Contacts of the helix formed by residues 676 - 686 (chain A) in PDB entry 6CNC
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 SER 676 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A PRO* 4.3 5.9 - - - +
626A LEU* 4.0 2.5 - - - -
667A SER 3.2 16.3 + - - -
668A VAL* 2.9 13.7 - - - +
669A LEU* 5.1 1.6 - - - -
670A GLY 4.0 6.6 + - - -
671A ASP* 5.6 0.4 - - - -
673A LYS 3.2 20.1 + - - -
674A LYS 2.7 5.3 + - - -
675A HIS* 1.3 72.0 + - - +
677A VAL* 1.3 55.8 + - - +
678A PHE* 4.2 3.1 - - - -
679A TYR* 3.6 20.6 - - - -
680A THR* 2.4 41.7 + - - -
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Residues in contact with VAL 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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610A PHE* 5.4 6.1 - - + -
614A ILE* 3.6 29.4 - - + -
624A ILE* 6.1 2.7 - - + -
626A LEU* 4.1 8.6 - - + +
652A VAL* 5.7 0.2 - - + -
654A ILE* 3.8 27.4 - - + -
659A ILE* 6.3 0.2 - - + -
664A MET* 5.5 7.6 - - - -
668A VAL* 2.4 43.7 + - + +
669A LEU* 4.8 6.1 - - + +
676A SER* 1.3 66.1 - - - +
678A PHE* 1.3 69.3 + - + +
680A THR* 4.6 0.9 - - - -
681A ILE* 2.9 47.4 + - + +
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Residues in contact with PHE 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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503A CYS* 6.0 1.3 - - - -
541A LEU* 5.2 6.3 - - + +
549A PRO* 5.8 2.7 - - + -
551A ILE 5.0 4.0 - - - +
552A ALA* 4.1 10.3 - - + -
553A ALA* 4.3 11.7 - - + -
610A PHE* 6.0 0.4 - + - -
613A LEU* 5.5 4.3 - - + -
614A ILE* 6.5 0.2 - - + -
668A VAL 4.0 1.0 + - - -
669A LEU* 4.0 27.8 - - + -
676A SER* 3.2 3.5 - - - -
677A VAL* 1.3 90.5 - - + +
679A TYR* 1.3 58.3 + - - +
681A ILE* 4.1 3.6 - - + +
682A LEU* 2.9 30.8 + - - +
690A ALA* 4.7 6.3 - - + +
693A ALA* 4.3 14.1 - - + -
694A MET* 3.4 59.9 - - + -
697A MET* 3.7 32.5 - - + -
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Residues in contact with TYR 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LEU* 5.8 0.7 - - - -
542A LEU* 3.6 38.3 - - + +
547A GLY 4.4 6.2 + - - -
549A PRO* 3.9 27.9 - - + +
674A LYS* 3.0 34.8 - - + +
676A SER* 3.0 13.5 + - - -
678A PHE* 1.3 79.9 - - - +
680A THR* 1.3 63.4 + - - +
682A LEU* 3.6 3.3 - - - +
683A ARG* 2.8 61.0 + - + +
926A MET 4.5 1.7 + - - -
927A GLU* 3.3 52.9 + - + +
937A ARG* 4.7 3.6 - - - -
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Residues in contact with THR 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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624A ILE* 3.7 26.2 - - + -
625A ASN 4.4 7.0 - - - +
626A LEU* 3.2 17.9 - - + +
676A SER 2.4 34.0 + - - -
677A VAL 4.1 1.6 - - - -
679A TYR* 1.3 72.3 - - - +
681A ILE* 1.3 63.0 + - - +
683A ARG* 4.0 2.3 - - - +
684A ASP* 2.9 36.6 + - + +
937A ARG* 2.6 32.6 + - - +
941A HIS* 6.0 2.0 - - + -
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Residues in contact with ILE 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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614A ILE* 3.7 29.6 - - + -
622A VAL* 4.6 15.9 - - + -
624A ILE* 3.9 23.6 - - + -
677A VAL* 2.9 35.7 + - + +
678A PHE* 4.1 4.5 - - - +
680A THR* 1.3 74.5 - - - +
682A LEU* 1.3 58.7 + - - +
684A ASP* 4.8 1.8 - - - -
685A TYR* 2.9 37.1 + - + +
686A GLY 3.7 1.4 + - - +
689A GLU* 4.6 7.2 - - + +
690A ALA* 4.2 20.4 - - - +
693A ALA* 4.4 17.0 - - + -
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Residues in contact with LEU 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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538A LYS 4.8 1.6 - - - +
541A LEU* 3.5 30.5 - - + -
542A LEU* 3.3 33.2 - - + -
678A PHE 2.9 19.6 + - - +
679A TYR* 3.6 3.8 - - - +
681A ILE* 1.3 76.5 - - - +
683A ARG* 1.3 68.6 + - - +
684A ASP 2.8 2.1 + - - -
686A GLY* 2.8 23.1 + - - +
687A PRO* 3.4 40.8 - - + -
690A ALA* 3.8 14.6 - - + +
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Residues in contact with ARG 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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542A LEU* 3.3 32.4 - - - +
679A TYR* 2.8 48.3 + - + +
680A THR* 4.2 2.5 - - - +
682A LEU* 1.3 77.5 - - - +
684A ASP* 1.3 62.0 + - - +
924A LEU* 3.7 4.0 + - - +
925A GLU* 3.3 54.5 + - - +
927A GLU* 4.1 20.4 - - - +
1077A LYS* 4.6 19.9 - - - +
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Residues in contact with ASP 684 (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 VAL 4.4 0.2 - - - +
624A ILE* 5.6 1.4 - - + +
680A THR* 2.9 24.4 + - + +
681A ILE* 4.1 0.7 - - - +
682A LEU 2.8 2.8 + - - -
683A ARG* 1.3 82.9 - - - +
685A TYR* 1.3 81.5 + - + +
686A GLY 3.4 1.4 + - - -
941A HIS* 2.6 46.1 + - - -
1073A ILE* 5.4 5.0 - - - +
1076A PHE* 6.1 1.0 - - - -
1077A LYS* 5.0 15.7 - - - +
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Residues in contact with TYR 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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621A PRO* 3.5 21.1 - - + +
622A VAL* 3.4 15.9 - - + -
623A VAL* 2.3 62.8 + - - +
624A ILE* 4.1 9.6 - - + -
681A ILE* 2.9 20.6 + - + +
684A ASP* 1.3 95.5 - - + +
686A GLY* 1.3 63.7 + - - +
689A GLU* 4.8 15.7 + - + +
941A HIS* 3.6 7.6 + + - -
945A ILE* 4.2 4.3 - - - +
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Residues in contact with GLY 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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681A ILE* 3.7 1.2 + - - +
682A LEU* 2.8 23.0 + - - +
684A ASP 3.4 2.4 + - - -
685A TYR* 1.3 83.3 - - - +
687A PRO* 1.3 78.5 - - - +
688A GLN 3.5 1.7 + - - -
689A GLU* 3.7 2.6 + - - +
690A ALA* 3.5 12.6 + - - +
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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