Contacts of the helix formed by residues 666 - 681 (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 ASP 666 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A LEU* 4.6 7.1 - - + +
659A LEU* 6.1 0.2 - - - +
664A HIS* 3.1 28.4 + - + +
665A PRO* 1.3 73.1 - - - +
667A ILE* 1.3 60.3 + - - +
668A GLU* 3.7 9.5 + - - +
669A ALA* 3.2 35.4 + - + +
670A GLN* 3.4 17.8 + - - +
672A ARG* 5.0 4.3 + - - -
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Residues in contact with ILE 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A HIS 4.7 1.6 - - - +
665A PRO* 3.1 17.2 + - + +
666A ASP* 1.3 71.8 - - - +
668A GLU* 1.3 57.1 + - - +
670A GLN* 3.1 12.8 + - - +
671A GLU* 2.8 31.1 + - + +
719A PHE* 4.4 0.2 - - + -
723A TYR* 3.7 44.0 - - + +
725A GLU* 5.4 2.2 - - - +
726A ARG* 3.4 51.4 - - - +
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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
----------------------------------------------------------
666A ASP* 3.2 8.0 - - - +
667A ILE* 1.3 80.1 - - - +
669A ALA* 1.3 60.6 + - - +
671A GLU* 3.3 21.6 + - - +
672A ARG* 3.1 40.0 + - - +
675A ARG* 6.3 0.2 - - - +
726A ARG* 4.7 10.6 + - - +
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Residues in contact with ALA 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A LEU* 3.6 22.9 - - + -
623A GLN* 3.0 32.1 + - - +
629A TRP* 4.8 3.4 - - - -
659A LEU* 5.6 0.4 - - + -
666A ASP* 3.2 25.0 + - - +
668A GLU* 1.3 71.9 - - - +
670A GLN* 1.3 65.7 + - + +
672A ARG* 3.3 34.8 + - - +
673A GLY* 3.4 2.6 + - - -
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Residues in contact with GLN 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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629A TRP* 6.0 0.2 - - - -
656A MET* 3.9 14.6 - - + +
659A LEU* 4.1 32.2 + - + +
660A MET* 3.3 22.7 - - + +
664A HIS* 2.9 34.2 + - - +
666A ASP 3.4 12.4 + - - +
667A ILE* 3.1 9.8 + - - +
669A ALA* 1.3 77.9 - - - +
671A GLU* 1.3 60.8 + - - +
673A GLY* 3.0 13.2 + - - -
674A VAL* 3.1 16.6 + - - +
719A PHE* 4.4 9.6 - - + -
723A TYR* 2.6 36.2 + - - -
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Residues in contact with GLU 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A ILE* 2.8 17.7 + - + +
668A GLU* 3.5 21.9 - - - +
669A ALA 3.3 0.2 - - - -
670A GLN* 1.3 73.8 - - - +
672A ARG* 1.3 56.4 + - - +
674A VAL* 3.3 6.8 + - - +
675A ARG* 3.0 51.8 + - - +
719A PHE* 3.5 19.8 - - + -
726A ARG* 3.1 44.6 + - - +
728A LEU* 3.6 31.6 + - + +
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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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620A LEU* 5.5 0.2 - - - +
623A GLN* 3.2 31.8 + - - +
624A MET 5.8 0.8 + - - -
625A ALA 6.0 1.8 - - - -
626A ASP 4.0 1.6 - - - +
627A GLY* 3.6 15.9 - - - -
666A ASP* 5.0 4.0 + - - -
668A GLU* 3.1 31.9 + - - +
669A ALA* 3.4 27.6 - - - +
670A GLN 3.3 0.4 - - - -
671A GLU* 1.3 75.3 - - + +
673A GLY* 1.3 57.0 + - - +
675A ARG* 3.6 15.0 + - - +
676A CYS* 3.1 26.5 + - - +
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Residues in contact with GLY 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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623A GLN* 4.6 0.4 - - - -
627A GLY 3.3 18.9 + - - -
652A THR* 4.3 2.4 - - - +
656A MET* 3.6 22.8 - - - +
669A ALA 3.4 5.3 + - - -
670A GLN 3.0 8.8 + - - -
672A ARG* 1.3 76.0 - - - +
674A VAL* 1.3 64.4 + - - +
676A CYS* 3.2 5.3 + - - +
677A LEU* 3.0 25.6 + - - +
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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
----------------------------------------------------------
73A ALA* 4.2 8.7 - - + -
656A MET* 3.5 17.0 - - + +
670A GLN 3.1 16.7 + - - +
671A GLU* 3.4 7.6 - - - +
673A GLY* 1.3 74.8 - - - +
