Contacts of the helix formed by residues 848 - 855 (chain A) in PDB entry 6ZGI
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 848 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A LYS* 4.1 9.6 + - - +
844A ILE* 3.1 24.6 + - + +
846A ALA 4.3 0.7 + - - -
847A ARG* 1.3 85.8 + - - +
849A LEU* 1.3 69.1 + - - +
850A ILE* 3.5 17.8 + - - +
851A CYS* 3.5 29.7 + - + +
852A ALA* 3.2 20.3 + - - +
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Residues in contact with LEU 849 (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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846A ALA 5.8 1.1 - - - +
847A ARG 3.6 15.0 - - - +
848A ASP* 1.3 74.9 + - - +
850A ILE* 1.3 65.0 + - + +
852A ALA* 3.4 8.9 + - + +
853A GLN* 3.0 35.6 + - - +
960A ASN* 3.6 36.2 - - - +
964A LYS* 5.9 3.6 - - - +
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Residues in contact with ILE 850 (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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829A ALA* 5.0 13.7 - - + +
830A ASP* 4.2 31.4 - - + +
835A LYS* 3.7 23.8 - - + -
848A ASP* 3.3 15.1 + - - +
849A LEU* 1.3 80.9 - - + +
851A CYS* 1.3 57.0 + - - +
853A GLN* 3.2 25.2 + - - +
854A LYS* 2.9 45.5 + - + +
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Residues in contact with CYS 851 (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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835A LYS* 3.4 25.4 - - - -
840A CYS* 2.0 52.5 - - + -
845A ALA* 4.5 7.9 - - - -
848A ASP* 3.5 17.2 + - + +
849A LEU 3.4 0.2 - - - -
850A ILE* 1.3 76.6 - - - +
852A ALA* 1.3 61.6 + - - +
854A LYS* 3.9 5.3 - - - +
855A PHE* 2.9 43.2 + - + -
592C PHE* 5.1 2.5 - - - -
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Residues in contact with ALA 852 (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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846A ALA* 4.3 22.1 - - - +
848A ASP 3.2 12.9 + - - +
849A LEU* 3.6 13.5 - - + +
850A ILE 3.3 0.2 - - - -
851A CYS* 1.3 80.7 - - - +
853A GLN* 1.3 59.9 + - - +
855A PHE* 3.8 7.3 + - - +
856A ASN* 2.8 26.6 - - - +
963A VAL* 4.4 16.4 - - + +
569C ILE* 5.8 5.4 - - + -
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Residues in contact with GLN 853 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849A LEU* 3.0 20.7 + - - +
850A ILE* 3.4 29.9 - - - +
852A ALA* 1.3 77.7 - - - +
854A LYS* 1.3 57.1 + - + +
856A ASN* 3.1 17.2 + - - +
857A GLY 3.6 0.2 + - - -
858A LEU* 3.3 35.6 + - + +
860A VAL* 5.4 2.9 - - - +
956A ALA* 4.5 3.4 + - - +
959A LEU* 3.3 40.0 - - + +
960A ASN* 3.3 25.8 + - - +
963A VAL* 4.0 22.9 - - + -
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Residues in contact with LYS 854 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740A MET* 5.4 0.5 - - - +
835A LYS* 4.5 14.1 - - + -
850A ILE* 2.9 36.3 + - + +
851A CYS* 3.2 3.1 + - - +
853A GLN* 1.3 72.1 - - + +
855A PHE* 1.3 61.0 + - - +
856A ASN 3.1 6.3 + - - -
857A GLY* 3.6 8.9 + - - -
858A LEU 4.0 14.1 - - - +
859A THR* 3.9 27.1 - - + +
860A VAL 5.3 1.4 - - - +
317C ASN* 4.5 9.2 + - - -
591C SER 5.2 0.5 - - - +
592C PHE* 3.6 46.3 - - + -
593C GLY* 5.2 2.7 + - - +
614C ASP* 3.5 32.4 + - - -
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Residues in contact with PHE 855 (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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740A MET* 4.0 15.4 - - - +
837A TYR* 4.0 10.5 - + - -
840A CYS* 4.0 22.7 - - - -
845A ALA* 3.6 28.5 - - + -
846A ALA 5.5 0.2 - - - -
851A CYS* 2.9 27.5 + - + +
852A ALA* 4.3 6.7 - - - +
853A GLN 3.3 0.2 - - - -
854A LYS* 1.3 76.0 - - - +
856A ASN* 1.3 66.4 + - - +
857A GLY 3.6 0.4 - - - -
588C THR* 3.9 18.6 - - + -
589C PRO* 3.9 47.8 - - + +
591C SER 4.3 9.1 - - - +
592C PHE* 3.7 26.7 - + + -
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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