Contacts of the helix formed by residues 1063 - 1071 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037D TRP* 3.4 19.7 - - + -
1062D SER* 1.3 78.9 - - - +
1064D TYR* 1.3 53.0 + - - +
1065D ALA 3.3 3.1 - - - -
1066D MET* 3.1 22.4 + - + +
1067D VAL* 2.6 36.5 + - + +
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Residues in contact with TYR1064 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D PHE* 5.5 4.0 - - + -
1037D TRP* 3.6 13.6 - - + -
1061D GLN* 3.4 35.8 + - + +
1062D SER 3.5 2.2 - - - -
1063D VAL* 1.3 76.8 - - - +
1065D ALA* 1.3 57.9 + - - +
1067D VAL 4.3 0.2 - - - +
1068D PHE* 2.9 47.0 + - + +
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Residues in contact with ALA1065 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063D VAL 3.3 0.4 - - - -
1064D TYR* 1.3 77.6 - - - +
1066D MET* 1.3 58.4 + - + +
1068D PHE* 5.5 0.4 - - - -
1069D THR* 2.6 41.6 + - - +
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Residues in contact with MET1066 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063D VAL* 3.1 25.4 + - + +
1065D ALA* 1.3 80.7 - - + +
1067D VAL* 1.3 54.6 + - - +
1069D THR* 4.9 0.4 - - - -
1070D LEU* 2.7 42.6 + - + +
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Residues in contact with VAL1067 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037D TRP* 3.5 48.0 - - + +
1063D VAL* 2.6 19.8 + - + +
1064D TYR 4.0 1.8 - - - +
1066D MET* 1.3 74.6 - - - +
1068D PHE* 1.3 59.5 + - - +
1071D LEU* 2.9 36.2 + - - +
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Residues in contact with PHE1068 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558D THR* 4.4 11.7 - - - -
561D GLY* 4.0 12.3 - - - -
562D HIS* 3.6 43.5 - - + -
565D PHE* 4.4 24.0 - + - -
1037D TRP* 3.3 37.2 - + - -
1064D TYR* 2.9 37.3 + - + +
1067D VAL* 1.3 76.1 - - - +
1069D THR* 1.3 60.0 + - - +
1071D LEU* 4.1 8.5 + - + +
1072D CYS* 4.4 11.1 + - - +
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Residues in contact with THR1069 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065D ALA* 2.6 25.5 + - - +
1066D MET* 4.9 0.4 - - - -
1068D PHE* 1.3 79.2 - - - +
1070D LEU* 1.3 62.1 + - - +
1071D LEU 3.3 0.6 + - - -
1072D CYS* 3.6 15.1 + - - +
1073D SER* 4.6 1.4 + - - -
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Residues in contact with LEU1070 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030D ILE* 5.2 2.8 - - - +
1066D MET* 2.7 30.8 + - + +
1067D VAL 4.3 0.2 - - - +
1069D THR* 1.3 76.3 - - - +
1071D LEU* 1.3 58.3 + - - +
1072D CYS 3.2 5.0 + - - -
1073D SER* 3.7 18.8 + - - -
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Residues in contact with LEU1071 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558D THR* 5.0 12.0 - - - -
1030D ILE* 3.4 42.6 - - + +
1033D TRP* 5.5 9.9 - - + -
1034D LEU* 5.6 7.4 - - + +
1067D VAL 2.9 20.4 + - - +
1068D PHE* 4.1 7.2 + - + +
1069D THR 3.3 0.6 - - - -
1070D LEU* 1.3 76.8 - - - +
1072D CYS* 1.3 57.7 + - - +
1073D SER 3.6 1.1 - - - -
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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