Contacts of the helix formed by residues 673 - 692 (chain A) in PDB entry 4G0U
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 LYS 673 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663A ALA* 3.8 12.3 + - - +
666A THR* 3.3 32.3 - - + +
667A LEU* 3.7 18.4 - - - +
670A SER* 3.2 18.3 + - - +
671A LYS 3.2 2.6 - - - -
672A LYS* 1.3 83.0 - - + +
674A ILE* 1.3 64.9 + - - +
675A ASP 3.3 2.0 - - - -
676A ASP* 3.2 35.1 + - + +
677A ARG* 3.1 42.3 + - - +
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Residues in contact with ILE 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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671A LYS* 3.6 20.0 - - + +
672A LYS 3.7 2.6 + - - -
673A LYS* 1.3 77.7 - - - +
675A ASP* 1.3 65.9 + - - +
677A ARG* 3.3 22.1 + - - +
678A LYS* 3.0 28.1 + - - +
875A GLY* 3.6 19.9 - - - +
17F G 3.9 28.7 - - + +
18F G 3.6 27.1 - - - +
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Residues in contact with ASP 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A LYS 5.4 1.1 + - - +
673A LYS 3.3 0.8 - - - -
674A ILE* 1.3 80.7 - - - +
676A ASP* 1.3 65.0 + - - +
678A LYS* 3.3 22.0 + - + +
679A GLU* 3.1 20.6 + - - +
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Residues in contact with ASP 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A LEU* 3.6 20.3 - - + +
672A LYS 4.6 1.7 - - - +
673A LYS* 3.2 38.1 - - + +
674A ILE 3.2 0.6 - - - -
675A ASP* 1.3 78.9 + - - +
677A ARG* 1.3 59.5 + - - +
679A GLU* 3.3 11.1 + - - +
680A TRP* 2.8 29.3 + - - +
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Residues in contact with ARG 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A LEU* 2.6 53.9 + - + +
668A ALA* 3.6 21.7 + - - +
669A PHE 4.9 1.0 - - - -
670A SER 2.7 31.9 + - - +
671A LYS* 4.2 2.0 - - - +
673A LYS* 3.1 15.3 + - - +
674A ILE* 3.3 22.3 + - - +
676A ASP* 1.3 71.9 - - - +
678A LYS* 1.3 59.3 + - - +
680A TRP* 3.3 17.0 - - + +
681A LEU* 2.8 37.9 + - + +
874A THR* 3.9 20.6 - - + -
875A GLY* 4.3 9.4 - - - +
16F C 4.4 2.5 + - - -
17F G 3.0 37.5 + - - -
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Residues in contact with LYS 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A ILE* 3.0 21.0 + - - +
675A ASP* 3.3 22.8 + - - +
676A ASP 3.2 0.2 - - - -
677A ARG* 1.3 75.3 - - - +
679A GLU* 1.3 54.5 + - - +
682A THR* 2.7 38.6 + - - +
875A GLY* 3.0 22.5 + - - +
876A TRP* 3.3 51.2 - - + +
17F G 3.8 0.2 + - - -
18F G 2.4 32.5 + - - -
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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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675A ASP 3.1 12.8 + - - +
676A ASP* 3.3 13.8 + - - +
678A LYS* 1.3 75.2 - - - +
680A TRP* 1.3 63.2 + - - +
682A THR* 3.3 7.0 + - - -
683A ASN* 3.0 45.7 + - - +
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Residues in contact with TRP 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A LEU* 3.7 23.9 - - + +
668A ALA* 4.8 7.0 - - + -
676A ASP 2.8 20.8 + - - +
677A ARG* 3.3 28.3 - - + +
679A GLU* 1.3 73.9 - - - +
681A LEU* 1.3 76.8 + - + +
683A ASN* 3.5 7.4 + - - +
684A PHE* 3.2 19.2 + - - +
715A ILE* 3.5 27.1 - - + -
716A ASN* 2.8 23.3 + - - -
719A LEU* 4.6 7.6 - - + -
720A ILE* 3.5 49.3 - - + +
723A SER* 3.6 26.5 - - - -
874A THR* 4.8 0.4 - - + -
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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
----------------------------------------------------------
677A ARG 2.8 21.8 + - - +
680A TRP* 1.3 78.7 - - + +
682A THR* 1.3 66.5 + - - +
684A PHE* 3.2 6.4 + - + +
685A MET* 2.9 31.8 + - + +
720A ILE* 3.7 26.0 - - + +
723A SER* 3.9 14.6 - - - -
724A ASN* 4.0 19.1 - - + +
727A ASN* 3.7 11.0 - - - +
874A THR* 3.3 44.9 - - + +
875A GLY* 4.6 0.9 - - - +
876A TRP* 3.6 15.7 - - + -
