Contacts of the strand formed by residues 206 - 215 (chain C) in PDB entry 2G4C
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 TYR 206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C GLN* 3.4 23.8 - - + +
126C PHE* 4.8 6.7 - + - -
193C TYR* 3.0 54.7 + + - -
196C CYS* 3.2 22.6 + - + +
197C LEU* 3.6 21.8 - - + -
200C VAL* 4.3 15.0 - - + -
203C ARG 4.0 17.0 - - - +
204C LEU* 4.7 4.7 - - + -
205C PRO* 1.3 77.3 - - - +
207C GLY* 1.3 63.7 + - - +
208C LEU* 3.5 23.8 - - + -
241C TRP* 3.2 9.0 - - - -
242C PHE* 3.4 28.4 + + + -
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Residues in contact with GLY 207 (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 GLN 3.4 8.9 + - - +
125C VAL* 3.3 9.1 - - - -
126C PHE 2.9 19.9 + - - -
206C TYR* 1.3 77.2 - - - +
208C LEU* 1.3 72.5 + - - +
209C ALA 4.1 0.2 - - - -
239C LEU* 4.2 3.8 - - - -
240C VAL 3.3 11.2 - - - -
241C TRP* 2.9 21.7 - - - -
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Residues in contact with LEU 208 (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 PHE* 3.4 17.0 - - + +
128C VAL* 3.9 18.6 - - + +
189C ALA* 3.3 38.6 - - + +
192C HIS* 3.5 20.0 - - + -
193C TYR* 4.1 7.4 - - - +
196C CYS* 4.2 13.2 - - + -
206C TYR* 3.5 19.7 - - + -
207C GLY* 1.3 85.2 - - - +
209C ALA* 1.3 62.6 + - - +
210C GLN* 4.9 0.5 + - - +
238C SER* 3.9 3.6 + - - +
239C LEU* 4.2 1.7 - - - +
240C VAL* 3.1 31.5 + - - +
242C PHE* 3.9 15.7 - - + -
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Residues in contact with ALA 209 (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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114C TRP* 4.2 5.6 - - + -
115C TRP* 3.7 16.0 - - + -
119C VAL* 3.6 32.3 - - + -
125C VAL* 3.7 11.4 - - + +
126C PHE 3.0 8.8 + - - +
127C PRO* 3.7 2.6 - - - +
128C VAL* 3.1 28.9 + - - +
208C LEU* 1.3 72.2 - - - +
210C GLN* 1.3 62.2 + - - +
238C SER 3.4 8.3 - - - +
239C LEU* 4.6 4.0 - - + +
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Residues in contact with GLN 210 (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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114C TRP* 4.4 0.9 - - - -
115C TRP* 4.1 6.0 - - - -
128C VAL* 3.6 28.6 - - + +
129C ASP* 4.2 0.3 - - - -
130C ALA* 2.9 41.4 + - - +
182C ARG* 4.5 2.1 + - - +
185C LEU* 3.7 49.6 + - + +
189C ALA* 4.8 4.4 - - - +
208C LEU 4.9 0.7 - - - +
209C ALA* 1.3 80.0 - - - +
211C ILE* 1.3 67.0 + - - +
212C GLY* 5.4 0.2 - - - -
237C ALA* 3.4 1.0 - - - -
238C SER* 2.6 43.1 + - - +
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Residues in contact with ILE 211 (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* 3.7 36.1 - - + +
114C TRP* 3.7 28.0 - - + -
115C TRP* 4.2 13.0 - - + -
185C LEU* 4.3 0.7 - - - -
210C GLN* 1.3 78.7 - - - +
212C GLY* 1.3 60.3 + - - +
235C THR* 4.2 9.2 - - + -
236C GLU 3.3 5.2 - - - +
237C ALA* 3.6 20.2 - - + -
342C LEU* 3.8 20.0 - - + -
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Residues in contact with GLY 212 (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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132C HIS* 6.0 0.2 - - - -
182C ARG* 4.5 4.9 - - - -
185C LEU* 3.7 15.5 - - - +
210C GLN* 5.4 0.4 - - - -
211C ILE* 1.3 77.8 - - - +
213C VAL* 1.3 60.7 + - - -
214C CYS* 4.3 0.5 - - - -
235C THR* 4.0 4.7 - - - -
236C GLU* 2.3 55.1 + - - +
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Residues in contact with VAL 213 (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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132A HIS* 3.4 37.0 - - + +
107C ARG* 5.7 0.7 - - - +
132C HIS* 4.2 6.8 + - - +
182C ARG* 2.5 34.8 + - - +
212C GLY* 1.3 73.6 - - - -
214C CYS* 1.3 67.3 + - - +
215C PHE* 4.2 12.8 - - + -
233C GLU* 4.0 23.8 - - + -
234C LYS 3.2 11.7 - - - +
235C THR* 3.7 22.4 - - + +
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Residues in contact with CYS 214 (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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182C ARG* 3.6 15.5 - - - +
183C GLU 3.4 11.2 - - - +
184C ASN* 3.7 20.4 - - - -
185C LEU* 4.1 11.2 - - - -
213C VAL* 1.3 80.1 - - - +
215C PHE* 1.3 64.2 + - - +
216C HIS* 3.2 27.8 + - + -
232C GLY 3.4 0.2 - - - +
233C GLU* 3.7 2.1 - - - -
234C LYS 2.9 27.7 + - - -
236C GLU* 3.1 28.5 - - - +
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Residues in contact with PHE 215 (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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132A HIS* 3.7 23.6 - + + -
133A HIS* 5.5 1.6 - + + -
181A LEU* 5.2 2.5 - - + -
215A PHE* 5.1 3.8 - + - -
132C HIS* 4.4 28.3 - + + -
145C PHE* 4.4 12.9 + - + -
181C LEU* 3.6 50.9 - - + +
182C ARG* 3.0 16.6 + - + +
183C GLU* 3.5 14.7 - - - +
213C VAL* 4.2 17.3 - - + -
214C CYS* 1.3 73.4 - - - +
216C HIS* 1.3 61.2 + - - +
231C ILE* 4.5 14.6 - - + -
232C GLY 3.3 5.8 - - - +
233C GLU* 3.3 43.1 - - + -
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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