Contacts of the strand formed by residues 205 - 219 (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 TRP 205 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B ARG* 3.5 43.7 - - + -
180B LYS* 5.3 1.1 - - - -
182B TYR* 3.6 28.5 - + - -
183B GLY* 3.4 29.2 - - - +
186B CYS 4.6 3.4 - - - +
187B SER* 3.5 24.5 + - - +
188B GLY 4.0 7.8 + - - -
233B ASN 3.6 15.6 + - - -
234B THR* 3.1 19.2 + - + -
236B ALA* 3.9 18.4 - - + -
197D SER* 4.1 8.1 - - - -
198D PHE* 3.4 41.3 - - - -
199D MET* 3.4 23.0 - - + +
203D SER 5.3 0.4 - - - -
204D THR* 1.3 80.7 - - - +
206D ARG* 1.3 66.5 + - - +
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Residues in contact with ARG 206 (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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187B SER* 3.6 3.6 + - - -
188B GLY* 5.6 7.3 - - - -
189B PRO* 5.6 4.6 - - - +
139D HIS* 3.6 41.9 + - + +
197D SER* 3.2 5.5 - - - -
198D PHE* 2.8 54.7 + - + -
200D ASP* 2.7 37.9 + - + +
202D ASN* 5.9 2.0 - - - +
204D THR* 3.6 29.9 + - - +
205D TRP* 1.3 79.2 + - - +
207D THR* 1.3 61.2 + - - +
208D VAL* 5.7 1.6 - - + -
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Residues in contact with THR 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLU* 4.0 16.9 - - + +
187B SER* 3.1 29.2 - - - -
188B GLY* 5.2 0.4 - - - +
190B HIS* 5.5 7.4 - - - +
195D ALA* 3.8 14.6 - - - +
196D VAL 3.2 6.8 + - - -
197D SER* 3.5 18.9 + - - -
206D ARG* 1.3 74.4 - - - +
208D VAL* 1.3 68.3 + - - +
209D ASP* 4.2 6.8 + - - +
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Residues in contact with VAL 208 (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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160C PRO* 5.4 4.7 - - + -
137D LEU* 4.3 28.9 - - + -
139D HIS* 5.6 7.4 - - + +
195D ALA* 3.2 3.5 - - - -
196D VAL* 2.7 34.1 + - + +
198D PHE* 4.7 8.5 - - + -
206D ARG* 5.7 0.9 - - + -
207D THR* 1.3 77.0 + - - +
209D ASP* 1.3 69.3 + - - +
211D LEU* 3.6 35.4 + - + +
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Residues in contact with ASP 209 (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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184B GLU* 4.2 8.8 - - - +
160C PRO* 4.6 8.1 - - - +
195D ALA* 3.8 16.0 - - + +
207D THR* 4.2 7.8 + - - +
208D VAL* 1.3 79.3 - - - +
210D ARG* 1.3 81.4 + - + +
211D LEU* 2.9 5.9 + - - +
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Residues in contact with ARG 210 (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* 4.1 12.5 - - - -
160C PRO* 4.0 29.1 - - + +
161C HIS* 3.9 11.8 + - - +
193D TYR* 3.5 54.4 - - + +
194D GLU* 3.8 12.9 + - - +
195D ALA* 3.9 1.0 - - - +
209D ASP* 1.3 81.4 - - + +
211D LEU* 1.3 60.4 + - - +
212D SER 3.5 1.8 - - - -
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Residues in contact with LEU 211 (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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160C PRO* 3.4 26.7 - - + +
161C HIS* 2.8 26.2 - - - +
164C SER* 3.2 33.9 - - - +
135D LEU* 4.2 20.0 - - + -
137D LEU* 4.2 16.2 - - + -
147D PHE* 3.2 11.7 - - + -
194D GLU 3.2 2.8 + - - -
196D VAL* 3.8 31.0 - - + -
208D VAL* 3.6 28.7 - - + +
209D ASP 2.9 2.0 + - - -
210D ARG* 1.3 79.9 - - - +
212D SER* 1.3 59.9 + - - +
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Residues in contact with SER 212 (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* 4.2 0.9 - - - -
146D ARG 4.2 2.8 + - - -
147D PHE* 3.8 6.5 - - - -
148D ARG* 2.9 40.3 + - - +
193D TYR* 3.0 5.7 - - - -
194D GLU* 2.6 51.5 + - - +
195D ALA 4.8 0.2 - - - -
196D VAL* 3.8 20.0 - - - -
211D LEU* 1.3 78.5 - - - +
213D ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 213 (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* 3.8 4.5 - - - +
125D LEU* 3.7 18.2 - - + +
148D ARG* 3.0 45.0 + - - +
149D PHE* 4.0 7.4 - - - -
150D CYS* 4.1 1.8 - - - -
190D PRO* 3.7 28.0 - - + -
192D ARG 3.6 6.5 - - - -
193D TYR* 4.3 2.5 - - - -
194D GLU* 4.5 0.5 - - - +
212D SER* 1.3 73.4 + - - +
214D THR* 1.3 63.3 + - - +
215D ALA 4.5 0.4 - - - +
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Residues in contact with THR 214 (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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125D LEU* 3.9 19.0 - - - +
148D ARG* 5.5 0.4 - - - +
192D ARG* 3.0 33.0 + - - +
193D TYR 3.6 3.3 + - - +
194D GLU* 3.4 53.4 - - + +
213D ALA* 1.3 73.7 - - - +
215D ALA* 1.3 62.2 + - - +
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Residues in contact with ALA 215 (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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125D LEU* 4.0 4.9 - - - +
150D CYS* 3.7 1.9 - - - -
190D PRO* 3.3 8.5 - - - +
191D THR* 2.9 36.6 + - - +
192D ARG* 3.6 34.4 + - + +
213D ALA 3.7 0.4 - - - -
214D THR* 1.3 84.0 + - - +
216D CYS* 1.3 64.6 + - - +
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Residues in contact with CYS 216 (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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123D CYS* 4.3 2.9 - - - +
124D ARG* 3.7 5.6 - - - -
125D LEU* 3.5 39.4 - - - +
150D CYS* 2.0 49.6 - - + -
188D CYS* 4.3 6.5 - - - -
189D ARG 3.3 5.4 - - - -
191D THR* 4.0 9.0 + - - +
215D ALA* 1.3 76.6 - - - +
217D GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 217 (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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123D CYS* 3.9 7.2 - - - -
187D CYS 3.5 0.3 - - - +
188D CYS* 3.5 4.2 - - - -
189D ARG 2.9 29.8 + - - -
191D THR* 3.9 4.9 - - - +
216D CYS* 1.3 76.9 - - - +
218D CYS* 1.3 58.9 + - - -
219D LEU* 3.1 17.9 - - - +
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Residues in contact with CYS 218 (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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123D CYS* 3.6 17.0 - - - -
153D SER 4.3 0.2 - - - -
154D CYS* 2.1 58.6 - - + -
186D PRO* 4.0 10.0 - - + +
187D CYS 3.7 0.4 - - - -
217D GLY* 1.3 70.3 - - - -
219D LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 219 (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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187C CYS* 3.9 5.5 - - - -
189C ARG* 5.0 3.7 - - - +
219C LEU* 4.9 24.7 - - + +
186D PRO* 3.2 12.8 - - - +
187D CYS* 3.0 43.6 + - - +
189D ARG* 3.8 30.3 - - + +
190D PRO 4.3 9.4 - - - +
191D THR* 3.9 13.2 - - + -
217D GLY* 3.1 43.3 - - - +
218D CYS* 1.3 75.0 - - - +
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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