Contacts of the helix formed by residues 555 - 566 (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 GLN 555 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A THR* 1.3 77.2 - - - +
556A ASP* 1.3 71.1 + - - +
558A ILE* 2.9 20.2 + - - +
559A THR* 3.1 10.5 + - - +
799A SER* 4.3 19.6 + - - +
800A LYS* 3.5 44.3 - - + +
767B ILE* 4.0 6.7 - - + +
768B GLU* 3.1 54.4 + - - +
769B ASP* 5.9 0.4 + - - -
947B HIS* 4.0 23.9 + - + +
952B ARG* 5.9 2.4 - - - +
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Residues in contact with ASP 556 (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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554A THR 3.1 2.0 + - - -
555A GLN* 1.3 79.0 - - - +
557A PHE* 1.3 57.5 + - - +
559A THR* 3.0 0.7 + - - +
560A GLY 2.6 32.6 + - - -
701A CYS* 3.2 17.6 - - - +
702A ALA* 5.1 0.2 - - - -
705A LEU* 3.2 23.7 - - - +
761B SER* 4.2 17.1 - - - +
762B TYR 5.2 1.4 + - - +
763B SER 4.3 13.2 - - - +
764B GLY* 4.8 1.2 - - - -
766B ASP* 5.7 0.3 - - - +
767B ILE* 2.8 37.1 + - + +
945B ASN* 5.6 0.2 - - - +
947B HIS* 3.6 19.2 + - + +
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Residues in contact with PHE 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A PRO* 3.6 23.6 - - + -
501A ASN* 4.3 1.8 - - - -
502A GLU* 3.0 42.2 - - + -
503A CYS* 3.9 22.2 - - - -
553A ALA* 3.4 24.2 - - + +
554A THR* 3.7 9.5 + - - +
555A GLN 3.1 0.4 + - - -
556A ASP* 1.3 75.7 - - - +
558A ILE* 1.3 61.9 + - - +
561A SER* 3.0 24.9 + - - -
697A MET* 4.3 5.8 - - + +
698A ALA* 3.7 34.3 - - + -
701A CYS* 3.4 24.6 - - + +
702A ALA* 4.3 8.1 - - + -
764B GLY* 5.0 0.4 - - - -
767B ILE* 4.4 8.7 - - + -
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Residues in contact with ILE 558 (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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553A ALA* 3.2 37.9 - - + +
554A THR* 3.9 8.7 - - + +
555A GLN* 2.9 15.1 + - - +
557A PHE* 1.3 71.9 - - - +
559A THR* 1.3 68.7 + - - +
561A SER* 2.9 17.0 + - - -
562A TYR* 3.0 9.4 + - - +
665A ASP* 3.7 18.6 - - - +
666A LYS* 3.4 49.6 - - + +
669A LEU* 4.1 8.1 - - + +
670A GLY* 4.5 0.9 - - - -
798A GLY 4.1 18.6 - - - +
799A SER* 4.6 1.8 - - - +
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Residues in contact with THR 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A GLN 3.1 3.2 + - - +
556A ASP* 3.0 18.9 + - - +
558A ILE* 1.3 78.8 - - - +
560A GLY* 1.3 68.0 - - - +
562A TYR* 2.9 19.3 + - - +
563A LEU* 3.1 18.9 + - + +
705A LEU* 4.5 6.3 - - + -
710A PHE* 5.0 6.1 - - + -
793A ILE* 3.7 25.8 + - - +
794A MET* 4.7 2.8 - - - +
797A CYS* 5.3 2.0 - - - -
799A SER* 4.3 10.3 - - - -
947B HIS* 3.3 38.2 - - + +
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Residues in contact with GLY 560 (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 ASP 2.6 19.7 + - - -
559A THR* 1.3 73.2 - - - +
561A SER* 1.3 62.5 + - - +
563A LEU* 2.9 16.6 + - - +
564A ILE* 3.2 16.2 + - - +
701A CYS* 3.6 11.0 - - - -
704A PHE* 4.5 3.7 - - - -
705A LEU* 3.5 26.2 - - - -
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Residues in contact with SER 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A PHE 3.0 10.0 + - - -
