Contacts of the helix formed by residues 664 - 683 (chain A) in PDB entry 6CIM
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 664 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A THR* 5.2 2.3 - - - +
660A ALA* 5.1 2.9 - - - +
661A ASP* 2.9 29.6 + - + +
662A GLU 3.3 0.6 - - - -
663A SER* 1.3 73.6 - - - +
665A HIS* 1.3 64.7 + - - +
666A GLU* 3.4 2.9 + - - +
667A THR* 2.5 29.9 + - - +
668A LEU* 3.0 20.3 + - - +
34B LYS* 2.9 31.1 + - - -
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Residues in contact with HIS 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A SER 3.3 5.1 + - - +
664A ASP* 1.3 74.2 + - - +
666A GLU* 1.3 65.7 + - - +
668A LEU* 3.7 5.4 - - + +
669A THR* 2.9 43.6 + - + +
714A GLU* 2.7 59.1 + - + +
782A LYS 5.0 2.6 + - - -
784A PHE* 4.2 14.0 - + - -
35B GLY* 4.9 8.1 - - - -
36B TRP* 3.5 27.4 + + + +
99B PRO* 3.8 6.1 - - + +
100B ASN* 3.1 28.8 + - - -
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Residues in contact with GLU 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A TYR* 4.5 10.5 - - + +
664A ASP* 3.1 2.3 + - - +
665A HIS* 1.3 80.4 + - - +
667A THR* 1.3 58.0 + - - +
669A THR* 3.1 3.8 + - - -
670A ALA* 3.0 28.5 + - - +
16B GLN* 3.9 3.3 + - - +
33B GLN 4.8 0.3 - - - +
34B LYS* 2.9 38.7 + - - +
35B GLY* 2.8 31.2 + - - -
73B ARG* 3.8 38.1 + - - +
99B PRO* 3.6 22.2 - - + +
101B ASN* 3.7 6.4 - - - +
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Residues in contact with THR 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LEU* 6.3 3.1 - - + -
548A TYR* 5.6 4.0 - - - -
552A THR* 3.7 36.7 - - + +
658A MET* 5.6 0.7 - - - -
660A ALA* 4.0 12.8 - - + -
664A ASP* 2.5 30.3 + - - -
666A GLU* 1.3 76.0 - - - +
668A LEU* 1.3 67.1 + - - +
670A ALA* 4.3 5.4 - - + -
671A ILE* 2.9 34.6 + - + +
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Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A CYS* 5.1 1.8 - - - -
620A VAL* 4.2 25.4 - - + -
658A MET* 4.5 10.8 - - + -
661A ASP 4.9 3.8 + - - +
662A GLU* 3.6 23.3 - - - +
664A ASP 3.0 16.6 + - - +
665A HIS* 3.7 6.7 - - - +
667A THR* 1.3 76.6 - - - +
669A THR* 1.3 58.6 + - + +
671A ILE* 4.0 0.3 - - - -
672A LEU* 3.0 63.3 + - + +
711A LEU* 4.2 18.6 - - + -
714A GLU* 4.5 9.4 - - + +
715A VAL* 4.3 15.7 - - + -
784A PHE* 4.2 7.9 - - + -
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Residues in contact with THR 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 HIS* 2.9 34.0 + - + +
666A GLU 3.1 10.6 + - - -
668A LEU* 1.3 72.1 - - + +
670A ALA* 1.3 69.3 + - - +
673A SER* 2.3 34.7 + - - -
784A PHE* 3.5 44.2 - - + -
99B PRO 3.3 10.4 + - - -
100B ASN* 3.4 27.1 - - - +
101B ASN* 4.0 1.1 + - - +
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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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537A GLY 4.8 0.2 - - - +
541A LEU* 4.5 19.5 - - + -
666A GLU 3.0 19.8 + - - +
667A THR* 3.3 6.9 + - + +
669A THR* 1.3 79.9 + - - +
671A ILE* 1.3 64.8 + - + +
673A SER* 4.7 0.4 - - - -
674A PRO* 3.6 8.7 - - - +
101B ASN* 4.0 25.4 - - - +
173B ASN* 3.0 31.1 + - - +
