Contacts of the helix formed by residues 193 - 201 (chain C) in PDB entry 3P71
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 GLY 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C SER* 4.8 3.1 - - - -
190C PRO* 6.2 0.2 - - - -
192C GLU* 1.3 77.3 - - - +
194C PRO* 1.3 79.3 - - - +
195C MET 3.4 1.8 - - - -
196C CYS* 3.0 13.0 + - - +
197C ASP* 3.1 23.1 + - - +
218C TYR* 6.1 0.2 - - - -
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Residues in contact with PRO 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C SER* 3.8 7.4 - - - +
173C SER* 3.7 24.7 - - - +
174C ILE* 3.9 21.2 - - + +
183C LEU* 3.8 28.0 - - + -
193C GLY* 1.3 80.2 - - - -
195C MET* 1.3 65.0 + - + +
197C ASP* 3.0 21.3 + - - +
198C LEU* 3.2 14.7 + - - +
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Residues in contact with MET 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ARG* 3.2 31.2 - - - +
155C LEU* 3.8 31.9 - - + -
183C LEU* 4.1 17.9 - - + +
184C ASP 4.2 0.9 - - - +
185C ARG* 3.4 24.0 - - - +
187C GLN* 3.8 25.1 - - - +
189C VAL* 4.3 13.7 - - + -
190C PRO* 3.8 22.0 - - + -
193C GLY 3.4 1.0 - - - -
194C PRO* 1.3 80.9 - - + +
196C CYS* 1.3 63.3 + - - +
198C LEU* 3.5 17.6 + - - +
199C LEU* 3.7 12.8 + - + +
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Residues in contact with CYS 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C VAL* 4.3 8.1 - - - -
190C PRO* 3.2 25.5 - - - +
191C HIS* 3.3 25.1 - - - -
192C GLU* 3.4 13.6 + - - +
193C GLY 3.0 10.8 + - - +
195C MET* 1.3 79.2 - - - +
197C ASP* 1.3 66.1 + - - +
199C LEU* 3.0 13.2 + - - +
200C TRP* 3.2 33.0 + - - -
216C ALA* 4.5 3.1 - - - -
217C GLY 4.2 15.7 - - - -
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Residues in contact with ASP 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C GLY 3.6 2.7 - - - +
170C LEU 4.0 0.9 - - - +
171C SER* 2.7 37.2 + - - -
172C PRO* 4.1 0.7 - - - +
173C SER* 4.4 2.9 + - - -
192C GLU* 5.3 0.7 - - - -
193C GLY* 3.1 26.2 + - - +
194C PRO 3.0 1.8 + - - +
196C CYS* 1.3 76.4 - - - +
198C LEU* 1.3 58.7 + - - +
201C SER* 2.9 46.4 + - - +
217C GLY* 3.4 17.4 + - - -
218C TYR* 3.4 31.3 - - + -
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LEU* 4.1 32.3 - - + +
156C THR* 4.7 2.2 - - - +
164C PHE* 5.3 1.1 - - + -
166C LEU* 3.6 28.1 - - + +
167C HIS 4.4 0.7 + - - -
168C GLY 3.0 21.8 + - - -
169C GLY 3.1 16.2 + - - +
170C LEU* 5.0 4.0 - - + -
171C SER* 4.9 3.8 - - - +
174C ILE* 3.7 30.3 - - + -
180C ILE* 4.5 19.1 - - + -
183C LEU* 4.1 8.7 - - + -
194C PRO 3.2 12.9 + - - +
195C MET* 3.6 7.6 - - - +
196C CYS 3.1 0.6 + - - -
197C ASP* 1.3 76.4 - - - +
199C LEU* 1.3 67.2 + - + +
228C PHE* 6.5 0.4 - - + -
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ARG* 3.3 37.7 - - + +
116C GLY* 3.7 17.9 - - - +
117C ASN* 3.3 23.9 - - + +
155C LEU* 4.5 22.9 - - + +
167C HIS* 3.3 13.6 - - + +
168C GLY* 3.9 5.4 - - - +
189C VAL* 3.7 34.1 - - + -
195C MET* 4.2 7.9 - - + +
196C CYS 3.0 9.2 + - - +
198C LEU* 1.3 92.4 - - + +
200C TRP* 1.3 61.9 + - + +
241C HIS* 3.3 10.6 + - - -
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Residues in contact with TRP 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ASN* 3.6 40.6 + - + +
120C SER* 6.4 0.2 - - - -
123C ILE* 4.1 18.4 - - + -
189C VAL* 4.2 14.8 - - + +
190C PRO 5.3 0.6 + - - -
196C CYS* 3.2 35.1 + - - +
199C LEU* 1.3 85.0 - - + +
201C SER* 1.3 66.3 + - - +
202C ASP* 3.8 1.0 - - - +
212C SER* 4.9 0.5 + - - -
214C ARG* 3.7 28.4 - - + -
216C ALA* 3.5 40.3 - - + +
217C GLY* 3.9 1.8 - - - +
241C HIS* 2.9 20.7 + - - -
301T PHE* 3.7 27.8 - + - -
303T ASP* 3.7 24.5 - - + -
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Residues in contact with SER 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C GLY 2.8 23.3 - - - +
169C GLY* 3.8 11.8 - - - +
170C LEU 3.0 23.4 + - - -
197C ASP* 2.9 24.9 + - - +
199C LEU 3.9 0.4 - - - -
200C TRP* 1.3 82.7 - - - +
202C ASP* 1.3 65.0 + - - +
212C SER* 5.5 0.4 - - - -
217C GLY* 3.7 1.9 - - - -
218C TYR* 2.9 34.8 + - - +
220C PHE* 4.0 4.0 - - - -
239C ARG* 3.4 0.9 + - - -
241C HIS* 3.5 0.7 - - - -
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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