Contacts of the helix formed by residues 132 - 137 (chain D) in PDB entry 3DVA
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 LEU 132 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ARG* 4.6 4.5 - - - +
139B GLN* 4.8 3.8 - - - +
83D PHE* 3.6 47.8 - - + +
84D GLY* 4.0 13.7 - - - +
86D VAL* 4.0 7.4 - - + -
87D TYR* 3.3 38.4 - - + +
118D PHE* 5.6 0.4 - - - -
127D LEU* 5.4 0.2 - - + -
130D ASP* 3.7 21.2 + - + +
131D SER* 1.3 81.3 - - - +
133D GLU* 1.3 63.9 + - - +
134D GLY 3.1 3.1 - - - +
135D LEU* 3.1 35.4 + - + +
136D VAL 4.0 1.2 + - - -
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Residues in contact with GLU 133 (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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83D PHE* 4.2 1.6 - - - -
118D PHE* 4.3 9.1 - - - -
131D SER* 3.1 36.0 + - - +
132D LEU* 1.3 79.4 + - - +
134D GLY* 1.3 60.8 + - - +
135D LEU 3.1 0.8 + - - -
136D VAL* 3.4 9.0 - - - +
137D ALA* 3.1 29.1 + - - +
144D VAL* 4.5 6.4 - - + +
146D ILE* 3.8 15.5 - - + -
170D LEU* 3.5 29.5 - - + +
209D TYR* 2.7 36.1 + - + +
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Residues in contact with GLY 134 (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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138B GLN* 2.9 32.3 + - - -
131D SER 5.2 0.4 + - - -
132D LEU* 3.1 2.0 - - - +
133D GLU* 1.3 86.7 - - - +
135D LEU* 1.3 60.2 + - - +
137D ALA* 4.0 8.8 - - - +
138D GLN* 3.4 13.7 + - - +
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Residues in contact with LEU 135 (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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90B MET* 4.3 11.0 - - + -
94B CYS* 6.1 1.1 - - - -
135B LEU* 3.5 55.5 - - + +
138B GLN* 3.6 13.7 + - + +
139B GLN* 6.4 0.4 - - + -
86D VAL* 4.9 2.5 - - + -
87D TYR* 4.0 25.8 - - + +
90D MET* 4.5 17.3 - - + -
94D CYS* 5.5 0.9 - - - -
132D LEU* 3.1 36.8 + - + +
133D GLU 3.1 1.2 - - - -
134D GLY* 1.3 76.9 - - - +
136D VAL* 1.3 61.8 + - + +
138D GLN* 3.0 25.5 + - - +
139D GLN* 4.0 2.9 + - - +
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Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 4.0 26.9 - - + -
86D VAL* 5.1 1.3 - - + -
90D MET* 4.9 10.5 - - - -
93D ILE* 4.3 5.2 - - + -
94D CYS* 4.2 13.9 - - - -
132D LEU 4.2 0.2 - - - +
133D GLU* 3.4 19.7 - - - +
135D LEU* 1.3 72.0 - - + +
137D ALA* 1.3 60.0 + - - +
138D GLN 3.0 6.1 + - - -
139D GLN* 3.3 15.5 + - - +
142D LEU* 3.8 22.5 - - + +
144D VAL* 3.7 19.1 - - + +
168D ILE* 3.3 36.1 - - + -
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Residues in contact with ALA 137 (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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265B GLN* 2.9 25.8 + - - +
133D GLU 3.1 18.5 + - - +
134D GLY* 4.1 11.0 - - - +
135D LEU 3.1 0.4 - - - -
136D VAL* 1.3 77.5 - - - +
138D GLN* 1.3 59.0 + - + +
139D GLN 3.4 0.2 - - - -
144D VAL* 4.2 13.2 - - + -
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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