Contacts of the helix formed by residues 192 - 201 (chain A) in PDB entry 3ULA
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 CYS 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A TYR* 1.3 74.9 - - - +
193A THR* 1.3 57.4 + - + +
194A ASP 2.5 15.3 + - - -
195A LEU* 3.1 9.2 + - - +
196A ARG* 4.1 3.0 + - - -
219A GLN* 2.5 20.2 + - - +
220A PRO 3.4 25.4 - - - -
221A GLY* 3.5 21.1 - - - -
222A ALA* 4.0 12.5 - - - +
224A LYS* 5.7 0.4 - - - -
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Residues in contact with THR 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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166A LYS* 3.9 26.7 - - - +
167A LEU 5.2 1.9 - - - +
191A TYR* 4.4 8.0 - - - +
192A CYS* 1.3 77.3 - - + +
194A ASP* 1.3 65.3 + - - -
195A LEU 2.7 2.4 + - - -
196A ARG* 2.7 46.7 + - + +
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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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164A SER* 4.4 3.0 + - - -
165A PHE* 2.3 50.0 + - + +
166A LYS* 3.5 19.6 - - - +
167A LEU* 3.3 30.3 + - - +
189A SER 3.8 7.4 - - - +
190A ILE* 4.5 1.8 - - + -
191A TYR* 3.1 49.1 + - - +
192A CYS 2.5 4.6 + - - -
193A THR* 1.3 75.6 + - - +
195A LEU* 1.3 59.6 + - - +
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Residues in contact with LEU 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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165A PHE* 3.6 30.5 - - + -
167A LEU* 3.6 27.8 - - + -
190A ILE* 5.3 3.8 - - + -
191A TYR 5.7 0.2 - - - +
192A CYS 3.1 4.6 + - - +
193A THR 2.7 1.6 + - - -
194A ASP* 1.3 74.9 - - + +
196A ARG* 1.3 68.3 + - - +
197A VAL* 3.5 5.4 - - - -
198A LEU* 2.9 37.5 + - + +
208A LEU* 4.3 15.5 - - + -
222A ALA 4.4 6.7 - - - +
223A PHE* 4.0 26.7 - - + -
226A ILE* 3.7 34.9 - - + +
228A LEU* 4.8 2.7 - - + -
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Residues in contact with ARG 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 CYS 4.1 2.0 + - - -
193A THR* 2.7 29.9 + - - +
195A LEU* 1.3 75.2 - - - +
197A VAL* 1.3 65.8 + - + +
198A LEU 2.6 14.0 + - - -
199A HIS* 2.7 47.7 + - + +
200A GLN* 3.5 31.2 + - - +
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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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167A LEU* 4.0 35.0 + - + +
168A PRO 4.2 2.0 - - - +
169A GLU* 3.8 39.9 - - + +
171A PHE* 4.1 17.3 - - + -
172A SER* 5.0 7.4 + - - +
195A LEU 4.0 4.9 - - - +
196A ARG* 1.3 84.1 - - + +
198A LEU* 1.3 65.7 + - + +
200A GLN* 3.0 28.2 + - - +
201A MET* 3.9 8.8 - - - +
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Residues in contact with LEU 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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167A LEU* 4.4 12.6 - - + -
171A PHE* 6.3 2.5 - - + -
195A LEU* 2.9 39.4 + - + +
196A ARG 2.6 5.5 + - - -
197A VAL* 1.3 79.4 - - + +
199A HIS* 1.3 51.3 + - - +
201A MET* 2.6 48.2 + - + +
204A LEU* 3.2 40.2 - - + -
206A LEU* 5.0 6.5 - - + -
226A ILE* 3.6 33.2 - - + -
227A ARG 5.8 1.6 - - - +
228A LEU* 5.0 9.4 - - + -
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Residues in contact with HIS 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 LEU 5.6 0.2 - - - -
196A ARG* 2.7 52.3 + - + +
198A LEU* 1.3 71.3 - - - +
200A GLN* 1.3 73.5 + - - +
201A MET* 3.0 9.2 + - - -
202A PRO* 4.5 4.3 - - - +
224A LYS* 3.3 32.3 - - + +
225A GLU* 3.2 30.5 + - + +
226A ILE* 4.2 11.4 - - + +
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Residues in contact with GLN 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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172A SER* 6.1 3.3 - - - -
196A ARG* 3.5 28.0 + - - +
197A VAL* 3.0 35.0 - - - +
198A LEU 3.0 1.2 - - - -
199A HIS* 1.3 94.6 - - - +
201A MET* 1.3 64.8 + - + +
202A PRO* 3.4 11.7 - - - +
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Residues in contact with MET 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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171A PHE* 3.6 20.4 - - - +
172A SER* 2.9 35.9 - - - +
174A LEU* 3.8 18.4 - - - +
175A THR* 3.8 10.1 - - - +
197A VAL 3.9 9.4 - - - +
198A LEU* 2.6 36.0 + - - +
199A HIS 3.0 4.2 + - - -
200A GLN* 1.3 78.5 - - + +
202A PRO* 1.3 64.5 - - - +
203A LEU 3.6 2.2 - - - -
204A LEU* 3.3 40.3 - - + +
227A ARG* 4.9 6.9 - - - +
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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