Contacts of the helix formed by residues 191 - 203 (chain A) in PDB entry 5A2E
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A THR 3.8 6.1 - - - +
190A TRP* 1.3 74.8 + - - +
192A LEU* 1.4 66.5 + - - +
193A GLU* 3.6 22.1 - - - +
194A ASP* 3.1 31.5 + - - +
195A ALA 3.1 17.0 + - - -
210A ALA* 3.4 15.4 - - - +
229A ASN* 5.7 2.1 - - - +
230A CYS 5.3 0.2 - - - +
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Residues in contact with LEU 192 (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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191A ASP* 1.4 74.1 - - - +
193A GLU* 1.3 65.7 + - - +
195A ALA* 3.8 2.1 - - - +
196A HIS* 2.9 31.0 + - - +
207A ALA* 3.7 24.4 - - + +
208A VAL 3.6 28.3 - - - +
209A GLN* 4.1 3.4 - - - +
210A ALA* 3.7 16.0 - - + +
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Residues in contact with GLU 193 (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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191A ASP* 3.2 19.9 - - - +
192A LEU* 1.3 84.6 - - - +
194A ASP* 1.3 60.7 + - - +
196A HIS* 3.8 9.8 + - - +
197A VAL* 3.7 19.2 + - - +
230A CYS* 3.6 24.0 - - - +
231A SER 3.8 16.7 - - - +
232A GLY* 4.1 8.4 - - - -
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Residues in contact with ASP 194 (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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189A THR 3.1 11.3 - - - +
190A TRP* 3.6 27.9 - - + -
191A ASP* 3.1 21.6 + - - +
193A GLU* 1.3 76.1 - - - +
195A ALA* 1.3 61.9 + - - +
197A VAL* 3.4 13.3 + - - +
198A VAL* 3.5 15.9 + - - +
228A VAL* 3.0 35.3 - - + +
229A ASN* 3.9 2.1 - - - +
230A CYS* 3.0 36.5 + - - +
237A LEU* 4.2 2.4 - - - +
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Residues in contact with ALA 195 (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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190A TRP* 4.4 9.1 - - + -
191A ASP 3.1 12.0 + - - +
192A LEU* 3.4 5.6 + - - +
194A ASP* 1.3 75.6 - - - +
196A HIS* 1.3 58.6 + - - +
198A VAL* 3.2 4.1 + - - +
199A CYS* 3.0 31.9 + - - -
207A ALA* 3.5 19.1 - - + -
210A ALA* 4.0 17.3 - - + +
257A VAL* 3.6 21.8 - - + -
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Residues in contact with HIS 196 (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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192A LEU 2.9 18.7 + - - +
193A GLU* 4.0 8.7 - - - +
194A ASP 3.4 0.2 - - - -
195A ALA* 1.3 74.5 - - - +
197A VAL* 1.3 61.7 + - - +
199A CYS* 3.6 1.5 + - - +
200A ARG* 3.3 54.1 + - + +
205A GLY 4.7 3.8 - - - -
206A TRP* 3.9 32.1 - - + +
207A ALA* 3.6 12.0 + - + +
232A GLY* 3.8 12.1 - - - +
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Residues in contact with VAL 197 (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 GLU 3.7 15.0 + - - +
194A ASP 3.4 8.7 + - - +
195A ALA 3.3 0.6 - - - -
196A HIS* 1.3 74.1 - - - +
198A VAL* 1.3 64.1 + - - +
200A ARG* 3.4 20.7 - - - +
201A GLN* 3.4 11.7 + - - +
230A CYS* 3.9 18.8 - - + -
232A GLY 3.8 17.9 - - - +
234A GLU* 3.6 25.1 - - + +
236A TYR* 3.4 36.6 - - - +
237A LEU* 3.6 9.9 - - + +
240A CYS* 4.3 1.3 - - - -
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Residues in contact with VAL 198 (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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161A LEU* 3.6 25.4 - - + -
163A LEU* 4.3 4.9 - - + -
174A VAL* 4.4 4.5 - - + -
190A TRP* 4.1 13.7 - - + -
194A ASP 3.5 13.7 + - - +
195A ALA* 3.2 10.2 + - - +
197A VAL* 1.3 78.1 - - - +
199A CYS* 1.3 61.2 + - - +
201A GLN* 3.4 12.8 - - - +
202A LEU* 3.2 36.6 - - + +
237A LEU* 4.0 24.5 - - + -
257A VAL* 4.0 24.7 - - + -
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Residues in contact with CYS 199 (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 ALA 3.0 20.1 + - - +
196A HIS 4.2 2.0 - - - +
197A VAL 3.5 0.2 - - - -
198A VAL* 1.3 76.5 - - - +
200A ARG* 1.4 59.0 + - - +
202A LEU* 3.7 1.9 + - - +
203A GLY 3.3 4.0 + - - -
204A CYS* 3.0 29.2 + - - +
205A GLY 3.5 16.1 - - - +
206A TRP 3.9 6.5 - - - +
207A ALA* 3.8 13.0 - - - +
257A VAL* 3.8 8.3 - - - -
259A CYS* 2.0 58.8 - - + -
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Residues in contact with ARG 200 (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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196A HIS* 3.3 37.0 + - + +
197A VAL* 3.4 14.1 - - - +
198A VAL 3.4 0.2 - - - -
199A CYS* 1.4 74.2 - - - +
201A GLN* 1.3 68.6 + - - +
203A GLY* 3.4 11.6 + - - -
204A CYS 5.2 0.2 - - - +
205A GLY* 3.7 10.7 + - - +
232A GLY 3.1 25.5 + - - -
233A ALA* 3.6 23.6 + - - +
234A GLU 3.8 15.6 + - - +
235A ALA* 4.5 9.7 - - - +
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Residues in contact with GLN 201 (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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51A SER 5.5 0.8 + - - -
161A LEU* 3.8 20.1 - - - +
197A VAL 3.4 11.2 - - - +
198A VAL* 3.4 12.6 - - - +
200A ARG* 1.3 80.0 - - - +
202A LEU* 1.3 69.4 + - + +
235A ALA 3.5 18.4 - - - +
236A TYR* 3.6 15.2 - - + +
237A LEU* 3.1 30.6 + - - +
238A TRP* 3.6 33.9 - - - -
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Residues in contact with LEU 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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161A LEU* 3.6 39.5 - - + +
163A LEU* 4.2 24.9 - - + -
198A VAL* 3.2 38.5 + - + +
199A CYS* 4.2 6.3 - - - +
200A ARG 3.3 0.6 - - - -
201A GLN* 1.3 82.0 - - + +
203A GLY* 1.3 60.4 + - - +
204A CYS* 4.2 14.3 - - - -
259A CYS* 5.3 0.9 - - - -
1372A EDO 4.7 14.4 - - - +
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Residues in contact with GLY 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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170A CYS* 4.6 1.9 - - - -
199A CYS 3.3 4.4 + - - -
200A ARG 3.4 10.9 + - - -
202A LEU* 1.3 79.8 - - - +
204A CYS* 1.3 64.0 + - - +
205A GLY 3.6 3.1 - - - -
261A GLU* 4.6 4.9 - - - +
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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