Contacts of the strand formed by residues 187 - 199 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C VAL* 4.2 17.5 - - + -
187C CYS* 2.1 50.1 - - + -
219C LEU 3.8 7.0 - - - -
154D CYS* 4.0 2.2 - - - -
183D VAL* 5.9 2.5 - - + -
185D GLN 3.6 1.4 + - - -
186D PRO* 1.3 73.2 - - - +
188D CYS* 1.3 63.8 + - - +
189D ARG* 3.3 33.4 + - + +
217D GLY 3.5 0.2 - - - +
219D LEU 3.0 33.3 + - - -
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Residues in contact with CYS 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C VAL* 4.0 10.2 + - - +
123D CYS* 2.1 49.4 - - + -
124D ARG 3.7 3.1 - - - -
150D CYS* 3.8 18.9 - - - +
151D SER* 3.4 24.2 - - - -
152D GLY 3.5 26.7 + - - +
154D CYS* 3.9 4.5 - - - -
186D PRO 4.1 0.2 + - - -
187D CYS* 1.3 69.9 - - - +
189D ARG* 1.3 67.2 + - - +
190D PRO* 4.9 0.2 - - - +
216D CYS* 4.3 1.6 - - - -
217D GLY 3.5 4.3 - - - -
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Residues in contact with ARG 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C SER* 5.0 1.2 + - - -
161C HIS* 5.2 0.8 + - - -
162C ASP* 2.8 43.8 + - - -
165C LEU* 5.4 1.0 - - - +
183C VAL* 3.6 26.6 + - - -
185C GLN 3.6 22.5 + - - +
186C PRO* 3.7 19.2 - - - +
219C LEU 4.7 3.7 + - - +
150D CYS* 3.7 6.1 - - - -
187D CYS* 3.3 30.9 + - - +
188D CYS* 1.3 80.3 - - - +
190D PRO* 1.4 82.1 - - + +
193D TYR* 5.3 4.4 + - - -
216D CYS* 3.3 0.7 - - - -
217D GLY 2.9 32.6 + - - +
219D LEU* 3.8 26.7 - - + +
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Residues in contact with PRO 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C HIS* 3.5 33.7 - - + +
150D CYS* 3.5 12.8 - - + -
189D ARG* 1.4 111.1 - - + +
191D THR* 1.3 60.8 + - - +
192D ARG 4.2 1.8 - - - +
193D TYR* 3.7 31.9 + - + +
213D ALA* 3.7 15.9 - - + -
215D ALA 3.3 8.3 - - - +
219D LEU* 4.3 6.4 - - - +
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Residues in contact with THR 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D PRO* 1.3 78.6 - - - +
192D ARG* 1.3 73.8 + - - +
193D TYR* 4.7 6.4 - - - -
215D ALA* 2.9 30.3 + - - +
216D CYS 3.7 4.1 + - - +
217D GLY* 3.9 12.3 - - - +
219D LEU* 3.9 27.4 - - + -
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Residues in contact with ARG 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D PRO* 3.7 0.6 - - - +
191D THR* 1.3 91.4 + - - +
193D TYR* 1.3 72.4 + - - +
213D ALA* 3.6 4.7 - - - -
214D THR* 3.0 33.4 + - - +
215D ALA* 3.6 28.5 + - + +
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Residues in contact with TYR 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C SER* 4.4 11.8 + - - -
161C HIS* 3.5 29.2 - + + -
162C ASP* 5.6 0.5 + - - -
189D ARG* 5.3 4.5 + - - -
190D PRO* 3.7 36.7 + - + +
191D THR 4.7 3.4 - - - -
192D ARG* 1.3 86.3 - - - +
194D GLU* 1.3 61.6 + - - +
210D ARG* 3.5 59.9 - - + +
212D SER 3.0 16.2 - - - +
213D ALA* 4.3 0.9 - - - -
214D THR* 3.9 7.9 + - - +
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Residues in contact with GLU 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LYS* 5.3 11.3 + - - +
148D ARG* 3.4 25.2 + - - -
193D TYR* 1.3 74.6 - - - +
195D ALA* 1.3 70.3 + - - +
210D ARG* 3.9 6.3 - - - +
211D LEU 3.2 4.0 + - - -
212D SER* 2.6 45.6 + - - +
213D ALA 4.5 2.1 - - - +
214D THR* 3.4 24.6 - - + +
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Residues in contact with ALA 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LYS* 4.7 9.9 - - - +
184B GLU* 3.8 30.2 + - + +
194D GLU* 1.3 88.8 - - - +
196D VAL* 1.3 65.9 + - - +
197D SER* 4.9 1.8 - - - +
207D THR* 3.8 13.0 - - - +
208D VAL 3.2 15.7 - - - +
209D ASP* 3.8 12.6 - - - +
210D ARG 3.9 4.0 - - - +
212D SER* 4.8 0.3 - - - -
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Residues in contact with VAL 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LYS* 5.5 3.1 - - - -
135D LEU* 4.4 3.6 - - + -
145D VAL* 4.0 32.3 - - + -
146D ARG 4.5 10.8 - - - +
147D PHE* 4.7 6.7 - - + -
195D ALA* 1.3 75.9 - - - +
197D SER* 1.3 63.6 + - - +
198D PHE* 4.2 13.3 - - + -
207D THR* 3.2 2.3 - - - -
208D VAL* 2.7 33.8 + - + +
211D LEU* 3.8 31.9 - - + -
212D SER* 3.8 24.0 - - - -
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Residues in contact with SER 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ARG* 5.0 4.0 + - - -
180B LYS* 3.8 26.3 + - - +
183B GLY 4.2 4.7 - - - -
184B GLU* 3.5 30.0 + - - +
143D GLU* 4.9 0.5 - - - +
145D VAL* 3.8 12.6 - - - +
195D ALA* 4.9 1.4 - - - +
196D VAL* 1.3 76.1 + - - +
198D PHE* 1.3 67.2 + - - +
205D TRP* 4.1 9.8 - - - -
206D ARG 3.2 11.0 - - - -
207D THR* 3.5 17.0 + - - -
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Residues in contact with PHE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ARG* 5.2 0.2 - - - +
132D VAL* 3.7 36.3 - - + -
137D LEU* 3.8 27.6 - - + -
139D HIS* 4.2 22.0 - - + -
141D SER* 3.6 21.8 - - - -
143D GLU* 3.6 16.8 - - - +
145D VAL* 4.1 2.7 - - + -
196D VAL* 4.2 13.0 - - + -
197D SER* 1.3 82.0 - - - +
199D MET* 1.3 64.2 + - - +
200D ASP* 4.4 2.9 - - + -
205D TRP* 3.4 13.4 - - - -
206D ARG* 2.8 61.7 + - + +
208D VAL* 4.7 10.1 - - + -
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Residues in contact with MET 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ARG* 4.2 1.8 - - - +
230B ARG* 3.8 38.1 + - + +
233B ASN* 3.5 31.6 - - + +
234B THR* 4.2 13.2 - - - -
141D SER* 2.8 19.4 + - - -
142D ASP 5.0 0.3 + - - -
143D GLU* 3.4 21.1 + - - +
198D PHE* 1.3 74.7 - - - +
200D ASP* 1.3 65.6 + - - +
203D SER* 3.5 27.4 - - - +
204D THR 3.4 5.8 - - - +
205D TRP* 3.4 40.4 - - + +
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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