Contacts of the helix formed by residues 747 - 754 (chain B) in PDB entry 6V3O
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 PRO 747 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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746B THR* 1.3 85.8 - - - +
748B GLU* 1.3 57.4 + - - +
749B THR 3.3 2.5 - - - -
750B GLU* 3.1 14.4 + - + +
751B TYR* 2.8 29.4 + - - +
779B PHE* 5.4 2.5 - - + -
780B SER* 3.9 13.0 - - - +
783B GLN* 4.1 15.7 - - + -
784B THR* 3.9 9.6 - - + -
844B TYR* 4.9 0.4 - - + -
905B GLN* 3.8 25.6 - - + +
909B LEU* 4.0 24.5 - - + -
913B ARG* 4.1 1.3 - - - +
955B LEU* 5.4 1.6 - - + -
959B MET* 5.0 11.9 - - + -
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Residues in contact with GLU 748 (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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742B PHE* 3.8 21.1 - - + +
743B ARG* 3.6 26.6 + - + +
746B THR* 3.1 16.9 + - - +
747B PRO* 1.3 77.3 - - - +
749B THR* 1.3 66.9 + - - +
751B TYR* 3.3 7.7 + - - +
752B GLY* 3.3 14.9 + - - -
761B ALA* 3.8 23.6 - - - +
762B LYS* 5.8 0.2 - - - +
772B LEU* 3.8 12.6 - - - +
776B PRO* 3.4 21.5 - - - +
780B SER* 2.6 37.0 + - - +
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Residues in contact with THR 749 (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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743B ARG* 3.5 43.4 + - - +
746B THR 4.8 1.2 + - - -
747B PRO 3.3 0.4 - - - -
748B GLU* 1.3 82.3 - - - +
750B GLU* 1.3 77.2 + - + +
752B GLY* 3.3 1.7 + - - -
753B ARG* 3.1 53.3 + - + +
913B ARG* 5.0 0.4 - - - -
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Residues in contact with GLU 750 (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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747B PRO* 3.1 10.7 + - + +
749B THR* 1.3 82.3 - - + +
751B TYR* 1.3 66.8 + - - +
753B ARG* 4.4 5.8 - - - +
754B MET* 3.0 35.2 + - + +
909B LEU* 3.5 17.3 - - + +
912B ILE* 4.5 11.3 - - + +
913B ARG* 2.8 53.3 + - - +
947B TYR* 4.3 13.7 - - - +
955B LEU* 3.6 24.2 - - + -
959B MET* 5.3 0.7 - - + -
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Residues in contact with TYR 751 (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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178B PRO* 4.2 8.2 + - - +
747B PRO 2.8 13.4 + - - +
748B GLU* 3.5 25.1 - - - +
750B GLU* 1.3 77.6 - - - +
752B GLY* 1.3 66.8 - - - +
754B MET 3.5 11.3 + - - +
756B ILE* 3.6 43.6 - - + +
757B GLY* 3.4 27.5 + - - -
759B ARG 6.0 1.6 - - - -
761B ALA* 5.1 4.7 - - + -
775B ILE* 4.5 14.6 - - - +
776B PRO* 4.4 25.4 - - + -
779B PHE* 3.5 48.5 - + + -
959B MET* 4.1 14.2 - - - -
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Residues in contact with GLY 752 (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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748B GLU 3.3 9.5 + - - -
749B THR 3.7 2.7 - - - -
750B GLU 3.2 0.2 - - - -
751B TYR* 1.3 88.1 - - - +
753B ARG* 1.3 62.6 + - - +
754B MET 3.0 8.1 + - - +
756B ILE 5.1 0.7 - - - +
759B ARG 6.0 1.6 - - - -
761B ALA* 4.8 15.3 - - - -
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Residues in contact with ARG 753 (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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749B THR* 3.1 39.2 + - + +
750B GLU* 3.5 3.0 + - - +
752B GLY* 1.3 74.2 - - - +
754B MET* 1.3 59.0 + - - +
946B GLU* 5.8 0.3 - - - +
947B TYR* 3.6 32.8 + - + +
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Residues in contact with MET 754 (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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750B GLU* 3.0 23.1 + - + +
751B TYR* 3.5 6.3 - - - +
752B GLY 3.0 11.9 + - - +
753B ARG* 1.3 81.6 - - - +
755B ASN* 1.3 62.2 + - - +
756B ILE* 3.1 13.4 + - + +
912B ILE* 4.0 11.9 - - + -
947B TYR* 4.0 25.4 - - + -
952B GLU* 3.7 55.2 - - + +
955B LEU* 3.6 34.5 - - + -
956B ILE* 4.2 11.2 - - + -
959B MET* 4.4 4.3 - - + -
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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