Contacts of the helix formed by residues 666 - 681 (chain A) in PDB entry 4RS6
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 666 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A ALA 4.0 0.9 - - - -
490A ASP 3.0 24.0 - - - -
491A CYS* 3.5 8.8 + - - -
492A ILE* 3.9 16.2 - - - +
665A CYS* 1.3 79.6 - - - +
667A SER* 1.3 59.9 + - - +
668A GLU* 3.6 7.8 + - - +
669A LEU* 3.1 23.6 + - - +
670A LYS* 2.9 22.1 + - - +
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Residues in contact with SER 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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488A GLU* 6.0 1.8 - - - -
489A ALA 4.3 5.5 + - - -
665A CYS 3.7 1.6 + - - -
666A SER* 1.3 73.9 - - - +
668A GLU* 1.3 61.1 + - - +
670A LYS* 4.1 9.9 - - - -
671A ASN* 2.8 46.8 + - - +
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Residues in contact with GLU 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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645A TYR* 4.3 6.6 + - + +
666A SER* 3.2 6.9 + - - +
667A SER* 1.3 82.9 + - - +
669A LEU* 1.3 62.9 + - - +
671A ASN* 3.4 6.7 + - - +
672A ARG* 3.1 56.7 + - - +
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Residues in contact with LEU 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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492A ILE* 4.8 6.5 - - + -
632A ILE* 4.0 17.9 - - + -
643A LEU* 5.0 4.9 - - + -
645A TYR* 3.6 47.4 - - + -
655A PHE* 4.6 15.0 - - + -
660A LEU* 4.4 9.6 - - + -
665A CYS* 3.4 26.9 - - + -
666A SER* 3.1 20.3 + - - +
668A GLU* 1.3 73.9 - - - +
670A LYS* 1.3 64.7 + - - +
672A ARG* 3.0 6.7 + - + +
673A MET* 2.9 36.8 + - + +
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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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483A LEU* 4.0 34.4 + - + +
486A MET* 4.3 25.6 - - + -
487A PRO 5.2 5.4 - - - +
488A GLU* 5.6 10.5 + - - +
665A CYS* 3.6 10.3 - - - +
666A SER 2.9 17.8 + - - +
667A SER* 3.3 10.3 + - - +
669A LEU* 1.3 75.9 - - - +
671A ASN* 1.3 61.5 + - - +
673A MET* 3.3 7.1 + - - +
674A GLU* 2.9 52.0 + - - +
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Residues in contact with ASN 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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667A SER* 2.8 30.9 + - - +
668A GLU* 3.8 8.0 - - - +
670A LYS* 1.3 82.0 - - - +
672A ARG* 1.3 58.4 + - + +
674A GLU* 3.3 16.0 + - - +
675A TYR* 2.9 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
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625A PHE* 3.8 31.7 - - + -
628A ASP* 2.5 31.5 + - - -
630A THR* 2.8 26.1 + - - +
632A ILE* 3.5 16.0 - - + +
645A TYR* 3.6 29.2 + - - -
668A GLU* 3.1 54.8 + - - +
669A LEU* 3.0 9.0 + - - +
671A ASN* 1.3 76.2 - - + +
673A MET* 1.3 64.8 + - - +
675A TYR* 4.2 1.6 - - - +
676A ALA* 2.9 24.9 + - - +
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Residues in contact with MET 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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479A LEU* 3.8 28.1 - - + +
482A CYS* 4.3 16.6 - - - -
483A LEU* 3.9 18.8 - - + +
486A MET* 4.5 4.3 - - - -
632A ILE* 3.9 16.6 - - + -
643A LEU* 4.1 20.9 - - + -
657A LEU* 5.2 0.7 - - + -
660A LEU* 4.2 13.7 - - + -
665A CYS* 4.3 10.8 - - - -
669A LEU* 2.9 41.8 + - + +
670A LYS* 3.5 9.4 - - - +
672A ARG* 1.3 74.3 - - - +
674A GLU* 1.3 65.2 + - - +
676A ALA* 3.3 5.1 + - - +
677A LEU* 3.0 22.2 + - - +
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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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483A LEU* 3.9 22.3 - - + +
