Contacts of the strand formed by residues 187 - 193 (chain C) in PDB entry 2CX9
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 ILE 187 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136C ALA 4.8 1.6 - - - +
137C ALA* 3.3 38.1 - - - +
139C LEU* 4.9 9.9 - - + -
171C MET* 4.2 13.0 - - + -
172C ALA 3.6 17.0 - - - +
173C ARG* 4.0 14.8 - - + +
183C LYS 3.6 15.5 - - - +
184C HIS 4.2 1.1 + - - +
185C GLN 3.4 0.2 - - - -
186C GLY* 1.3 79.3 - - - +
188C SER* 1.3 75.3 + - - +
235C GLY* 3.0 22.9 - - - -
236C LYS 3.0 3.1 + - - -
237C GLY 3.0 6.7 + - - -
238C PHE* 3.9 36.1 - - + +
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Residues in contact with SER 188 (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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170C VAL 3.8 0.3 - - - +
171C MET* 3.3 3.8 - - - -
172C ALA 2.8 31.2 + - - +
174C THR* 3.1 31.2 + - - +
187C ILE* 1.3 74.6 - - - +
189C ALA* 1.3 60.1 + - - +
190C PHE* 3.8 13.6 - - - -
230C LEU* 4.4 12.8 - - - -
233C GLU 5.1 0.9 - - - -
234C ARG* 3.6 3.8 - - - +
235C GLY 2.8 26.1 + - - +
237C GLY* 4.3 6.5 - - - +
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Residues in contact with ALA 189 (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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99C HIS* 3.5 35.9 - - + +
169C VAL* 4.6 0.7 - - + -
170C VAL 3.5 4.5 - - - -
171C MET* 3.7 11.9 - - + -
188C SER* 1.3 73.9 - - - +
190C PHE* 1.3 61.5 + - - +
230C LEU* 3.4 6.1 - - - +
231C LEU* 2.6 52.1 + - + +
237C GLY* 4.4 6.1 - - - -
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Residues in contact with PHE 190 (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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143C ALA* 3.4 34.1 - - + -
150C TRP* 3.5 38.8 - + + -
152C LEU* 4.2 25.6 - - + -
168C TYR 3.6 1.4 - - - +
169C VAL* 3.1 3.8 - - - -
170C VAL 2.7 47.0 + - - +
172C ALA* 4.1 6.7 - - + -
174C THR* 3.9 11.7 - - + -
188C SER* 3.8 26.7 - - - -
189C ALA* 1.3 75.0 - - - +
191C ALA* 1.3 60.2 + - - +
192C PHE* 4.0 7.6 - - + -
225C VAL* 5.1 0.2 - - + -
229C ALA* 3.3 16.4 - - + +
230C LEU* 3.8 22.9 - - + -
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Residues in contact with ALA 191 (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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100C ILE* 4.3 14.4 - - + -
108C GLN* 5.6 2.2 - - - +
112C PHE* 3.9 25.2 - - + -
168C TYR 3.1 8.3 - - - +
169C VAL* 4.1 15.0 - - + +
189C ALA 4.3 0.2 - - - -
190C PHE* 1.3 73.3 - - - +
192C PHE* 1.3 67.1 + - - +
226C PRO* 5.7 0.5 - - - +
228C GLU 4.8 0.7 - - - +
229C ALA* 3.1 27.2 + - - +
231C LEU* 4.5 13.8 - - + +
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Residues in contact with PHE 192 (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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112C PHE* 3.7 16.6 - - - -
152C LEU* 3.8 24.0 - - + -
167C VAL* 3.5 2.4 - - - +
168C TYR* 2.7 61.3 + + + -
170C VAL* 4.3 13.0 - - + -
190C PHE* 4.0 13.9 - - + -
191C ALA* 1.3 79.3 - - - +
193C PHE* 1.3 71.3 + - - +
195C PRO* 3.7 22.0 - - + -
199C LEU* 4.4 4.9 - - + -
223C LEU* 3.8 20.6 - - + -
225C VAL* 3.4 33.7 - - + -
226C PRO* 5.3 3.1 - - + -
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Residues in contact with PHE 193 (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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111C ALA* 3.4 28.7 - - + -
112C PHE* 3.4 28.7 - + - -
115C LYS* 3.8 36.8 - - + -
121C ALA* 5.3 2.0 - - + -
166C GLY 3.3 15.9 - - - +
167C VAL* 3.8 14.1 - - + -
192C PHE* 1.3 81.8 - - - +
194C ARG* 1.3 69.1 + - - +
195C PRO* 2.8 12.8 - - - +
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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