Contacts of the helix formed by residues 198 - 207 (chain Z) in PDB entry 5V09
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 ALA 198 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196Z ASP* 2.9 13.6 + - - +
197Z GLN* 1.3 79.3 - - - +
199Z ARG* 1.3 61.7 + - + +
200Z LEU 3.3 2.2 + - - -
201Z GLY* 4.3 4.2 + - - -
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Residues in contact with ARG 199 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z GLU 4.0 6.7 + - - -
13Z ALA* 3.4 38.1 + - - +
14Z SER 3.8 10.7 + - - -
15Z GLU* 4.0 25.2 + - - +
196Z ASP* 3.3 29.5 + - + +
197Z GLN 3.2 1.0 - - - -
198Z ALA* 1.3 79.7 - - + +
200Z LEU* 1.3 55.8 + - - +
201Z GLY 3.0 6.7 - - - -
202Z MET* 2.9 62.8 + - + +
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Residues in contact with LEU 200 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Z ILE* 4.1 25.1 - - + -
13Z ALA* 4.2 13.5 - - + -
175Z LEU* 5.6 4.9 - - + -
195Z ILE* 4.8 4.5 - - + -
196Z ASP 3.8 5.6 + - - +
197Z GLN* 3.4 32.1 - - + +
198Z ALA 3.3 1.6 - - - -
199Z ARG* 1.3 77.3 - - - +
201Z GLY* 1.3 58.8 + - - +
202Z MET 3.1 1.1 - - - -
203Z CYS* 3.3 13.3 + - - +
206Z LEU* 3.4 31.5 - - + +
210Z PHE* 3.9 29.1 - - + +
215Z PHE* 4.0 32.3 - - + -
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Residues in contact with GLY 201 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198Z ALA 4.3 4.7 + - - -
199Z ARG* 3.0 2.6 - - - +
200Z LEU* 1.3 74.3 - - - +
202Z MET* 1.3 64.5 + - - +
203Z CYS* 3.1 8.9 + - - +
204Z ARG* 5.3 1.2 - - - -
207Z GLY 5.7 1.3 - - - -
210Z PHE* 4.4 19.9 - - - +
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Residues in contact with MET 202 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z GLU* 2.9 39.2 - - + +
199Z ARG* 2.9 51.9 + - + +
201Z GLY* 1.3 79.0 - - - +
203Z CYS* 1.3 58.8 + - - +
204Z ARG* 3.3 2.1 + - - +
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Residues in contact with CYS 203 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Z PHE 4.8 4.3 - - - +
10Z ILE* 3.6 35.2 - - - -
12Z GLU* 3.4 9.4 - - + +
13Z ALA* 3.5 33.9 - - - -
200Z LEU* 3.6 14.1 - - - +
201Z GLY* 3.1 5.8 - - - +
202Z MET* 1.3 75.5 - - - +
204Z ARG* 1.3 66.0 + - - +
205Z GLN* 3.2 2.0 - - + +
206Z LEU* 3.3 30.2 + - + +
207Z GLY 3.9 3.6 + - - +
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Residues in contact with ARG 204 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z GLU* 3.2 16.7 + - - +
201Z GLY 5.3 1.1 - - - -
202Z MET 3.3 3.7 + - - +
203Z CYS* 1.3 72.3 - - - +
205Z GLN* 1.3 62.9 + - + +
206Z LEU 3.3 0.5 + - - -
207Z GLY* 3.3 26.4 + - - -
243Z ARG* 5.9 0.2 - - - -
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Residues in contact with GLN 205 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A C 4.8 9.0 + - - -
8Z GLN 5.0 1.2 + - - -
9Z PHE* 3.1 58.9 + - + +
12Z GLU* 5.8 2.2 - - - -
203Z CYS* 3.2 1.8 - - + -
204Z ARG* 1.3 79.0 - - + +
206Z LEU* 1.3 61.8 + - - +
207Z GLY 3.4 0.3 + - - -
239Z CYS* 3.3 14.8 - - - -
243Z ARG* 4.1 7.8 - - - -
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Residues in contact with LEU 206 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Z PHE* 3.7 24.5 - - + -
10Z ILE* 3.9 17.7 - - + -
200Z LEU* 3.4 32.5 - - + +
201Z GLY* 6.2 0.2 - - - -
203Z CYS* 3.3 22.3 + - + +
204Z ARG 3.2 1.0 - - - -
205Z GLN* 1.3 79.5 - - - +
207Z GLY* 1.3 65.2 + - - +
209Z VAL* 3.2 50.2 + - - +
210Z PHE* 4.9 0.9 - - + -
215Z PHE* 4.1 9.6 - - + -
218Z MET* 3.9 24.5 - - + -
239Z CYS* 3.5 7.6 - - - -
243Z ARG* 3.8 2.5 - - - +
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Residues in contact with GLY 207 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201Z GLY* 5.7 1.4 - - - -
203Z CYS 3.9 3.7 + - - +
204Z ARG* 3.3 27.7 + - - -
205Z GLN 3.3 0.4 - - - -
206Z LEU* 1.3 78.5 - - - +
208Z ASP* 1.3 57.4 + - - -
209Z VAL 3.2 0.6 + - - -
210Z PHE* 3.2 20.4 - - - -
243Z ARG* 4.3 16.4 - - - -
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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