670A LYS* 2.9 44.6 + - - +
671A ASN* 3.5 16.5 - - - +
672A ARG 3.2 0.2 - - - -
673A MET* 1.3 75.7 - - - +
675A TYR* 1.3 64.7 + - - +
677A LEU* 3.2 5.1 + - - +
678A ASN* 3.0 30.2 + - - +
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Residues in contact with TYR 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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608A SER* 2.5 29.9 + - - -
609A ASP* 4.9 1.6 + - - -
610A LYS* 3.4 31.7 - - + +
611A ALA* 4.0 3.1 - - + -
625A PHE* 3.9 24.9 - + + -
671A ASN 2.9 16.9 + - - +
672A ARG* 3.8 4.3 - - - +
673A MET 3.2 0.4 - - - -
674A GLU* 1.3 77.6 - - - +
676A ALA* 1.3 63.2 + - - +
678A ASN* 3.1 19.0 + - + +
679A MET* 3.0 53.1 + - + +
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Residues in contact with ALA 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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479A LEU* 4.6 3.1 - - + -
621A PHE* 3.9 20.8 - - + -
623A VAL* 3.9 32.3 - - + -
625A PHE* 4.7 0.6 - - - -
632A ILE* 4.8 9.0 - - + -
672A ARG 2.9 16.5 + - - +
673A MET* 3.5 8.1 - - - +
675A TYR* 1.3 76.7 - - - +
677A LEU* 1.3 62.7 + - - +
679A MET* 2.9 17.9 + - - +
680A LEU 3.0 9.0 + - - -
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Residues in contact with LEU 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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476A ALA* 4.0 35.4 - - + +
479A LEU* 3.9 17.6 - - + +
480A ARG* 4.0 27.6 - - + +
483A LEU* 3.8 21.1 - - + -
673A MET 3.0 12.8 + - - +
674A GLU* 3.5 8.1 - - - +
676A ALA* 1.3 73.9 - - - +
678A ASN* 1.3 60.0 + - - +
680A LEU* 2.7 24.3 + - + +
681A LEU* 3.0 39.5 + - + +
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Residues in contact with ASN 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* 3.0 23.2 + - - +
675A TYR* 3.1 19.1 + - + +
677A LEU* 1.3 78.9 - - - +
679A MET* 1.3 64.9 + - + +
681A LEU* 3.5 10.7 + - - +
682A GLN* 3.4 16.8 - - - +
682B GLN* 2.8 38.1 + - - +
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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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606A LEU* 3.8 29.5 - - + +
608A SER* 3.7 23.8 - - - +
611A ALA* 3.6 32.5 - - - +
613A MET* 2.9 36.8 - - + +
623A VAL* 4.5 5.4 - - - -
675A TYR* 3.0 38.7 + - + +
676A ALA* 2.9 10.5 + - - +
678A ASN* 1.3 77.7 - - + +
680A LEU* 1.3 63.7 + - - +
682A GLN* 3.3 21.2 + - - +
606B LEU* 5.1 0.7 - - + -
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Residues in contact with LEU 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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472A ALA* 3.9 31.2 - - + +
475A VAL* 3.9 15.3 - - + +
476A ALA* 3.3 42.0 - - + +
479A LEU* 5.2 1.8 - - + -
604A GLN* 6.0 0.4 - - - +
613A MET* 3.5 11.7 - - + +
615A LEU* 4.7 7.0 - - + -
621A PHE* 3.6 29.8 - - + -
676A ALA 3.0 7.3 + - - +
677A LEU* 2.7 18.1 + - + +
679A MET* 1.3 78.3 - - - +
681A LEU* 1.3 57.1 + - - +
682A GLN* 2.9 9.2 + - - -
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Residues in contact with LEU 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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476A ALA* 4.2 24.0 - - + -
480A ARG* 4.6 22.7 - - - +
677A LEU* 3.0 50.8 + - + +
678A ASN* 3.5 9.6 + - - +
679A MET 3.4 1.0 - - - -
680A LEU* 1.3 74.3 - - - +
682A GLN* 1.3 60.2 + - - +
682B GLN* 2.9 52.8 - - + +
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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