Contacts of the strand formed by residues 187 - 199 (chain C) in PDB entry 2GH0
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 187 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C CYS* 4.0 2.2 - - - -
183C VAL* 6.0 1.1 - - + -
185C GLN 3.7 0.4 + - - -
186C PRO* 1.3 73.2 - - - +
188C CYS* 1.3 62.6 + - - +
189C ARG* 3.4 28.5 + - + +
217C GLY 3.2 1.6 - - - +
218C CYS 3.6 0.2 - - - -
219C LEU* 2.8 43.7 + - - -
183D VAL* 4.5 14.6 - - + -
187D CYS* 2.1 55.5 - - + -
219D LEU 3.9 5.2 - - - -
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Residues in contact with CYS 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C CYS* 2.0 49.4 - - + -
124C ARG 3.7 2.9 - - - -
150C CYS* 3.8 19.7 - - - +
151C SER* 3.3 28.0 - - - -
152C GLY 3.5 24.0 + - - +
154C CYS* 3.9 4.3 - - - -
186C PRO 4.0 0.4 + - - -
187C CYS* 1.3 70.0 - - - +
189C ARG* 1.3 67.3 + - - +
190C PRO* 4.8 0.2 - - - +
217C GLY 3.3 4.7 - - - -
183D VAL* 4.3 8.9 + - - +
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Residues in contact with ARG 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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150C CYS* 3.6 7.2 - - - +
187C CYS* 3.4 27.8 + - + +
188C CYS* 1.3 81.1 - - - +
190C PRO* 1.3 80.9 - - + +
191C THR* 4.4 0.5 - - - +
193C TYR* 4.3 11.9 + - - -
216C CYS* 3.4 0.7 - - - -
217C GLY* 2.8 31.8 + - - +
219C LEU* 4.0 19.8 - - + +
159D SER* 4.9 0.8 + - - -
161D HIS* 5.1 0.8 + - - -
162D ASP* 2.7 44.0 + - - -
165D LEU* 5.0 2.2 - - - +
183D VAL* 3.2 34.5 + - - -
185D GLN 3.5 17.0 + - - +
186D PRO* 4.0 15.6 - - - +
219D LEU 5.0 4.4 + - - +
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Residues in contact with PRO 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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150C CYS* 3.4 9.8 - - + +
188C CYS 4.8 0.2 - - - +
189C ARG* 1.3 103.6 - - + +
191C THR* 1.3 59.4 + - - +
192C ARG 4.1 4.3 - - - +
193C TYR* 3.5 39.4 + - + +
213C ALA* 3.8 19.1 - - + -
215C ALA 3.3 9.2 - - - +
219C LEU* 3.9 12.1 - - - +
161D HIS* 3.6 29.8 - - + -
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Residues in contact with THR 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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189C ARG 3.6 0.2 + - - -
190C PRO* 1.3 73.9 - - - +
192C ARG* 1.3 65.3 + - - +
193C TYR* 5.1 3.8 - - - -
215C ALA* 2.9 29.9 + - - +
216C CYS 3.6 3.1 + - - +
217C GLY* 3.8 21.5 - - - +
219C LEU* 3.8 25.6 - - + -
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Residues in contact with ARG 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C PRO* 3.6 2.5 - - - +
191C THR* 1.3 86.3 + - - +
193C TYR* 1.3 69.1 + - - +
213C ALA* 3.5 6.1 - - - -
214C THR* 3.0 54.2 + - - +
215C ALA* 3.5 30.5 + - + +
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Residues in contact with TYR 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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189C ARG* 4.3 13.3 + - - -
190C PRO* 3.5 40.1 + - + +
191C THR 5.1 1.3 - - - -
192C ARG* 1.3 82.1 - - - +
194C GLU* 1.3 63.0 + - - +
210C ARG* 3.6 45.4 - - + +
212C SER 3.2 15.5 - - - +
214C THR* 4.1 7.4 + - - -
159D SER* 4.8 7.6 + - - -
161D HIS* 3.4 35.2 + + + +
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Residues in contact with GLU 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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177A ARG* 5.5 10.0 + - - -
180A LYS* 5.3 8.1 + - - +
148C ARG* 3.6 23.4 + - - -
193C TYR* 1.3 76.0 - - - +
195C ALA* 1.3 70.4 + - - +
210C ARG 3.9 6.5 - - - +
211C LEU 3.2 4.9 + - - -
212C SER* 2.8 43.5 + - - +
213C ALA 4.7 0.3 - - - +
214C THR* 3.3 26.0 - - + +
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Residues in contact with ALA 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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180A LYS* 4.6 8.8 + - - +
184A GLU* 3.8 23.7 + - - +
194C GLU* 1.3 90.8 - - - +
196C VAL* 1.3 65.3 + - - +
197C SER* 4.9 1.3 - - - +
207C THR* 3.4 28.0 - - + -
208C VAL 3.3 11.4 - - - +
209C ASP* 3.9 11.0 - - + +
210C ARG 4.0 3.9 - - - +
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS* 4.1 14.4 - - - +
135C LEU* 4.8 1.1 - - + -
145C VAL* 3.8 35.7 - - + -
146C ARG 4.5 3.8 - - - +
147C PHE* 5.0 4.5 - - + -
195C ALA* 1.3 76.8 - - - +
197C SER* 1.3 65.4 + - - +
198C PHE* 4.2 13.4 - - + -
206C ARG 4.1 0.3 - - - +
207C THR* 3.4 2.1 - - - +
208C VAL* 3.0 32.1 + - - +
211C LEU* 3.8 31.2 - - + +
212C SER* 3.7 25.6 - - - -
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Residues in contact with SER 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 4.9 5.4 + - - -
180A LYS* 3.9 26.9 + - - +
183A GLY 4.2 0.4 - - - -
184A GLU* 3.6 24.5 + - - +
143C GLU* 4.7 0.5 - - - +
145C VAL* 4.0 11.1 - - - +
195C ALA* 4.9 1.2 - - - +
196C VAL* 1.3 73.4 - - - +
198C PHE* 1.3 65.3 + - - +
205C TRP* 4.1 14.5 - - - -
206C ARG 3.2 11.2 - - - -
207C THR* 3.1 26.2 + - - +
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Residues in contact with PHE 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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179A ARG* 4.9 0.2 - - - +
132C VAL* 4.0 31.0 - - + -
137C LEU* 3.8 23.8 - - + -
139C HIS* 3.8 32.3 - + + -
141C SER* 3.6 26.0 - - - -
143C GLU* 3.3 17.7 - - - +
145C VAL* 4.3 2.9 - - + -
196C VAL* 4.2 12.8 - - + -
197C SER* 1.3 81.5 - - - +
199C MET* 1.3 63.5 + - - +
200C ASP* 4.4 2.7 - - + -
205C TRP* 3.5 12.9 - - - -
206C ARG* 2.9 54.0 + - + +
208C VAL* 4.4 9.9 - - + -
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Residues in contact with MET 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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179A ARG* 4.8 0.4 - - - -
230A ARG* 3.6 48.8 + - + +
233A ASN* 3.6 20.9 - - + +
234A THR* 4.2 13.7 - - - -
141C SER* 2.8 25.3 + - - -
142C ASP 4.7 0.3 + - - -
143C GLU* 3.2 22.9 + - - +
198C PHE* 1.3 74.3 - - - +
200C ASP* 1.3 62.1 + - - +
203C SER* 3.4 31.2 - - - +
204C THR 3.5 5.2 - - - +
205C TRP* 3.5 40.3 - - + +
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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