Contacts of the helix formed by residues 1063 - 1071 (chain B) in PDB entry 5TWV
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 VAL1063 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037B TRP* 3.4 20.1 - - + -
1062B SER* 1.3 77.9 - - - +
1064B TYR* 1.3 53.5 + - - +
1065B ALA 3.3 2.2 - - - -
1066B MET* 3.1 23.0 + - + +
1067B VAL* 2.6 35.8 + - + +
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Residues in contact with TYR1064 (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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565B PHE* 5.5 3.8 - - + -
1037B TRP* 3.6 13.8 - - + -
1061B GLN* 3.4 36.7 + - + +
1062B SER 3.5 2.4 - - - -
1063B VAL* 1.3 77.7 - - - +
1065B ALA* 1.3 58.4 + - - +
1067B VAL* 4.3 0.7 - - - +
1068B PHE* 2.9 48.1 + - + +
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Residues in contact with ALA1065 (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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1063B VAL 3.3 0.4 - - - -
1064B TYR* 1.3 77.2 - - - +
1066B MET* 1.3 59.1 + - + +
1068B PHE* 5.5 0.7 - - - -
1069B THR* 2.6 41.0 + - - +
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Residues in contact with MET1066 (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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1063B VAL* 3.1 24.7 + - + +
1065B ALA* 1.3 81.0 - - + +
1067B VAL* 1.3 55.5 + - - +
1069B THR* 4.9 0.2 - - - -
1070B LEU* 2.7 41.7 + - + +
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Residues in contact with VAL1067 (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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1037B TRP* 3.5 47.6 - - + +
1063B VAL* 2.6 19.9 + - + +
1064B TYR 4.0 1.6 - - - +
1065B ALA 3.3 0.2 - - - -
1066B MET* 1.3 73.8 - - - +
1068B PHE* 1.3 61.2 + - + +
1070B LEU* 4.3 0.4 - - - +
1071B LEU* 2.9 35.4 + - - +
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Residues in contact with PHE1068 (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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558B THR* 4.4 11.5 - - - -
561B GLY* 4.0 11.9 - - - -
562B HIS* 3.6 43.7 - - + -
565B PHE* 4.4 24.7 - + + -
1037B TRP* 3.3 36.6 - + - -
1064B TYR* 2.9 36.2 + - + +
1065B ALA* 5.5 0.4 - - - -
1067B VAL* 1.3 76.2 - - - +
1069B THR* 1.3 59.7 + - - +
1071B LEU* 4.1 8.3 + - + +
1072B CYS* 4.4 11.3 + - - +
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Residues in contact with THR1069 (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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1065B ALA* 2.6 25.7 + - - -
1066B MET* 4.9 0.2 - - - -
1068B PHE* 1.3 77.9 - - - +
1070B LEU* 1.3 61.1 + - - +
1071B LEU 3.3 1.0 + - - -
1072B CYS* 3.6 15.3 + - - +
1073B SER* 4.6 1.4 + - - -
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Residues in contact with LEU1070 (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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1030B ILE* 5.2 2.6 - - - +
1066B MET* 2.7 31.2 + - + +
1067B VAL 4.3 0.2 - - - +
1069B THR* 1.3 74.6 - - - +
1071B LEU* 1.3 59.1 + - - +
1072B CYS 3.2 4.2 + - - -
1073B SER* 3.7 19.2 + - - -
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Residues in contact with LEU1071 (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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558B THR* 5.0 11.5 - - - -
1030B ILE* 3.4 41.5 - - + +
1033B TRP* 5.5 10.1 - - + -
1034B LEU* 5.6 7.9 - - + +
1067B VAL 2.9 20.4 + - - +
1068B PHE* 4.5 7.6 - - + +
1069B THR 3.3 0.8 - - - -
1070B LEU* 1.3 76.5 - - - +
1072B CYS* 1.3 57.0 + - - +
1073B SER 3.6 1.3 - - - -
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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