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Residues in contact with ILE 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A GLY 3.1 38.2 - - - +
538A LEU* 3.7 25.1 - - + -
539A SER* 4.9 0.3 + - - -
541A LEU* 5.6 2.9 - - + -
552A THR* 4.6 4.7 - - - +
554A ALA* 4.1 10.8 - - + -
556A ARG* 5.0 2.5 - - - -
656A CYS* 3.8 17.9 - - - -
658A MET* 3.8 35.7 - - + -
667A THR* 2.9 34.4 + - + +
668A LEU 4.1 0.4 - - - +
670A ALA* 1.3 78.2 - - + +
672A LEU* 1.3 63.5 + - + +
674A PRO* 3.5 12.1 - - - +
675A LEU* 4.6 6.9 + - - +
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Residues in contact with LEU 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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599A CYS* 4.3 8.5 - - - -
622A PHE* 3.8 32.1 - - + -
658A MET* 3.7 21.3 - - + -
668A LEU* 3.0 44.8 + - + +
671A ILE* 1.3 79.4 - - + +
673A SER* 1.3 64.0 + - - +
674A PRO 3.4 0.4 - - - -
675A LEU* 3.1 22.4 + - + +
676A ILE* 3.0 24.0 + - + +
715A VAL* 5.7 0.7 - - + -
784A PHE* 4.1 10.3 - - + -
785A ILE* 3.9 24.7 - - + -
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Residues in contact with SER 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A THR* 2.3 35.1 + - - -
670A ALA* 4.7 1.3 - - - -
672A LEU* 1.3 75.3 - - - +
674A PRO* 1.3 65.0 - - - +
676A ILE* 3.1 10.3 + - - +
677A ALA* 2.9 27.7 + - - +
784A PHE* 4.3 8.9 - - - -
100B ASN 4.6 5.5 + - - -
101B ASN* 5.6 1.3 - - - +
172B TRP* 4.2 17.5 + - - -
173B ASN* 5.5 0.9 - - - -
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Residues in contact with PRO 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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539A SER* 3.5 20.2 - - - +
556A ARG* 3.7 12.6 - - - +
670A ALA 3.6 10.8 - - - +
671A ILE 3.5 11.7 - - - +
673A SER* 1.3 91.8 - - - +
675A LEU* 1.3 64.5 + - - +
677A ALA* 3.3 5.4 + - + +
678A GLU* 3.0 30.2 + - - +
169B THR* 3.4 22.1 - - - +
172B TRP* 3.5 30.5 - - + -
173B ASN* 4.4 0.9 - - - +
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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
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556A ARG* 3.3 35.4 - - + +
557A PHE 3.8 10.5 - - - +
559A TYR* 3.6 10.8 - - + -
622A PHE* 3.4 38.4 - - + -
655A LEU* 4.1 18.2 - - + -
656A CYS* 3.7 23.3 - - + -
671A ILE 4.6 2.5 - - - +
672A LEU* 3.1 22.9 + - + +
674A PRO* 1.3 77.1 - - - +
676A ILE* 1.3 65.4 + - - +
678A GLU* 3.2 9.4 + - - +
679A ARG* 2.9 22.2 + - - +
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Residues in contact with ILE 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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597A GLU* 4.8 1.1 - - - +
622A PHE* 4.1 20.2 - - + -
672A LEU* 3.0 19.3 + - + +
673A SER* 3.1 8.0 + - - +
675A LEU* 1.3 74.8 - - - +
677A ALA* 1.3 57.1 + - - +
679A ARG* 3.1 31.6 + - - +
680A GLU* 2.8 36.7 + - + +
784A PHE* 4.5 13.5 - - + +
785A ILE* 3.7 42.2 - - + -
786A GLU 5.8 0.2 - - - +
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Residues in contact with ALA 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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524A LYS 5.0 1.3 - - - +
525A ASN* 6.3 0.2 - - + -
673A SER 2.9 11.7 + - - +
