Contacts of the helix formed by residues 648 - 662 (chain A) in PDB entry 1W6J
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 GLN 648 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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629A TRP 2.8 8.3 + - - +
630A GLY* 3.9 4.7 - - - -
631A GLU 4.2 6.1 - - - +
644A SER* 4.0 5.9 + - - +
646A GLN* 3.1 27.5 + - - +
647A SER* 1.3 80.0 + - - +
649A ILE* 1.3 65.4 + - - +
650A HIS* 3.2 14.1 + - + +
651A ASN* 3.2 29.4 - - - +
652A THR* 2.8 26.3 + - - -
680A LYS* 4.3 0.9 - - - -
690A GLU* 3.3 12.3 - - - +
691A ASN* 2.9 55.0 + - - +
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Residues in contact with ILE 649 (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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648A GLN* 1.3 70.8 - - - +
650A HIS* 1.3 60.0 + - - +
652A THR* 3.3 6.3 + - - -
653A CYS* 2.9 35.8 + - - -
677A LEU* 4.3 10.3 - - + -
680A LYS* 3.7 21.5 - - + +
687A TRP* 3.8 27.8 - - + -
688A PRO* 3.7 26.2 - - + +
690A GLU* 2.7 28.3 + - - +
707A TYR 4.8 0.2 - - - +
708A ARG* 4.2 15.3 - - + +
712A PRO* 3.4 34.8 - - + -
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Residues in contact with HIS 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A VAL* 4.2 4.1 + - - +
631A GLU 5.3 1.6 + - - -
648A GLN* 3.7 22.3 - - + +
649A ILE* 1.3 81.5 + - + +
651A ASN* 1.3 95.7 + - - +
653A CYS* 3.3 5.1 + - - +
654A TRP* 3.0 58.5 + + + +
690A GLU* 5.1 2.3 + - + +
691A ASN* 3.3 27.1 - - + +
692A ILE 4.0 4.2 + - - -
693A ALA* 3.7 31.8 - - + +
707A TYR* 4.7 14.1 - - + +
711A PHE* 5.3 3.6 - - + -
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Residues in contact with ASN 651 (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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583A VAL* 2.7 27.2 + - - +
586A THR* 3.0 24.1 + - + +
629A TRP* 3.6 23.4 - - + +
630A GLY* 4.0 0.9 - - - +
631A GLU* 3.0 35.7 + - - +
648A GLN* 3.2 25.0 + - - +
650A HIS* 1.3 87.7 + - - +
652A THR* 1.3 62.7 + - - +
654A TRP* 3.4 1.5 + - - -
655A ALA* 3.1 24.9 + - - +
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Residues in contact with THR 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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628A GLY* 3.4 21.3 - - - -
629A TRP* 3.0 27.5 + - + +
647A SER* 4.1 2.3 - - - -
648A GLN 2.8 23.3 + - - -
649A ILE* 3.4 5.8 - - - -
651A ASN* 1.3 79.3 - - - +
653A CYS* 1.3 60.9 + - - +
655A ALA* 3.5 1.7 + - - +
656A MET* 3.1 46.4 + - - +
673A GLY* 4.3 7.4 - - - +
676A CYS* 4.7 5.2 - - - -
677A LEU* 4.0 16.6 - - + -
680A LYS* 5.2 0.5 + - - -
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Residues in contact with CYS 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ILE* 2.9 24.9 + - - +
650A HIS 3.8 2.2 - - - +
652A THR* 1.3 75.7 - - - +
654A TRP* 1.3 59.1 + - - +
656A MET* 3.4 3.4 + - - +
657A MET* 2.8 38.2 + - - +
677A LEU* 3.9 17.3 - - - -
711A PHE* 3.4 29.4 - - + +
712A PRO* 3.4 40.6 - - - -
715A ALA* 4.1 8.5 - - + -
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Residues in contact with TRP 654 (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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583A VAL 3.3 23.8 - - - -
586A THR* 3.6 28.3 - - - +
587A TYR* 3.4 42.8 - + + -
590A TRP* 3.6 38.9 - + + +
619A LEU* 5.4 0.2 - - - +
650A HIS* 3.0 47.1 + + + +
651A ASN 3.8 2.7 - - - +
653A CYS* 1.3 78.3 - - - +
655A ALA* 1.3 62.1 + - - +
657A MET* 4.6 0.7 - - - -
658A GLY* 3.1 18.9 + - - -
693A ALA 4.1 13.9 - - - -
707A TYR* 3.6 28.7 - + - -
711A PHE* 3.5 36.1 - + - -
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Residues in contact with ALA 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A THR* 4.5 3.7 - - + -
619A LEU* 4.0 24.5 - - + +