675A ARG* 1.3 58.0 + - - +
677A LEU* 3.1 4.7 + - - +
678A LEU* 2.9 33.5 + - + +
716A LEU* 3.9 21.9 - - + +
719A PHE* 3.6 36.6 - - + -
728A LEU* 3.6 30.1 - - + +
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Residues in contact with ARG 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 GLU* 3.0 44.3 + - - +
672A ARG* 3.9 13.1 - - - +
673A GLY 3.3 0.2 - - - -
674A VAL* 1.3 76.4 - - - +
676A CYS* 1.3 62.5 + - - +
678A LEU* 3.4 8.7 + - + +
679A GLU* 3.0 27.2 + - - +
728A LEU* 3.5 36.2 - - + +
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Residues in contact with CYS 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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626A ASP* 3.4 31.8 + - - +
627A GLY 4.2 0.2 - - - -
628A GLY* 3.9 18.2 - - - +
647A SER* 3.6 24.0 - - - -
652A THR* 4.7 6.7 - - + -
672A ARG 3.1 10.5 + - - +
673A GLY* 3.2 10.1 + - - +
675A ARG* 1.3 76.6 - - - +
677A LEU* 1.3 61.9 + - - +
679A GLU* 3.6 9.3 + - - +
680A LYS* 3.4 37.2 + - - +
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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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649A ILE* 4.2 24.0 - - + +
652A THR* 4.0 18.4 - - + -
653A CYS* 3.9 33.4 - - - -
656A MET* 3.9 22.2 - - + -
673A GLY 3.0 14.0 + - - +
674A VAL 3.1 5.4 + - - +
676A CYS* 1.3 74.4 - - - +
678A LEU* 1.3 66.3 + - - +
680A LYS* 3.2 11.9 + - + +
687A TRP* 3.0 28.0 + - - +
712A PRO* 4.4 6.1 - - + -
715A ALA* 4.4 4.3 - - + -
716A LEU* 4.1 31.2 - - + -
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Residues in contact with LEU 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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69A LYS* 4.8 7.3 + - - -
70A ALA* 4.3 16.7 - - + +
71A HIS* 3.7 31.6 - - - +
72A THR* 3.4 25.8 - - - +
76A GLY* 3.7 21.5 - - - -
674A VAL* 2.9 24.6 + - + +
675A ARG* 3.8 8.5 - - + +
677A LEU* 1.3 76.0 - - - +
679A GLU* 1.3 63.3 + - - +
681A GLN* 3.3 22.7 + - - +
716A LEU* 4.0 15.5 - - + -
728A LEU* 4.0 13.5 - - + -
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Residues in contact with GLU 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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69A LYS* 5.0 12.0 + - - +
626A ASP* 5.7 4.0 - - - +
675A ARG 3.0 17.8 + - - +
676A CYS* 3.9 9.9 - - - +
677A LEU 3.3 0.2 - - - -
678A LEU* 1.3 76.2 - - - +
680A LYS* 1.3 60.5 + - + +
681A GLN 3.8 4.2 + - - +
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Residues in contact with LYS 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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626A ASP* 4.8 2.5 - - - -
647A SER* 2.8 42.9 + - - -
648A GLN 4.0 1.0 - - - +
649A ILE* 3.7 20.9 - - + +
652A THR* 5.2 0.2 + - - -
676A CYS* 3.4 23.5 + - - +
677A LEU* 3.2 11.1 + - + +
678A LEU 3.2 0.8 - - - -
679A GLU* 1.3 77.6 - - + +
681A GLN* 1.3 65.5 + - - +
682A LEU* 3.5 5.2 + - - +
687A TRP* 3.8 10.3 - - + -
688A PRO* 3.2 25.5 - - + +
690A GLU* 2.8 31.7 + - - +
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Residues in contact with GLN 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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69A LYS* 6.1 0.7 - - - -
70A ALA* 3.7 14.4 + - - +
76A GLY* 3.0 38.0 + - - -
79A ASN* 3.6 12.2 + - - +
80A GLY 3.4 6.5 - - - +
677A LEU 3.3 4.8 + - - +
678A LEU* 3.3 18.1 + - - +
679A GLU 4.2 4.7 - - - +
680A LYS* 1.3 78.3 - - - +
682A LEU* 1.3 73.5 + - - +
683A PRO* 4.2 1.4 - - - +
685A GLY* 3.2 14.5 + - - +
686A ASP 3.5 9.2 - - - +
687A TRP* 3.2 39.2 - - + +
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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
------------------------------------------------------------
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