Contacts of the helix formed by residues 201 - 210 (chain A) in PDB entry 1PVS
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 ASP 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A PRO* 3.1 5.0 - - - +
200A GLY* 1.3 75.8 - - - +
202A VAL* 1.3 60.9 + - - +
203A GLU* 3.3 8.8 + - - +
204A GLN* 2.7 51.7 + - + +
205A ALA* 3.2 19.4 + - - +
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 4.1 21.8 - - + -
199A PRO* 3.9 21.1 - - + +
200A GLY 4.0 2.4 + - - +
201A ASP* 1.3 69.3 - - - +
203A GLU* 1.3 65.4 + - + +
205A ALA* 3.1 3.3 + - - +
206A MET* 2.8 49.6 + - + +
224A ALA* 4.2 8.1 - - + -
228A TRP* 4.1 15.5 - - + -
230A ALA* 4.4 11.9 - - + -
233A VAL* 4.8 4.7 - - + -
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Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ASP* 3.3 6.2 + - - +
202A VAL* 1.3 79.7 - - + +
204A GLN* 1.3 63.5 + - - +
206A MET* 3.2 30.6 + - - +
207A LYS* 3.0 23.8 + - - +
217A ARG* 4.0 12.4 + - - -
232A ASP 5.2 5.2 - - - +
233A VAL* 5.3 2.9 - - - +
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Residues in contact with GLN 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ASP* 2.7 37.8 + - + +
203A GLU* 1.3 72.8 - - - +
205A ALA* 1.3 62.7 + - - +
207A LYS* 2.9 49.5 + - - +
208A THR* 3.0 20.5 + - - -
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A PRO* 5.0 6.5 - - + -
199A PRO* 3.5 33.0 - - + -
201A ASP 3.2 4.3 + - - +
202A VAL 3.1 7.9 + - - +
204A GLN* 1.3 79.9 - - - +
206A MET* 1.3 56.8 + - - +
208A THR* 3.1 10.8 + - - -
209A LEU* 2.8 27.4 + - - +
228A TRP* 3.5 14.9 - - + -
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Residues in contact with MET 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A VAL* 2.8 30.8 + - + +
203A GLU* 3.2 42.6 - - - +
205A ALA* 1.3 71.8 - - - +
207A LYS* 1.3 63.9 + - - +
209A LEU* 2.9 20.7 + - + +
210A GLN* 2.9 20.6 + - - +
217A ARG* 4.0 22.7 - - - +
220A ALA* 3.9 13.6 - - + +
221A ASN* 3.7 21.3 - - - +
224A ALA* 3.8 22.0 - - + -
228A TRP* 4.1 11.0 - - + -
233A VAL* 4.9 8.1 - - + -
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Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLU 3.0 13.4 + - - +
204A GLN* 2.9 56.0 + - - +
206A MET* 1.3 77.4 - - - +
208A THR* 1.3 75.1 + - - +
210A GLN* 3.2 18.6 + - - +
211A THR* 3.3 16.4 + - + +
217A ARG* 5.2 1.7 - - - +
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Residues in contact with THR 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A THR 5.9 2.7 - - - +
204A GLN 3.0 12.0 + - - -
205A ALA* 3.4 10.5 - - - -
207A LYS* 1.3 92.0 + - - +
209A LEU* 1.3 61.6 + - - +
211A THR* 2.7 35.2 + - + +
212A PHE* 3.6 13.4 - - + -
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 5.4 0.9 - - + -
194A LEU* 4.5 15.5 - - + -
195A PRO* 5.8 2.9 - - + -
205A ALA 2.8 13.0 + - - +
206A MET* 3.1 15.0 - - - +
208A THR* 1.3 78.0 - - - +
210A GLN* 1.3 55.7 + - - +
212A PHE* 3.1 34.9 - - + +
215A ILE* 3.5 30.7 - - + +
220A ALA* 4.5 16.4 - - + +
223A PHE* 3.0 46.0 - - + -
228A TRP* 4.5 8.1 - - + -
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Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A MET 2.9 18.6 + - - +
207A LYS* 3.2 10.9 + - - +
209A LEU* 1.3 72.8 - - - +
211A THR* 1.3 58.7 + - - +
212A PHE 2.9 17.1 + - - +
215A ILE* 3.6 21.9 - - + +
216A GLY* 3.8 0.9 - - - +
217A ARG* 2.9 61.9 + - - +
220A ALA* 3.6 22.3 - - + +
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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