.8 6.3 - - + +
657A SER* 1.3 80.9 - - - +
659A ILE* 1.3 59.6 + - + +
661A ASP* 4.6 3.4 - - - +
662A ALA* 3.0 30.7 + - - +
679A LEU* 4.6 2.5 - - + -
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Residues in contact with ILE 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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643A LEU* 5.5 4.7 - - + -
655A ARG* 2.9 24.5 + - + +
656A ALA* 3.7 4.5 - - - +
658A LEU* 1.3 74.1 - - + +
660A ASP* 1.3 65.9 + - - +
662A ALA* 3.5 0.5 + - - +
663A PHE* 3.1 48.5 + - + +
679A LEU* 4.6 25.4 - - + +
680A THR* 5.8 1.8 - - + -
682A TYR* 3.5 33.4 - - + +
683A LEU* 5.0 0.2 - - + -
691A PRO* 4.6 6.1 - - + +
694A ARG* 4.5 5.8 - - + +
695A VAL* 3.9 42.8 - - + +
698A ALA* 5.4 0.2 - - + -
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Residues in contact with ASP 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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446A LEU* 3.4 29.0 - - + +
628A ARG* 2.9 29.6 + - - -
656A ALA 2.8 18.3 + - - +
657A SER 3.3 4.2 + - - +
659A ILE* 1.3 79.6 - - - +
661A ASP* 1.3 63.3 + - - +
663A PHE* 4.0 2.8 - - - +
664A ALA* 3.0 25.7 + - - +
694A ARG* 2.9 46.7 + - + +
698A ALA* 6.2 1.1 - - - -
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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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620A ASN* 5.5 0.5 + - - -
623A HIS* 3.2 23.4 + - - -
628A ARG* 3.0 38.3 + - - +
629A VAL* 3.1 36.7 + - - +
636A TRP* 4.5 4.5 - - + -
657A SER* 2.9 21.4 + - - +
658A LEU* 4.0 5.7 - - + +
660A ASP* 1.3 76.6 - - - +
662A ALA* 1.3 52.2 + - - +
664A ALA* 3.3 1.4 + - - +
665A LEU* 2.7 44.4 + - + +
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Residues in contact with ALA 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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636A TRP* 4.0 10.9 - - + -
658A LEU 3.0 19.3 + - - +
659A ILE 3.8 2.7 - - - +
661A ASP* 1.3 75.8 - - - +
663A PHE* 1.3 58.9 + - + +
665A LEU* 3.3 3.5 + - - +
666A ALA* 2.8 29.5 + - - +
671A LEU* 3.9 21.2 - - + +
676A ALA* 4.1 8.5 - - + -
679A LEU* 3.4 26.9 - - + -
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Residues in contact with PHE 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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659A ILE* 3.1 41.3 + - + +
660A ASP* 4.2 2.5 - - - +
662A ALA* 1.3 81.3 - - + +
664A ALA* 1.3 57.6 + - - +
666A ALA* 3.5 4.0 + - - +
667A ARG* 3.0 28.9 + - - +
673A TYR* 4.3 10.6 + + - -
676A ALA* 3.6 33.0 - - + -
677A LEU* 3.7 24.2 - - + -
679A LEU* 5.2 2.5 - - + -
680A THR* 3.5 30.3 - - + -
695A VAL* 6.3 0.7 - - - -
698A ALA* 3.8 26.5 - - + -
699A VAL* 5.9 2.9 - - + -
702A ILE* 3.8 24.2 - - + -
720A PHE* 5.6 2.5 - + - -
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Residues in contact with ALA 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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560A PHE* 3.6 8.8 - - + -
562A LEU* 4.0 4.0 - - + +
628A ARG* 3.3 42.6 - - - +
660A ASP* 3.0 15.4 + - - +
661A ASP 3.7 1.1 - - - +
663A PHE* 1.3 74.6 - - - +
665A LEU* 1.3 60.1 + - - +
667A ARG* 3.2 11.1 + - - +
668A ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 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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546A VAL* 3.9 21.8 - - + -
560A PHE* 3.5 26.0 - - + -
628A ARG* 4.3 7.4 - - + -
629A VAL 3.7 20.2 - - - +
630A ASN* 3.7 31.4 - - + +
636A TRP* 3.9 10.1 - - + -
661A ASP* 2.7 32.9 + - + +
662A ALA* 3.5 4.9 - - - +
664A ALA* 1.3 73.0 - - - +
666A ALA* 1.3 60.3 + - - +
668A ALA* 3.2 7.0 + - - +
670A LEU* 2.8 33.0 + - + -
671A LEU* 3.8 13.5 - - + +
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Residues in contact with ALA 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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662A ALA 2.8 20.1 + - - +
663A PHE 3.7 2.9 - - - +
665A LEU* 1.3 72.6 - - - +
667A ARG* 1.3 62.9 + - - +
669A GLN* 3.1 11.4 + - - -
671A LEU* 3.1 22.7 + - - +
673A TYR* 3.4 47.0 - - + -
676A ALA* 4.0 11.7 - - + -
942A HIS* 3.7 8.0 + - - -
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Residues in contact with ARG 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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450A GLU* 3.0 34.3 + - - +
562A LEU* 3.7 42.0 - - + +
564A PRO* 5.4 1.2 - - - +
663A PHE 3.0 15.0 + - - +
664A ALA* 3.2 13.4 + - - +
666A ALA* 1.3 76.9 - - - +
668A ALA* 1.3 58.7 + - - +
669A GLN* 3.3 1.8 + - - +
673A TYR* 3.5 10.7 + - - +
701A TYR* 3.4 52.9 + - + +
931A THR* 5.3 8.1 - - - +
934A ASN* 6.2 1.6 - - - +
935A ASN* 4.6 3.6 + - - -
938A TRP* 3.8 30.6 - - + +
942A HIS* 4.2 4.3 - - - -
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Residues in contact with ALA 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A PHE* 3.7 20.2 - - + -
561A LEU 3.6 22.2 - - - +
562A LEU* 3.6 14.1 - - + +
564A PRO* 4.0 15.2 - - - +
664A ALA 2.9 15.7 + - - +
665A LEU 3.6 4.9 - - - +
666A ALA 3.1 0.4 - - - -
667A ARG* 1.3 78.5 - - - +
669A GLN* 1.3 68.2 + - - +
670A LEU* 3.5 13.1 + - + +
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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
------------------------------------------------------------
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