Contacts of the helix formed by residues 671 - 690 (chain A) in PDB entry 4H1J
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 671 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A GLU* 3.5 22.9 + - - +
542A SER* 6.3 1.4 - - - +
608A VAL* 4.6 1.1 - - - -
669A ARG 3.8 0.9 + - - +
670A PRO* 1.3 76.7 - - - +
672A PHE* 1.3 65.8 + - - +
673A THR* 4.1 22.3 + - - +
674A GLU* 3.1 44.8 + - - +
675A LEU* 2.9 20.8 + - - +
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Residues in contact with PHE 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A CYS* 3.8 15.9 - - - +
537A MET* 3.6 51.1 - - + -
538A ALA* 3.7 16.6 - - - +
541A GLU* 2.8 23.6 + - - +
550A ILE* 4.1 0.2 - - + -
604A THR* 3.9 10.3 - - + -
607A ASP* 3.6 21.3 - - + -
608A VAL* 3.6 35.6 - - + +
611A PHE* 3.5 29.8 - + + -
670A PRO 3.9 1.0 + - - -
671A ARG* 1.3 71.5 - - - +
673A THR* 1.3 62.4 + - - +
675A LEU* 3.2 8.9 + - + +
676A VAL* 3.0 27.5 + - - +
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Residues in contact with THR 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ALA* 4.1 19.1 + - + +
541A GLU* 2.6 23.5 + - - +
542A SER* 5.6 2.1 + - - -
671A ARG* 3.3 17.8 + - - +
672A PHE* 1.3 77.8 - - - +
674A GLU* 1.3 73.8 + - - +
676A VAL* 3.6 14.4 - - - +
677A CYS* 3.9 10.4 - - - -
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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
----------------------------------------------------------
670A PRO* 5.1 5.2 - - + -
671A ARG* 3.1 57.3 + - + +
672A PHE 3.3 0.4 - - - -
673A THR* 1.3 82.0 - - - +
675A LEU* 1.3 60.8 + - - +
676A VAL 3.1 1.8 - - - -
677A CYS* 3.0 28.0 + - - +
678A SER* 3.2 14.8 + - - +
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Residues in contact with LEU 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A CYS* 3.9 11.7 - - - -
608A VAL* 4.7 5.4 - - + -
611A PHE* 3.7 34.3 - - + -
615A MET* 4.9 2.5 - - + -
657A LEU* 4.5 21.1 - - + +
661A CYS* 4.0 21.1 - - - -
670A PRO* 4.1 21.9 - - + +
671A ARG 2.9 17.4 + - - +
672A PHE* 3.2 14.1 + - + +
674A GLU* 1.3 72.0 - - - +
676A VAL* 1.4 54.6 + - - +
678A SER* 3.3 13.3 + - - -
679A LEU* 2.8 48.2 + - + +
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Residues in contact with VAL 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 3.6 6.3 - - + +
534A CYS* 3.7 33.9 - - + +
535A LYS* 3.9 31.4 - - + +
538A ALA* 3.9 12.8 - - + -
672A PHE 3.0 18.0 + - - +
673A THR* 3.6 11.9 - - - +
674A GLU 3.1 0.4 - - - -
675A LEU* 1.4 74.9 - - - +
677A CYS* 1.4 58.1 + - - +
679A LEU 3.4 0.2 + - - -
680A SER* 2.9 37.5 + - - +
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Residues in contact with CYS 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A THR 3.9 14.4 - - - -
674A GLU* 3.0 15.1 + - + +
676A VAL* 1.4 78.5 - - - +
678A SER* 1.3 56.1 + - - +
680A SER* 3.5 7.5 + - - -
681A ASP* 3.1 26.7 + - - +
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Residues in contact with SER 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A LEU* 3.7 32.6 - - - +
670A PRO* 6.1 0.7 - - - +
674A GLU* 3.2 12.0 + - - +
675A LEU* 3.3 12.3 + - - +
677A CYS* 1.3 75.2 - - - +
679A LEU* 1.3 62.0 + - - +
681A ASP* 3.4 8.5 + - - +
682A VAL* 3.2 26.2 + - - +
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Residues in contact with LEU 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A VAL* 4.3 7.2 - - + +
530A SER* 4.0 11.4 - - - +
531A LEU* 3.7 19.5 - - + -
534A CYS* 3.6 37.7 - - + -
611A PHE* 3.9 17.7 - - + -
615A MET* 4.0 10.8 - - + -
654A LEU* 3.5 32.8 - - + -
657A LEU* 4.0 9.0 - - + -
675A LEU* 2.8 26.2 + - + +
678A SER* 1.3 70.2 - - - +
680A SER* 1.4 58.5 + - - +
682A VAL* 3.2 6.0 + - + +
683A TYR* 2.9 28.9 + - - +
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Residues in contact with SER 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 3.5 25.1 - - - +
535A LYS* 4.8 3.6 + - - -