558A ILE 2.9 10.4 + - - -
560A GLY* 1.3 72.8 - - - +
562A TYR* 1.3 51.2 + - - +
564A ILE* 2.9 11.9 + - - +
565A SER* 2.5 37.9 + - - -
610A PHE* 4.0 5.9 - - - -
664A MET* 4.2 18.1 - - - +
665A ASP 5.8 0.2 - - - -
669A LEU* 4.4 11.0 - - - -
697A MET* 2.9 34.1 - - - +
700A LEU* 5.9 2.1 - - - +
701A CYS* 4.2 4.8 - - - +
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Residues in contact with TYR 562 (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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558A ILE 3.0 7.5 + - - +
559A THR* 2.9 13.9 + - - +
561A SER* 1.3 75.5 - - - +
563A LEU* 1.3 67.0 + - + +
565A SER* 2.8 21.9 + - - -
566A HIS* 2.9 46.4 + + - +
663A VAL* 3.4 41.1 - - + +
664A MET 4.8 0.2 - - - -
665A ASP* 4.0 18.1 - - + +
792A LEU* 5.7 2.1 - - - +
793A ILE* 3.8 31.7 - - + +
796A THR* 5.3 7.9 - - + +
797A CYS* 3.3 35.7 - - - -
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Residues in contact with LEU 563 (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 THR* 3.1 14.1 + - - +
560A GLY 2.9 8.2 + - - +
562A TYR* 1.3 82.5 - - + +
564A ILE* 1.3 60.0 + - - +
566A HIS* 3.7 14.8 - - + +
569A SER* 4.1 11.8 - - - -
571A TYR* 4.1 2.0 + - - -
704A PHE* 4.7 4.7 - - + -
705A LEU* 4.6 13.7 - - + -
708A ARG* 3.4 43.4 + - - +
709A GLY 5.0 0.2 - - - +
710A PHE* 4.0 28.3 - - + -
788A TRP* 4.1 20.9 - - + -
793A ILE* 3.8 25.6 - - + -
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Residues in contact with ILE 564 (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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560A GLY 3.2 6.6 + - - +
561A SER* 2.9 10.4 + - - +
563A LEU* 1.3 72.5 - - - +
565A SER* 1.3 59.3 + - - +
566A HIS 3.1 7.2 + - - +
569A SER* 4.9 0.7 - - - -
571A TYR* 3.4 22.1 + - + +
579A LEU* 5.0 4.5 - - + -
606A GLY* 3.1 26.1 - - - +
609A VAL* 3.6 29.8 - - + -
610A PHE* 5.0 8.7 - - + +
700A LEU* 3.9 31.6 - - + -
701A CYS* 5.7 1.3 - - - -
704A PHE* 3.4 44.6 - - + -
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Residues in contact with SER 565 (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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561A SER 2.5 19.6 + - - -
562A TYR* 2.8 12.9 + - - -
564A ILE* 1.3 72.1 - - - +
566A HIS* 1.3 57.4 + - - +
606A GLY 4.8 4.3 - - - -
607A LYS* 3.1 30.7 - - - +
610A PHE* 5.7 0.9 - - - -
659A ILE* 5.5 0.2 - - - +
662A GLY 3.6 2.4 + - - -
663A VAL* 3.1 9.4 - - - +
664A MET* 3.0 52.7 + - - +
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Residues in contact with HIS 566 (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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562A TYR* 2.9 44.2 + + + +
563A LEU* 3.7 14.8 - - + +
564A ILE 3.1 4.5 - - - +
565A SER* 1.3 77.2 - - - +
567A LYS* 1.3 69.5 + - - +
568A ASP* 3.0 35.9 + - + +
569A SER* 3.0 21.5 + - - +
606A GLY* 5.1 3.6 + - - -
607A LYS* 4.7 1.3 + - - +
663A VAL* 3.7 6.8 - - + +
787A ASN* 5.8 0.6 + - - -
788A TRP* 4.2 27.7 + + - -
793A ILE* 6.2 3.1 - - + +
19H ARG 5.1 3.2 + - - -
20H TYR* 3.5 30.5 - + - -
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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