Contacts of the strand formed by residues 205 - 219 (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 TRP 205 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ARG* 3.7 39.7 - - + -
180A LYS* 5.6 0.4 - - - -
182A TYR* 3.7 28.1 - + - -
183A GLY* 3.5 29.4 - - - +
186A CYS 4.9 2.7 - - - +
187A SER* 3.8 24.2 + - - +
188A GLY* 4.2 8.3 + - - -
233A ASN* 3.5 17.4 + - + -
234A THR* 3.3 18.6 + - + -
236A ALA* 3.8 19.0 - - + +
197C SER* 4.1 8.3 - - - -
198C PHE* 3.5 39.0 - - - -
199C MET* 3.5 23.5 - - + +
203C SER 5.3 0.4 - - - -
204C THR* 1.3 81.3 - - - +
206C ARG* 1.3 65.5 + - - +
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Residues in contact with ARG 206 (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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187A SER* 3.8 2.4 + - - -
188A GLY* 5.8 3.6 - - - -
189A PRO* 5.8 6.3 - - - +
139C HIS* 3.5 40.7 + - + +
197C SER* 3.2 5.0 - - - -
198C PHE* 2.9 53.0 + - + -
200C ASP* 2.8 33.8 + - + +
202C ASN* 5.8 2.0 - - - +
204C THR* 3.6 31.8 + - - +
205C TRP* 1.3 79.6 + - - +
207C THR* 1.3 65.1 + - - +
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Residues in contact with THR 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLU* 3.7 16.5 - - + -
187A SER* 2.7 33.5 + - - -
139C HIS* 5.6 2.1 + - - -
195C ALA* 3.4 25.4 - - + -
196C VAL 3.4 4.0 - - - +
197C SER* 3.1 24.5 + - - +
206C ARG* 1.3 72.7 + - - +
208C VAL* 1.3 67.9 + - - +
209C ASP* 4.1 11.5 + - - +
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Residues in contact with VAL 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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137C LEU* 4.0 39.5 - - + -
139C HIS* 4.5 15.7 - - + -
195C ALA* 3.3 1.7 - - - -
196C VAL 3.0 29.6 + - - +
198C PHE* 4.4 10.1 - - + -
207C THR* 1.3 76.7 - - - +
209C ASP* 1.3 72.0 + - - +
211C LEU* 3.8 21.3 - - + +
160D PRO* 5.1 8.3 - - + -
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Residues in contact with ASP 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLU* 4.9 2.9 - - - +
195C ALA* 3.9 15.0 - - - +
207C THR* 4.1 10.7 - - - +
208C VAL* 1.3 81.4 - - - +
210C ARG* 1.3 79.7 + - + +
211C LEU* 3.0 5.2 + - - -
160D PRO* 4.1 9.9 - - - +
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Residues in contact with ARG 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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193C TYR* 3.6 43.5 - - + -
194C GLU* 3.7 12.4 + - - +
195C ALA 4.1 0.2 - - - +
209C ASP* 1.3 80.0 - - + +
211C LEU* 1.3 59.5 + - - +
212C SER 3.6 2.2 - - - -
160D PRO* 4.1 12.4 - - + +
161D HIS* 3.7 13.0 + - - +
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Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C LEU* 3.9 21.3 - - + -
137C LEU* 4.0 19.3 - - + -
147C PHE* 3.1 23.1 - - + -
194C GLU 3.2 3.0 + - - -
196C VAL* 3.8 27.8 - - + -
208C VAL* 3.8 28.3 - - + +
209C ASP 3.0 3.5 + - - +
210C ARG* 1.3 77.8 - - - +
212C SER* 1.3 54.6 + - - +
160D PRO* 4.3 8.3 - - + +
161D HIS* 2.8 31.1 - - - +
164D SER* 3.4 25.6 - - - +
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Residues in contact with SER 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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180A LYS* 5.4 1.3 + - - -
146C ARG 4.2 3.1 + - - -
147C PHE* 3.9 7.2 - - - -
148C ARG* 3.0 38.9 + - - +
193C TYR* 3.2 5.3 - - - -
194C GLU* 2.8 44.7 + - - +
196C VAL* 3.7 22.2 - - - -
210C ARG 3.6 0.2 - - - -
211C LEU* 1.3 77.2 - - - +
213C ALA* 1.3 62.6 + - - +
161D HIS* 4.2 1.3 - - - -
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Residues in contact with ALA 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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125C LEU* 3.7 16.3 - - + +
148C ARG* 3.0 43.2 + - - +
149C PHE* 4.0 5.2 - - - -
150C CYS* 4.1 4.0 - - - -
190C PRO* 3.8 31.0 - - + -
192C ARG 3.5 6.7 - - - -
193C TYR* 4.4 3.1 - - - +
194C GLU* 4.7 0.5 - - - +
212C SER* 1.3 75.4 + - - +
214C THR* 1.3 63.2 + - - +
215C ALA 4.3 1.1 - - - +
161D HIS* 3.9 4.3 - - - +
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Residues in contact with THR 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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125C LEU* 3.7 20.0 - - - +
148C ARG* 5.4 1.3 - - - +
192C ARG* 3.0 49.3 + - - +
193C TYR 3.8 2.8 + - - +
194C GLU* 3.3 50.9 - - + +
213C ALA* 1.3 73.2 - - - +
215C ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 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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125C LEU* 4.0 4.6 - - - +
150C CYS* 3.7 0.9 - - - -
190C PRO* 3.3 9.2 - - - +
191C THR* 2.9 34.6 + - - +
192C ARG* 3.5 35.5 + - + +
213C ALA* 3.8 0.9 - - - +
214C THR* 1.3 78.8 + - - +
216C CYS* 1.3 66.7 + - - +
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Residues in contact with CYS 216 (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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123C CYS* 4.2 11.0 - - - -
124C ARG* 4.1 11.7 - - - -
125C LEU* 3.5 29.1 - - + +
150C CYS* 2.0 55.4 - - + -
189C ARG 3.4 4.5 - - - -
191C THR* 4.0 8.8 + - - +
215C ALA* 1.3 75.3 - - - +
217C GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 217 (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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123C CYS* 3.6 6.7 - - - -
187C CYS 3.2 2.6 - - - +
188C CYS* 3.3 4.2 - - - -
189C ARG 2.8 33.8 + - - +
191C THR* 3.8 5.7 - - - +
216C CYS* 1.3 75.1 - - - +
218C CYS* 1.3 62.1 - - - -
219C LEU* 3.4 17.6 + - - +
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Residues in contact with CYS 218 (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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123C CYS* 3.6 16.2 - - - -
153C SER 4.2 0.7 - - - -
154C CYS* 2.1 57.4 - - + -
157C ALA* 4.3 14.2 - - + +
186C PRO* 3.7 11.5 - - + +
187C CYS 3.6 0.2 - - - -
217C GLY* 1.3 70.0 - - - -
219C LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 219 (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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186C PRO* 3.6 9.2 - - - +
187C CYS* 2.8 46.8 + - - +
189C ARG* 4.0 16.2 - - + -
190C PRO 3.9 21.8 - - - +
191C THR* 3.8 15.5 - - + -
217C GLY* 3.8 27.1 - - - +
218C CYS* 1.3 77.7 - - - +
187D CYS* 3.8 5.0 - - - -
189D ARG* 4.7 4.3 - - - +
219D LEU* 5.1 26.0 - - + -
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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