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Residues in contact with THR 682 (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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678A LYS* 2.7 25.6 + - - +
679A GLU* 3.5 8.5 - - - -
681A LEU* 1.3 75.8 - - - +
683A ASN* 1.3 66.4 + - - +
685A MET* 3.1 15.5 + - + +
686A GLU* 3.0 43.8 + - + +
876A TRP* 3.6 15.1 - - - -
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Residues in contact with ASN 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A GLU* 3.0 42.3 + - - +
680A TRP* 3.7 6.5 - - - +
682A THR* 1.3 78.7 - - - +
684A PHE* 1.3 61.8 + - - +
686A GLU* 3.4 10.9 + - - +
687A ASP* 3.0 37.9 + - - +
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Residues in contact with PHE 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A TRP 3.2 4.1 + - - +
681A LEU* 3.2 10.1 + - + +
683A ASN* 1.3 77.6 - - - +
685A MET* 1.3 68.9 + - + +
687A ASP* 3.5 7.3 + - + +
688A ARG* 3.1 53.5 + - + +
716A ASN 5.6 0.7 - - - -
720A ILE* 3.6 40.4 - - + -
721A LEU* 3.6 31.6 - - + -
724A ASN* 3.8 40.2 - - + -
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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
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681A LEU* 2.9 23.2 + - + +
682A THR* 3.1 11.9 + - + +
684A PHE* 1.3 81.8 - - + +
686A GLU* 1.3 57.5 + - - +
688A ARG* 3.5 7.3 + - - +
689A ARG* 3.0 48.6 + - - +
724A ASN* 3.9 22.9 - - + +
727A ASN* 5.5 3.6 - - - -
876A TRP* 3.6 34.3 - - + -
1019A PHE* 5.2 7.2 - - - -
1025A LEU* 4.3 28.3 - - + -
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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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682A THR* 3.0 39.6 + - + +
683A ASN* 3.9 10.6 - - - +
685A MET* 1.3 74.2 - - - +
687A ASP* 1.3 63.5 - - - +
689A ARG* 3.1 27.4 + - - +
690A GLN* 3.0 42.1 + - + +
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Residues in contact with ASP 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A ASN* 3.0 26.7 + - - +
684A PHE* 3.9 7.6 - - + +
686A GLU* 1.3 78.9 - - - +
688A ARG* 1.3 57.2 + - - +
690A GLN* 4.5 12.0 - - - +
691A ARG* 3.0 55.3 + - - +
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Residues in contact with ARG 688 (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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684A PHE* 3.1 42.0 + - + +
685A MET* 3.9 8.0 - - - +
687A ASP* 1.3 76.1 - - - +
689A ARG* 1.3 60.9 + - - +
690A GLN 3.4 0.2 - - - -
691A ARG* 3.5 10.1 + - + +
692A ARG* 3.0 71.4 + - + +
721A LEU* 5.6 2.6 - - - +
724A ASN* 3.3 24.7 + - - +
728A GLU* 3.1 26.5 + - - -
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Residues in contact with ARG 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* 3.0 40.7 + - - +
686A GLU* 3.4 36.8 - - - +
688A ARG* 1.3 76.8 - - - +
690A GLN* 1.3 63.6 + - + +
692A ARG* 3.2 26.8 + - - +
1024A CYS* 3.2 42.3 - - - +
1025A LEU 5.1 2.4 + - - +
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Residues in contact with GLN 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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686A GLU* 3.0 26.6 + - + +
687A ASP* 4.5 12.9 - - - +
689A ARG* 1.3 76.1 - - + +
691A ARG* 1.3 62.3 + - - +
692A ARG 3.0 3.1 + - - -
693A LEU* 3.3 30.6 + - + +
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Residues in contact with ARG 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ASP* 3.0 50.1 + - - +
688A ARG* 3.6 13.9 - - + +
689A ARG 3.3 0.2 - - - -
690A GLN* 1.3 77.5 - - - +
692A ARG* 1.3 56.4 + - + +
693A LEU* 2.9 16.5 + - - +
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Residues in contact with ARG 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A ARG* 3.0 69.9 + - + +
689A ARG* 3.5 19.9 - - - +
690A GLN 3.0 1.4 - - - -
691A ARG* 1.3 74.2 - - - +
693A LEU* 1.3 58.0 + - - +
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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