Contacts of the helix formed by residues 885 - 890 (chain A) in PDB entry 6VSB
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 GLY 885 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880A GLY 3.6 6.3 + - - -
881A THR* 3.7 6.6 + - - +
884A SER* 1.3 78.1 - - - +
886A TRP* 1.3 64.8 + - - -
887A THR 3.0 1.2 + - - -
888A PHE* 2.8 29.2 - - - -
901A GLN* 3.2 31.3 + - - +
905A ARG* 3.3 8.1 - - - -
1033A VAL 5.5 0.2 - - - -
1034A LEU 5.3 0.7 - - - -
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Residues in contact with TRP 886 (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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884A SER 4.7 2.2 - - - -
885A GLY* 1.3 73.9 - - - -
887A THR* 1.3 78.5 + - + +
889A GLY* 3.3 7.4 + - - -
890A ALA* 4.2 4.2 + - - +
896A ILE* 5.2 3.1 - - + -
901A GLN* 3.9 23.8 - - + -
904A TYR* 3.2 44.6 + + - -
905A ARG* 3.5 19.2 - - + +
1034A LEU 3.2 22.0 - - - +
1035A GLY* 3.6 24.7 - - - -
1036A GLN* 4.7 3.8 - - + +
1040C VAL* 5.2 7.2 - - + +
1047C TYR* 3.4 35.1 + + - -
1107C ARG* 3.7 30.5 - - + -
1108C ASN* 5.2 4.6 + - - -
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Residues in contact with THR 887 (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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884A SER* 2.6 32.0 + - - +
885A GLY 3.0 0.4 + - - -
886A TRP* 1.3 98.2 - - + +
888A PHE* 1.3 57.5 + - - -
889A GLY 2.6 13.9 + - - -
890A ALA* 2.8 21.4 + - - +
891A GLY 3.5 4.3 + - - -
892A ALA 4.4 3.8 - - - +
894A LEU* 3.9 36.9 + - + +
896A ILE* 6.2 1.6 - - + -
1047C TYR* 4.3 12.8 - - - +
1069C PRO* 6.1 0.3 - - - +
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Residues in contact with PHE 888 (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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785A VAL* 4.7 10.5 - - + -
786A LYS* 3.3 22.3 + - - -
789A TYR* 3.7 34.8 - + + +
877A LEU* 3.7 13.9 - - + -
880A GLY* 3.8 12.8 - - - -
881A THR* 3.1 35.4 - - - -
884A SER* 3.9 14.6 - - - -
885A GLY 2.8 27.8 + - - -
887A THR* 1.3 78.1 + - - +
889A GLY* 1.3 56.6 + - - +
890A ALA 3.3 1.8 - - - -
891A GLY 3.9 9.9 - - - -
893A ALA* 3.9 13.7 - - + +
1033A VAL* 4.8 3.8 - - + -
1034A LEU* 3.5 33.4 - - + -
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Residues in contact with GLY 889 (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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786A LYS* 5.3 0.9 - - - -
886A TRP 3.3 8.9 + - - -
887A THR 2.6 8.5 + - - -
888A PHE* 1.3 82.1 - - - +
890A ALA* 1.3 56.6 + - - +
1034A LEU* 4.5 25.7 + - - +
1040C VAL* 4.4 14.5 - - - +
1041C ASP* 4.5 10.2 - - - +
1045C LYS* 4.4 12.3 - - - +
1046C GLY 4.5 2.4 + - - -
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Residues in contact with ALA 890 (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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786A LYS* 5.3 1.1 - - - -
886A TRP 4.6 2.9 - - - +
887A THR 2.8 10.4 + - - +
888A PHE 3.3 0.4 - - - -
889A GLY* 1.3 79.0 - - - +
891A GLY* 1.3 57.2 + - - +
1040C VAL* 5.9 3.1 - - + -
1045C LYS* 3.5 24.1 - - - +
1046C GLY* 3.7 29.9 + - - +
1047C TYR* 3.8 29.4 - - + -
1068C VAL* 4.0 10.9 - - - +
1069C PRO* 5.0 3.1 - - + -
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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