Contacts of the helix formed by residues 566 - 576 (chain A) in PDB entry 6C90
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 THR 566 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ARG* 4.4 4.2 + - - -
264A VAL* 4.6 6.3 - - + -
268A GLU* 5.5 0.3 + - - -
564A HIS* 3.7 26.6 + - + +
565A LEU* 1.3 79.3 - - - +
567A TYR* 1.3 64.2 + - - +
568A ASN* 3.8 4.0 + - - +
569A MET* 3.1 30.4 + - + +
570A VAL* 3.0 26.5 + - - +
854A ARG* 3.8 8.7 - - - +
885A GLU* 3.9 8.9 + - - -
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Residues in contact with TYR 567 (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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566A THR* 1.3 71.5 - - - +
568A ASN* 1.3 58.3 + - - +
570A VAL* 3.2 4.2 + - + +
571A LEU* 2.9 37.8 + - + +
854A ARG* 3.5 55.1 - - + +
857A VAL* 3.7 15.3 - - + +
858A LEU* 3.7 27.1 - - + -
884A ASP* 5.6 0.9 - - - -
885A GLU* 3.2 22.1 + - + +
886A LEU* 3.7 42.1 - - + +
946A SER* 4.5 3.1 + - - -
951A LEU* 3.3 27.9 - - - +
1104A MLI 4.4 15.6 + - - -
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Residues in contact with ASN 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 2.9 27.7 + - - +
566A THR* 4.2 4.5 - - - +
567A TYR* 1.3 73.2 - - - +
569A MET* 1.3 61.4 + - - +
571A LEU* 4.1 4.3 - - - +
572A ASN* 2.9 39.6 + - - -
877A ALA 3.3 7.9 + - - -
878A CYS* 3.0 24.6 + - - +
880A ILE 2.6 32.5 + - - +
881A SER* 4.0 7.8 - - - +
885A GLU* 2.7 25.2 + - + +
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Residues in contact with MET 569 (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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233A ARG* 3.9 7.2 - - - +
237A TYR* 3.8 10.5 + - - +
264A VAL* 3.5 21.8 - - + -
268A GLU* 3.5 22.4 - - + +
563A PHE* 3.6 30.1 - - + -
564A HIS 3.4 21.5 - - - +
565A LEU* 3.8 22.7 - - - -
566A THR* 3.1 21.0 + - - +
568A ASN* 1.3 77.0 + - - +
570A VAL* 1.3 64.4 + - + +
572A ASN* 3.4 1.0 + - - +
573A LEU* 3.1 41.1 + - + +
581A PRO* 6.2 0.4 - - + +
584A MET* 4.0 6.5 - - - +
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Residues in contact with VAL 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A LEU* 4.2 20.4 - - + -
566A THR 3.0 23.0 + - - +
567A TYR* 3.2 5.4 + - - +
569A MET* 1.3 75.1 - - + +
571A LEU* 1.3 57.6 + - - +
573A LEU 3.3 1.0 + - - -
574A LEU* 2.9 41.2 + - + +
581A PRO* 3.6 24.3 - - + +
851A LEU* 4.0 25.8 - - + -
854A ARG* 5.1 8.7 - - + +
855A LYS* 4.2 6.7 - - + +
858A LEU* 4.0 22.4 - - + -
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Residues in contact with LEU 571 (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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567A TYR* 2.9 25.3 + - + +
568A ASN* 4.1 1.8 - - - +
570A VAL* 1.3 76.2 - - - +
572A ASN* 1.3 57.4 + - - +
574A LEU* 3.3 12.6 + - + +
575A ARG* 2.8 29.6 + - - +
858A LEU* 3.8 41.1 - - + -
863A PHE* 4.1 26.7 - - + +
864A ALA* 4.7 0.9 - - + -
870A ILE* 3.6 15.2 - - + +
874A GLY* 3.9 4.5 - - - +
877A ALA* 3.5 32.1 - - + -
878A CYS* 3.8 15.0 - - - -
886A LEU* 5.6 0.7 - - + -
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Residues in contact with ASN 572 (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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233A ARG* 4.7 1.0 - - - +
237A TYR* 3.6 32.6 - - + +
568A ASN* 2.9 40.9 + - - +
569A MET 4.0 0.2 - - - +
571A LEU* 1.3 76.6 - - - +
573A LEU* 1.3 59.6 + - - +
575A ARG* 2.7 34.6 + - - +
576A VAL* 3.0 34.9 + - - +
878A CYS* 3.2 32.2 + - - +
670B ILE* 3.6 4.8 - - - +
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Residues in contact with LEU 573 (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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237A TYR* 4.0 21.3 - - + +
272A LEU* 4.6 2.7 - - + -
569A MET* 3.1 32.0 + - + +
570A VAL 3.8 2.2 - - - +
572A ASN* 1.3 75.7 - - - +
574A LEU* 1.3 52.9 + - - +
576A VAL 3.1 4.7 - - - +
579A ILE* 3.0 43.6 - - + +
580A ASN 3.9 2.5 - - - +
581A PRO* 3.7 31.4 - - + -
584A MET* 3.7 37.2 - - + -
1103A MG 2.3 27.5 - - - -
666B PHE* 5.0 2.9 - - + -
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Residues in contact with LEU 574 (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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570A VAL* 2.9 31.5 + - + +
571A LEU* 3.5 17.3 - - + +
573A LEU* 1.3 76.1 - - - +
575A ARG* 1.3 60.5 + - - +
577A GLU* 5.4 0.2 - - - -
580A ASN* 5.5 1.8 - - + -
581A PRO* 3.7 22.4 - - + -
855A LYS* 4.6 11.9 - - + +
858A LEU* 4.7 3.4 - - + -
864A ALA* 4.4 20.0 - - + -
868A ASP* 3.6 44.1 - - + +
869A VAL* 6.0 0.3 - - - -
870A ILE* 4.9 8.8 + - + +
1103A MG 2.6 17.1 - - - -
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Residues in contact with ARG 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TYR* 2.9 25.5 + - - +
571A LEU 2.8 19.3 + - - +
572A ASN* 2.7 34.2 + - - +
573A LEU 3.3 0.2 - - - -
574A LEU* 1.3 76.2 - - - +
576A VAL* 1.3 81.5 + - - +
577A GLU* 3.4 4.3 + - - +
870A ILE* 3.9 21.6 - - + +
875A ARG* 3.7 35.7 + - - +
878A CYS* 4.1 9.7 - - - -
1107A MLI 5.4 4.0 - - - +
665B LYS 4.4 0.2 + - - -
666B PHE 2.9 21.6 + - - -
668B THR 3.3 18.6 + - - +
669B GLY 3.7 8.7 - - - -
670B ILE* 3.6 17.6 - - - +
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Residues in contact with VAL 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TYR* 5.5 0.4 - - + -
572A ASN 3.0 17.2 + - - +
573A LEU* 3.1 3.7 + - - +
575A ARG* 1.3 97.7 - - - +
577A GLU* 1.3 69.1 + - - +
579A ILE* 3.2 23.0 - - + +
1103A MG 2.2 30.3 - - - -
661B PRO* 3.8 13.0 - - + -
665B LYS* 3.9 19.3 - - + +
666B PHE* 3.5 33.7 - - + -
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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