674A PRO* 3.5 9.4 - - + +
675A LEU 3.1 0.2 - - - -
676A ILE* 1.3 73.8 - - - +
678A GLU* 1.3 64.3 + - - +
680A GLU* 3.6 6.8 - - - +
681A ALA* 2.9 24.5 + - - +
169B THR* 3.9 16.6 - - + -
172B TRP* 4.0 26.5 - - + -
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Residues in contact with GLU 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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523A LEU* 6.0 0.7 - - + -
526A VAL* 3.7 22.1 - - + +
556A ARG* 3.1 28.7 + - - -
558A ARG* 3.3 16.2 - - + +
559A TYR* 3.0 34.6 + - + +
560A ASP* 5.1 2.9 - - + +
674A PRO 3.0 15.8 + - - +
675A LEU* 3.7 5.5 - - - +
677A ALA* 1.3 75.1 - - - +
679A ARG* 1.3 63.0 + - - +
681A ALA* 3.4 1.9 + - - +
682A MET* 3.0 31.7 + - + +
169B THR* 2.6 36.4 + - + +
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Residues in contact with ARG 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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559A TYR* 3.7 13.4 - - + -
597A GLU* 3.0 35.8 + - - +
675A LEU 2.9 12.8 + - - +
676A ILE* 3.1 30.0 + - - +
678A GLU* 1.3 74.3 - - - +
680A GLU* 1.3 84.8 + - - +
682A MET* 3.2 12.8 + - - +
683A LYS* 3.1 44.0 + - + +
702A PHE* 3.6 37.7 + - + +
704A GLY 4.7 6.1 - - - +
785A ILE* 5.3 0.2 - - - +
786A GLU* 3.4 43.4 + - - +
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Residues in contact with GLU 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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676A ILE* 2.8 22.2 + - + +
677A ALA* 3.6 7.9 - - - +
679A ARG* 1.3 98.2 + - - +
681A ALA* 1.3 55.1 + - - +
683A LYS* 2.7 55.9 + - + +
684A SER* 3.9 5.0 + - - -
786A GLU* 4.8 3.2 - - - +
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Residues in contact with ALA 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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523A LEU* 3.3 21.1 - - + +
524A LYS* 3.5 41.3 + - + +
526A VAL* 4.0 4.5 - - + -
677A ALA 2.9 18.0 + - - +
678A GLU 3.7 4.5 - - - +
679A ARG 3.4 0.2 - - - -
680A GLU* 1.3 73.5 - - - +
682A MET* 1.3 61.7 + - - +
684A SER* 3.2 20.1 + - - +
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Residues in contact with MET 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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519A TRP* 3.6 28.1 - - + -
523A LEU* 3.4 22.2 - - + -
559A TYR* 3.4 41.1 - - + -
560A ASP* 3.6 23.1 - - + +
563A LEU* 3.7 13.7 - - + -
678A GLU 3.0 23.1 + - - +
679A ARG* 3.6 6.5 - - - +
680A GLU 3.2 0.2 - - - -
681A ALA* 1.3 70.5 - - - +
683A LYS* 1.3 63.5 + - - +
684A SER 2.9 8.0 + - - -
685A SER 3.5 16.5 + - - +
700A PHE* 5.0 6.8 + - + +
702A PHE* 3.5 24.2 - - + -
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Residues in contact with LYS 683 (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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679A ARG* 3.1 37.4 + - - +
680A GLU* 2.7 49.8 + - - +
682A MET* 1.3 71.3 - - - +
684A SER* 1.3 58.9 + - - +
685A SER 3.7 1.0 + - - -
700A PHE 5.3 7.8 - - - +
702A PHE* 4.0 28.5 + - + +
786A GLU* 3.4 24.9 + - - -
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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