Contacts of the helix formed by residues 886 - 890 (chain B) 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 TRP 886 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047A TYR* 4.6 15.8 + + - -
1107A ARG* 6.1 2.5 - - - -
1108A ASN* 5.9 2.2 - - - +
884B SER 3.3 0.2 + - - -
885B GLY* 1.3 72.6 - - - -
887B THR* 1.3 78.6 + - + +
888B PHE* 3.3 6.2 + - - -
889B GLY* 3.6 9.4 + - - -
890B ALA* 4.2 7.4 + - - +
901B GLN* 6.2 1.6 - - + -
904B TYR* 4.5 31.4 - + + -
905B ARG* 4.0 34.7 - - + +
1033B VAL 5.9 0.2 - - - -
1034B LEU 3.7 25.3 - - - +
1035B GLY* 4.3 6.1 - - - -
1036B GLN* 3.8 36.3 - - + -
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Residues in contact with THR 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A TYR* 5.2 6.7 - - - +
1108A ASN* 6.2 1.8 - - - +
884B SER* 2.8 22.6 + - - +
885B GLY 3.5 0.2 - - - -
886B TRP* 1.3 93.6 - - + +
888B PHE* 1.3 63.3 + - - +
890B ALA* 3.1 17.7 + - - +
891B GLY 3.3 9.2 + - - -
892B ALA 3.6 7.3 - - - +
894B LEU* 3.1 49.6 + - + +
896B ILE* 6.4 0.7 - - + -
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Residues in contact with PHE 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A LYS* 6.1 0.5 - - - -
785B VAL* 4.3 26.8 - - + +
789B TYR* 4.0 27.2 + + + +
877B LEU* 4.1 13.7 - - + -
880B GLY* 3.8 10.8 - - - -
881B THR* 3.7 30.1 - - + -
884B SER* 3.5 20.0 - - - +
885B GLY 3.5 24.0 - - - -
886B TRP* 4.5 3.1 - - - -
887B THR* 1.3 81.4 + - - +
889B GLY* 1.3 63.1 + - - +
890B ALA 3.3 0.4 - - - -
891B GLY 3.4 18.6 + - - +
893B ALA* 3.8 19.5 - - + +
1034B LEU* 3.7 26.5 - - + -
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Residues in contact with GLY 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040A VAL* 5.2 5.6 - - - +
1041A ASP* 4.2 17.7 - - - +
1045A LYS* 4.5 13.1 - - - +
1046A GLY 5.1 0.3 + - - -
785B VAL* 5.6 2.0 - - - -
886B TRP 3.6 6.8 + - - -
887B THR 3.1 1.2 - - - -
888B PHE* 1.3 86.2 - - - +
890B ALA* 1.3 56.4 + - - +
1034B LEU* 4.2 30.3 - - - +
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Residues in contact with ALA 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A LYS* 4.8 8.3 - - - +
1046A GLY* 4.0 30.9 + - - +
1047A TYR* 4.2 32.1 - - + +
1068A VAL* 4.3 13.3 - - - +
1069A PRO* 4.7 6.5 - - + +
886B TRP 4.2 6.1 + - - +
887B THR 3.1 8.0 + - - +
889B GLY* 1.3 76.6 - - - +
891B GLY* 1.3 57.0 + - - +
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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