Contacts of the helix formed by residues 661 - 675 (chain A) in PDB entry 1R49
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 ALA 661 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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657A GLN 3.2 19.0 + - - +
658A LEU 3.1 2.8 + - - +
660A ASP* 1.3 76.5 - - - +
662A ARG* 1.3 61.9 + - - +
663A ARG 3.0 5.3 + - - -
664A ASP* 3.4 26.0 + - - +
665A LEU* 3.7 4.3 + - - +
687A LYS* 5.2 2.6 - - - +
690A ALA* 6.0 1.7 - - + +
691A VAL* 3.9 10.1 - - + +
694A LEU* 3.4 24.0 - - + -
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Residues in contact with ARG 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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658A LEU* 2.7 50.9 + - - +
659A ALA* 3.5 12.1 + - - +
661A ALA* 1.3 76.1 - - - +
663A ARG* 1.3 57.9 + - - +
664A ASP 3.4 0.4 - - - -
665A LEU* 3.7 15.1 + - + +
666A LYS* 3.1 23.6 + - - +
691A VAL* 3.6 29.0 - - + +
695A GLU* 3.3 29.9 + - - +
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Residues in contact with ARG 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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656A GLU* 5.8 0.8 + - - -
659A ALA* 3.1 27.1 + - - +
660A ASP* 3.2 34.8 + - - +
661A ALA 3.0 0.2 - - - -
662A ARG* 1.3 77.9 - - - +
664A ASP* 1.3 65.7 + - - +
665A LEU 3.3 0.2 - - - -
666A LYS* 3.2 21.7 - - + +
667A SER* 3.1 24.1 + - - -
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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 ASP 3.7 14.9 - - - +
661A ALA* 3.4 15.2 + - - +
662A ARG 3.4 0.4 - - - -
663A ARG* 1.3 78.6 - - - +
665A LEU* 1.3 56.8 + - - +
667A SER* 3.4 8.3 + - - -
668A ALA* 2.9 29.7 + - - +
687A LYS* 3.4 37.1 + - + +
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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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661A ALA 3.7 5.7 + - - +
662A ARG* 3.7 22.1 + - + +
663A ARG 3.3 0.4 - - - -
664A ASP* 1.3 76.2 - - - +
666A LYS* 1.3 62.1 + - - +
668A ALA* 3.7 6.7 - - - -
669A LYS* 2.9 36.1 + - + +
684A VAL* 3.5 31.8 - - + +
687A LYS* 3.7 14.3 - - + +
688A LYS* 3.5 35.7 - - + +
691A VAL* 5.1 6.7 - - + -
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Residues in contact with LYS 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 ARG 3.1 15.7 + - - +
663A ARG* 3.1 28.2 + - + +
665A LEU* 1.3 78.2 - - - +
667A SER* 1.3 63.8 + - - +
669A LYS* 3.2 42.7 + - - +
670A ALA* 3.7 4.3 + - - +
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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
----------------------------------------------------------
663A ARG 3.1 8.9 + - - -
664A ASP* 3.4 9.7 + - - -
666A LYS* 1.3 81.1 - - - +
668A ALA* 1.3 64.2 + - - +
669A LYS 3.2 1.0 + - - -
670A ALA* 3.6 11.9 + - - +
671A ASP* 3.3 18.8 + - - +
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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
----------------------------------------------------------
664A ASP 2.9 19.7 + - - +
665A LEU* 3.7 8.7 - - - +
667A SER* 1.3 76.5 + - - +
669A LYS* 1.3 64.3 + - - +
670A ALA 3.4 0.2 - - - -
671A ASP* 3.4 25.5 - - + +
672A ALA 3.7 0.7 + - - -
680A THR* 5.3 0.2 - - - +
683A VAL* 5.1 7.6 - - + -
684A VAL* 3.2 27.8 - - + +
687A LYS* 4.5 18.2 - - + -
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Residues in contact with LYS 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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665A LEU* 2.9 20.5 + - + +
666A LYS* 3.2 36.2 - - - +
667A SER 3.2 0.2 - - - -
668A ALA* 1.3 78.5 - - - +
670A ALA* 1.3 66.4 + - + +
671A ASP 3.3 0.7 + - - -
672A ALA* 3.4 12.6 + - - +
673A LYS* 3.4 14.4 + - + +
684A VAL* 4.4 7.6 - - - -
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Residues in contact with ALA 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 LYS 3.7 4.9 + - - +
667A SER* 3.6 11.5 + - - +
668A ALA 3.4 0.2 - - - -
669A LYS* 1.3 82.5 - - + +
671A ASP* 1.3 66.8 + - - +
673A LYS* 3.6 21.1 + - + +
674A VAL* 4.0 10.7 + - - +
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Residues in contact with ASP 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A SER 3.3 15.8 + - - +
668A ALA* 3.4 17.0 - - - +
669A LYS 3.1 0.4 - - - -
670A ALA* 1.3 81.0 - - - +
672A ALA* 1.3 58.2 + - - +
674A VAL* 4.2 0.9 - - - +
675A MET* 3.1 54.8 + - + +
680A THR* 4.2 10.7 - - + +
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Residues in contact with ALA 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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668A ALA 3.7 0.4 + - - -
669A LYS 3.4 7.8 + - - +
671A ASP* 1.3 78.9 - - - +
673A LYS* 1.3 66.7 + - - +
674A VAL 3.2 0.7 + - - -
675A MET 3.3 22.8 - - - +
676A LYS* 3.5 8.8 + - - +
680A THR* 3.8 17.9 - - + +
681A LYS* 5.2 6.7 - - + +
684A VAL* 4.1 19.3 - - + -
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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 LYS* 3.4 13.9 + - + +
670A ALA* 3.7 17.5 - - + +
671A ASP 3.3 0.6 - - - -
672A ALA* 1.3 79.7 - - - +
674A VAL* 1.3 69.1 + - + +
676A LYS* 4.1 9.0 + - - +
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Residues in contact with VAL 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 ALA 4.0 6.7 + - - +
671A ASP* 3.8 4.2 + - - +
673A LYS* 1.3 89.6 - - + +
675A MET* 1.3 75.5 + - + +
676A LYS* 3.4 27.2 + - - +
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Residues in contact with MET 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 ASP* 3.1 50.9 + - + +
672A ALA* 3.3 16.5 - - - +
674A VAL* 1.3 84.9 - - + +
676A LYS* 1.3 56.1 + - - +
677A ASP* 3.0 27.2 + - - +
680A THR* 3.9 13.6 - - + +
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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