Contacts of the helix formed by residues 658 - 674 (chain A) in PDB entry 4KHW
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 ARG 658 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604A TYR* 3.2 33.3 + - + +
608A VAL* 4.6 13.9 - - - +
654A PHE* 2.9 46.2 + - + +
657A GLU* 1.3 87.7 - - + +
659A MET* 1.3 64.8 + - - +
661A PRO* 3.3 10.5 - - - +
662A ALA* 3.4 11.3 + - - +
665A ARG* 5.0 1.2 + - - -
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Residues in contact with MET 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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408A MET* 4.5 6.3 - - - +
410A PHE* 3.7 36.8 - - + -
601A VAL* 4.3 17.9 - - + -
604A TYR* 4.3 15.3 - - + -
605A LEU* 3.9 29.4 - - + -
627A VAL* 4.4 4.5 - - + -
632A ILE* 4.4 6.5 - - - -
654A PHE* 3.2 41.2 + - + +
655A ALA* 3.6 10.3 - - - +
658A ARG* 1.3 73.0 - - - +
660A GLU* 1.3 62.5 + - - +
662A ALA* 3.0 6.3 + - - +
663A ILE* 2.8 34.8 + - + +
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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
----------------------------------------------------------
410A PHE* 4.1 10.8 - - + -
655A ALA 2.9 24.0 + - - +
656A ARG* 4.2 19.7 - - - +
659A MET* 1.3 71.8 - - - +
661A PRO* 1.3 61.2 - - + +
663A ILE* 3.1 9.1 + - - +
664A ASP* 2.7 34.2 + - - +
683A MET 4.0 11.8 - - - +
684A ASP* 3.4 7.7 - - - +
685A ARG* 3.2 29.2 + - - +
1005A CA 2.4 32.5 - - - -
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Residues in contact with PRO 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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656A ARG 3.7 12.8 - - - +
657A GLU* 3.4 19.7 - - - +
658A ARG 3.3 15.0 - - - +
660A GLU* 1.3 94.1 - - + +
662A ALA* 1.3 56.1 + - - +
664A ASP* 3.2 11.7 + - + +
665A ARG* 2.9 46.8 + - - +
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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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600A LYS* 5.7 2.1 - - - +
604A TYR* 3.6 32.1 - - + -
658A ARG 3.4 8.2 + - - +
659A MET 3.0 10.0 + - - +
661A PRO* 1.3 77.9 - - - +
663A ILE* 1.3 57.6 + - + +
665A ARG* 3.2 32.2 + - - +
666A GLY* 2.8 25.8 + - - -
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Residues in contact with ILE 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A PHE* 3.9 37.2 - - + -
597A ILE* 3.9 11.8 - - + +
600A LYS* 6.1 0.9 - - - -
601A VAL* 4.0 27.6 - - + -
659A MET* 2.8 24.6 + - + +
660A GLU* 3.4 9.6 - - - +
662A ALA* 1.3 75.0 - - + +
664A ASP* 1.3 59.3 + - - +
666A GLY* 3.2 1.0 + - - -
667A PHE* 2.9 52.4 + - + +
683A MET* 3.8 28.7 - - + +
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Residues in contact with ASP 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A GLU 2.7 20.6 + - - +
661A PRO* 3.2 13.3 + - + +
663A ILE* 1.3 74.4 - - - +
665A ARG* 1.3 57.3 + - + +
667A PHE* 3.8 4.1 - - - +
668A ARG* 2.8 49.0 + - - +
679A HIS* 3.5 22.5 + - - -
681A MET 4.5 2.9 - - - +
682A PHE* 4.5 9.9 - - - -
683A MET 5.8 0.8 + - - -
1005A CA 4.1 14.4 - - - -
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Residues in contact with ARG 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A TYR* 3.9 16.6 - - - -
658A ARG 5.0 0.8 + - - -
661A PRO* 2.9 39.0 + - - +
662A ALA* 3.3 32.8 - - - +
664A ASP* 1.3 73.4 - - + +
666A GLY* 1.3 65.2 + - - +
668A ARG* 3.3 8.8 + - - +
669A GLU* 3.0 26.0 + - - +
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Residues in contact with GLY 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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596A TRP* 2.7 27.4 + - - -
597A ILE* 4.3 3.1 - - - -
600A LYS* 4.1 30.3 - - - -
662A ALA 2.8 14.7 + - - -
663A ILE 3.2 4.0 + - - -
665A ARG* 1.3 77.1 - - - +
667A PHE* 1.3 55.4 + - - +
669A GLU* 3.6 3.5 - - - +