629A TRP* 3.4 47.8 - - + +
651A ASN 3.1 11.9 + - - +
654A TRP* 1.3 75.3 - - - +
656A MET* 1.3 63.0 + - - +
658A GLY* 3.4 1.0 + - - -
659A LEU* 3.0 29.7 + - - +
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Residues in contact with MET 656 (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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629A TRP* 4.1 15.5 - - + -
652A THR* 3.1 25.6 + - - +
653A CYS* 3.6 5.4 - - - +
655A ALA* 1.3 79.8 - - - +
657A MET* 1.3 57.3 + - - +
659A LEU* 3.3 9.2 + - + +
660A MET* 2.9 54.1 + - + +
670A GLN* 3.9 13.9 - - - +
673A GLY* 3.6 24.7 - - - +
674A VAL* 3.5 37.2 - - + +
677A LEU* 3.9 16.6 - - + -
715A ALA* 4.4 9.0 - - + +
716A LEU* 5.2 0.2 - - + -
719A PHE* 5.7 0.2 - - + -
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Residues in contact with MET 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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590A TRP* 3.6 37.2 - - + +
653A CYS 2.8 25.3 + - - +
654A TRP* 3.9 1.3 - - - +
656A MET* 1.3 73.2 - - - +
658A GLY* 1.3 58.3 + - - +
660A MET* 3.8 6.7 - - + -
661A ALA* 2.9 25.1 + - - +
711A PHE* 3.8 24.7 - - - -
714A TRP* 3.6 46.4 - - + +
715A ALA* 3.8 23.3 - - + -
718A ARG* 3.0 29.0 + - - +
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Residues in contact with GLY 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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590A TRP* 3.7 13.6 - - - -
593A LEU* 3.6 30.4 - - - +
619A LEU* 5.1 0.9 - - - -
654A TRP 3.1 14.8 + - - -
655A ALA 3.8 2.5 - - - -
657A MET* 1.3 74.1 - - - +
659A LEU* 1.3 64.4 + - - +
661A ALA* 3.4 11.9 + - - +
662A VAL* 3.4 16.5 + - - +
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Residues in contact with LEU 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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593A LEU* 4.2 0.6 - - - +
616A CYS* 3.9 35.0 - - + +
619A LEU* 4.3 9.0 - - + -
620A LEU* 4.0 37.2 - - + -
629A TRP* 4.1 22.2 - - + -
655A ALA 3.0 22.0 + - - +
656A MET* 3.7 6.7 - - - +
658A GLY* 1.3 76.1 - - - +
660A MET* 1.3 60.8 + - - +
662A VAL* 3.6 4.8 + - - +
663A ARG 3.3 3.1 + - - -
664A HIS* 3.0 34.5 + - + +
666A ASP 6.1 0.2 - - - +
669A ALA* 5.6 0.2 - - + -
670A GLN* 4.1 25.0 + - + +
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Residues in contact with MET 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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656A MET* 2.9 44.4 + - + +
657A MET* 3.9 6.7 - - - +
659A LEU* 1.3 74.4 - - - +
661A ALA* 1.3 63.5 + - - +
663A ARG* 2.9 35.2 + - - +
670A GLN* 3.3 29.6 - - + +
715A ALA* 3.6 23.8 - - - +
718A ARG* 3.8 19.5 - - + -
719A PHE* 3.6 35.7 - - - -
722A LEU* 3.7 16.7 - - + +
723A TYR* 4.5 0.7 - - - -
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Residues in contact with ALA 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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593A LEU 4.6 4.0 - - - +
594A GLU* 3.5 31.0 - - + +
597A ALA* 3.4 22.3 - - + +
602A THR* 4.2 6.1 - - - +
657A MET 2.9 19.8 + - - +
658A GLY* 3.6 7.9 - - - +
659A LEU 3.3 0.2 - - - -
660A MET* 1.3 76.8 - - - +
662A VAL* 1.3 59.1 + - - +
663A ARG* 3.6 16.7 + - - +
718A ARG* 3.9 6.5 - - - +
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Residues in contact with VAL 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A LEU* 3.8 36.6 - - + +
597A ALA* 4.3 1.6 - - + -
601A GLN 3.8 18.2 - - - +
602A THR* 3.8 8.3 - - - -
603A TYR* 2.8 32.3 + - + +
612A VAL* 3.8 17.9 - - + -
616A CYS* 3.6 29.2 - - - -
658A GLY 3.4 14.1 + - - +
659A LEU 3.6 6.5 - - - +
661A ALA* 1.3 76.7 - - - +
663A ARG* 1.3 66.1 + - - +
664A HIS 3.3 1.2 + - - +
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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