Contacts of the strand formed by residues 165 - 173 (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 ALA 165 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C LEU* 3.4 12.8 - - - +
124C ALA* 3.8 14.6 - - + +
161C GLN* 2.8 23.6 - - + +
163C SER 2.5 7.9 + - - -
164C VAL* 1.3 72.5 - - - +
166C GLY* 1.3 60.2 + - - +
167C VAL 4.2 0.4 - - - +
168C TYR* 3.1 38.9 + - + -
194C ARG* 3.3 20.3 + - - +
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Residues in contact with GLY 166 (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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121C ALA* 4.4 9.2 - - - -
122C LEU 2.7 19.1 + - - +
164C VAL 3.6 3.6 + - - -
165C ALA* 1.3 73.7 - - - +
167C VAL* 1.3 60.7 + - - +
168C TYR* 4.3 0.7 - - - -
193C PHE* 3.3 11.1 - - - +
194C ARG* 2.8 38.4 + - - +
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Residues in contact with VAL 167 (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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96C ALA* 5.0 0.8 - - + +
100C ILE* 4.1 18.6 - - + -
112C PHE* 3.5 28.9 - - + +
115C LYS* 5.6 0.7 - - + -
116C LEU* 3.6 28.9 - - + -
121C ALA* 4.1 9.4 - - + -
122C LEU 2.9 3.5 + - - +
123C GLY* 3.1 5.1 - - - -
124C ALA 3.0 23.2 + - - +
165C ALA* 4.2 0.2 - - - +
166C GLY* 1.3 81.5 - - - +
168C TYR* 1.3 74.6 + - - +
169C VAL* 5.0 1.1 - - + -
192C PHE 3.5 7.0 - - - +
193C PHE* 3.8 25.1 - - + -
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Residues in contact with TYR 168 (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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124C ALA* 3.6 14.8 - - + -
162C GLY 2.8 26.4 + - - -
163C SER* 4.5 1.4 - - - -
165C ALA* 3.1 41.0 + - + +
167C VAL* 1.3 80.7 - - - +
169C VAL* 1.3 64.2 + - - +
170C VAL* 4.6 5.8 - - + -
190C PHE 3.6 1.2 - - - +
191C ALA* 3.1 4.2 - - - +
192C PHE* 2.7 60.9 + + + -
194C ARG* 4.0 29.2 - - + -
199C LEU* 3.7 25.5 - - + +
201C VAL* 4.2 9.5 - - - +
218C LEU* 3.9 24.2 - - + -
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Residues in contact with VAL 169 (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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96C ALA* 3.9 25.4 - - + +
99C HIS* 3.8 18.4 - - + +
100C ILE* 4.1 11.9 - - + -
124C ALA 2.9 12.2 + - - +
125C TRP* 3.5 7.2 - - + -
126C GLY 2.7 31.9 + - - -
167C VAL* 5.0 1.6 - - + -
168C TYR* 1.3 79.4 - - - +
170C VAL* 1.3 58.4 + - - +
171C MET* 3.4 24.3 - - + +
189C ALA* 4.6 1.6 - - + -
190C PHE 3.1 9.2 - - - +
191C ALA* 4.1 12.3 - - + -
231C LEU* 4.3 10.8 - - + -
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Residues in contact with VAL 170 (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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126C GLY* 3.7 9.2 - - - +
141C THR* 4.6 6.1 - - + -
152C LEU* 4.6 12.6 - - + -
156C LYS* 3.5 26.9 - - + -
168C TYR* 4.6 9.2 - - + -
169C VAL* 1.3 84.1 - - - +
171C MET* 1.3 73.9 + - - +
172C ALA* 5.1 0.7 - - + -
189C ALA* 3.5 1.4 - - - -
190C PHE* 2.7 43.6 + - - +
192C PHE* 4.3 21.1 - - + -
199C LEU* 5.9 0.7 - - + -
218C LEU* 5.4 4.3 - - + -
220C LEU* 4.4 23.8 - - + -
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Residues in contact with MET 171 (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* 3.7 8.5 - - - +
125C TRP* 3.0 36.8 - - + +
126C GLY 3.0 14.7 + - - +
127C LEU* 3.6 21.1 - - + -
139C LEU* 3.3 21.6 - - + +
141C THR* 4.0 3.5 - - - -
156C LYS* 3.1 18.9 + - - -
169C VAL* 3.4 35.4 - - + +
170C VAL* 1.3 76.9 - - - +
172C ALA* 1.3 64.3 + - - +
187C ILE* 4.2 8.5 - - + -
188C SER 3.3 6.1 - - - +
189C ALA* 3.7 21.8 - - - -
237C GLY 5.4 0.4 - - - +
241C VAL* 4.0 13.0 - - + -
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Residues in contact with ALA 172 (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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139C LEU* 5.0 2.7 - - - -
141C THR* 3.5 21.1 - - + +
142C LYS 3.8 7.2 - - - +
143C ALA* 3.7 24.5 - - + -
152C LEU* 5.2 2.7 - - + -
170C VAL* 5.0 2.5 - - + +
171C MET* 1.3 76.4 - - - +
173C ARG* 1.3 63.8 + - - +
174C THR* 3.5 3.8 + - - +
187C ILE* 4.0 5.2 - - - +
188C SER* 2.8 35.7 + - - +
190C PHE* 4.1 7.9 - - + -
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Residues in contact with ARG 173 (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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137C ALA 3.1 17.2 + - - -
138C ALA* 5.0 0.6 - - - +
139C LEU* 4.3 17.5 + - + +
140C LYS 5.9 0.2 - - - -
141C THR 3.1 12.7 + - - +
142C LYS* 3.7 17.7 - - + +
143C ALA 3.2 19.6 + - - +
172C ALA* 1.3 71.6 - - - +
174C THR* 1.3 59.1 + - - +
175C ASP 3.0 31.5 + - - +
176C PRO* 5.0 0.4 - - - -
177C PRO* 3.9 17.5 - - - +
183C LYS* 2.6 39.6 + - - +
185C GLN 3.0 24.5 + - - -
186C GLY* 3.4 9.3 - - - +
187C ILE* 4.0 11.4 - - + +
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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