670A MET 3.2 12.5 + - - -
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Residues in contact with PHE 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 3.6 31.9 - - + -
422A GLN* 5.3 0.2 + - - -
593A ALA* 3.5 24.0 - - + -
596A TRP* 4.4 1.8 - + - -
597A ILE* 3.4 38.8 - - + -
663A ILE* 2.9 32.3 + - + +
664A ASP* 4.1 0.4 - - - +
666A GLY* 1.3 72.8 - - - +
668A ARG* 1.3 60.0 + - - +
669A GLU 3.1 1.6 - - - -
670A MET* 3.1 31.0 + - + +
671A CYS* 2.8 29.8 + - - +
679A HIS* 3.6 21.4 - - - +
681A MET* 3.5 27.1 - - + +
683A MET* 4.0 4.5 - - + -
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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
----------------------------------------------------------
664A ASP* 2.8 46.4 + - - +
665A ARG* 3.7 8.8 - - - +
667A PHE* 1.3 76.2 - - - +
669A GLU* 1.3 61.2 + - - +
671A CYS* 3.4 5.5 - - + +
672A GLU* 3.3 19.6 + - - +
679A HIS* 3.7 36.6 + - + +
682A PHE* 5.8 0.4 - - - -
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Residues in contact with GLU 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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445A ALA* 4.8 6.9 - - - +
596A TRP* 3.5 22.4 - - + -
599A ARG* 5.3 0.3 + - - -
600A LYS* 2.7 30.2 + - - -
665A ARG 3.0 16.6 + - - +
666A GLY 3.6 4.3 - - - +
668A ARG* 1.3 75.4 - - - +
670A MET* 1.3 59.4 + - - +
672A GLU* 3.0 10.4 + - + +
673A TYR* 2.9 27.1 + - + +
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Residues in contact with MET 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A GLN* 4.5 4.5 - - - +
589A PHE* 3.6 35.9 - - + -
592A MET* 3.9 18.6 - - + -
593A ALA* 3.7 28.7 - - + -
596A TRP* 3.6 51.3 - - + +
666A GLY 3.2 3.2 + - - +
667A PHE* 3.1 29.0 + - + +
669A GLU* 1.3 79.6 - - - +
671A CYS* 1.3 61.9 + - - +
673A TYR* 3.1 7.3 + - + +
674A MET* 3.0 25.3 + - + +
681A MET* 4.0 8.3 - - + -
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Residues in contact with CYS 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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422A GLN* 3.9 8.7 - - - +
667A PHE 2.8 13.6 + - - +
668A ARG* 3.4 11.7 - - + +
670A MET* 1.3 77.4 - - - +
672A GLU* 1.3 57.7 + - - +
674A MET 3.6 0.3 + - - -
675A ASN* 3.0 5.2 + - - -
676A ASN* 2.9 62.3 + - - -
678A GLN* 4.0 1.1 - - - -
679A HIS* 3.6 40.4 - - + -
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Residues in contact with GLU 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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449A ARG* 2.8 43.0 + - - +
668A ARG 3.3 8.6 + - - +
669A GLU* 3.0 11.9 + - + +
671A CYS* 1.3 76.5 - - - +
673A TYR* 1.3 65.2 + - - +
675A ASN* 3.0 4.2 + - - +
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Residues in contact with TYR 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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442A TYR* 3.3 33.5 - + - -
445A ALA* 3.8 15.7 - - + -
447A ALA* 2.6 48.0 + - - +
449A ARG* 3.2 45.6 - - + +
450A PRO* 3.6 8.8 - - + +
592A MET* 5.3 0.9 - - - -
596A TRP* 3.5 25.4 - + + -
669A GLU* 2.9 13.4 + - + +
670A MET* 3.2 14.6 - - + +
672A GLU* 1.3 77.2 - - - +
674A MET* 1.3 71.2 + - + +
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Residues in contact with MET 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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442A TYR* 4.0 9.6 - - + -
450A PRO* 3.7 29.6 - - + -
451A SER 5.2 0.4 - - - -
454A TYR 3.8 0.2 - - - +
455A SER* 3.8 0.2 - - - -
456A CYS* 2.9 43.0 + - - +
458A PRO* 4.0 23.8 - - - -
589A PHE* 3.9 4.5 - - + -
592A MET* 3.8 23.8 - - + -
670A MET* 3.0 15.2 + - + +
673A TYR* 1.3 108.3 - - + +
675A ASN* 1.3 69.6 + - - +
676A ASN* 3.3 24.0 - - - +
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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