676A VAL* 2.9 25.9 + - - +
677A CYS* 3.7 7.8 - - - -
678A SER 3.4 0.2 - - - -
679A LEU* 1.4 72.5 - - - +
681A ASP* 1.3 59.3 + - - +
683A TYR* 3.4 2.3 + - - +
684A GLN* 3.0 38.3 + - - +
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Residues in contact with ASP 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A CYS 3.1 14.3 + - - +
678A SER* 3.5 11.9 - - - +
679A LEU 3.2 0.2 - - - -
680A SER* 1.3 75.2 - - - +
682A VAL* 1.3 57.3 + - + +
684A GLN* 3.4 7.0 + - - +
685A MET* 3.0 45.4 + - - +
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Residues in contact with VAL 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A VAL* 3.9 22.2 - - + -
651A PRO* 5.0 4.5 - - + -
653A VAL* 3.9 24.7 - - + -
654A LEU* 4.2 26.7 - - + +
657A LEU* 3.8 20.4 - - + -
678A SER 3.2 14.7 + - - +
679A LEU* 3.6 8.5 - - - +
681A ASP* 1.3 71.7 - - + +
683A TYR* 1.3 61.1 + - - +
685A MET* 3.4 12.5 + - + +
686A GLU* 2.9 35.4 + - + +
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Residues in contact with TYR 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A LEU* 3.5 39.7 - - + +
527A VAL* 3.8 11.0 - - + +
528A LEU* 3.8 47.2 - - + +
531A LEU* 4.3 13.5 - - + -
679A LEU 2.9 16.1 + - - +
680A SER* 3.7 8.5 - - - +
681A ASP 3.4 0.2 - - - -
682A VAL* 1.3 76.5 - - - +
684A GLN* 1.3 80.8 + - - +
686A GLU* 3.3 2.6 + - - -
687A LYS* 2.9 57.4 + - + +
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Residues in contact with GLN 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A SER* 3.0 23.1 + - - +
681A ASP* 3.8 7.6 - - - +
683A TYR* 1.3 95.7 - - - +
685A MET* 1.3 64.4 + - - +
687A LYS* 3.5 12.2 + - - +
688A ASP* 3.1 39.3 + - - +
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Residues in contact with MET 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A PRO* 6.4 1.3 - - + -
653A VAL* 3.9 39.5 - - + -
681A ASP* 3.0 40.7 + - - +
682A VAL* 3.5 13.0 - - + +
684A GLN* 1.3 77.4 - - - +
686A GLU* 1.4 66.8 + - - +
688A ASP* 3.6 8.0 + - - +
689A ILE* 3.3 33.9 + - + +
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Residues in contact with GLU 686 (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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523A VAL* 4.3 12.1 - - + +
524A LEU* 3.8 20.0 + - + +
527A VAL* 4.3 12.6 - - + -
651A PRO* 3.6 37.6 - - + +
682A VAL* 2.9 22.9 + - + +
683A TYR* 3.3 5.1 + - - +
685A MET* 1.4 80.7 - - - +
687A LYS* 1.3 58.0 + - - +
689A ILE* 3.4 22.9 + - - +
690A ALA* 3.0 29.3 + - - +
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Residues in contact with LYS 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A LEU* 3.5 25.7 - - + +
683A TYR* 2.9 47.2 + - + +
684A GLN* 3.5 16.8 + - - +
686A GLU* 1.3 73.7 - - - +
688A ASP* 1.4 65.2 + - - +
690A ALA* 3.2 21.3 + - - +
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Residues in contact with ASP 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A GLN* 3.1 30.3 + - - +
685A MET* 3.7 7.9 - - - +
686A GLU 3.4 0.2 - - - -
687A LYS* 1.4 78.0 - - - +
689A ILE* 1.3 61.3 + - + +
690A ALA 4.5 2.4 - - - -
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Residues in contact with ILE 689 (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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685A MET* 3.3 20.6 - - + +
686A GLU* 3.4 27.3 + - - +
687A LYS 3.3 0.4 - - - -
688A ASP* 1.3 76.6 - - + +
690A ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 690 (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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524A LEU* 4.7 16.6 - - + -
686A GLU 3.0 18.4 + - - +
687A LYS* 3.2 18.6 + - + +
688A ASP 4.5 1.8 - - - -
689A ILE* 1.3 80.3 - - - +
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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
------------------------------------------------------------
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