Contacts of the helix formed by residues 191 - 204 (chain D) in PDB entry 1URP
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 ASP 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D ASN* 1.3 70.9 - - - +
192D GLU* 1.3 57.7 + - - +
194D ALA* 3.1 5.6 + - - -
195D LEU* 2.7 44.7 + - + +
213D GLY* 3.7 3.1 - - - -
214D PHE 2.9 23.3 + - - +
215D ASP* 4.6 1.0 + - - -
216D GLY* 3.0 9.5 + - - -
217D THR* 2.9 51.1 + - + +
220D GLY* 3.8 17.4 - - - +
229D LEU* 4.4 2.6 - - + +
232D THR* 2.6 24.6 + - - -
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Residues in contact with GLU 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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164D PHE 3.7 17.9 - - - +
165D ASP* 5.2 0.4 - - - -
166D ARG* 3.1 61.6 + - - +
190D ASN* 3.3 13.1 + - - +
191D ASP* 1.3 78.2 - - - +
193D MET* 1.3 58.1 + - - +
195D LEU* 3.7 6.3 - - - +
196D GLY 2.8 25.8 + - - -
217D THR* 5.2 4.2 + - - +
219D ASP* 4.7 4.2 - - - +
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Residues in contact with MET 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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129D LEU* 3.6 19.4 - - + +
130D GLN 3.1 26.9 - - - +
131D GLY 3.8 0.4 - - - +
162D ALA* 3.3 17.9 - - + -
164D PHE* 3.2 33.0 - - + -
165D ASP 3.4 27.6 - - - +
169D GLY* 4.2 3.0 - - - -
188D ALA* 3.9 9.0 - - + -
189D GLN* 3.5 25.1 - - + +
190D ASN* 2.7 25.7 + - - +
192D GLU* 1.3 72.1 - - - +
194D ALA* 1.3 52.0 + - - +
196D GLY* 3.2 0.9 + - - -
197D ALA* 2.7 36.0 + - - +
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Residues in contact with ALA 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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188D ALA* 3.4 12.9 - - + +
190D ASN 3.0 14.9 + - - +
191D ASP* 3.1 9.4 + - - +
193D MET* 1.3 75.3 - - - +
195D LEU* 1.3 53.7 + - - +
197D ALA* 3.2 4.0 + - - +
198D LEU* 2.8 37.8 + - - +
211D VAL* 3.8 16.1 - - + +
213D GLY* 3.7 24.7 - - - -
229D LEU* 4.1 10.3 - - + -
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Residues in contact with LEU 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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166D ARG* 3.9 32.5 - - - +
191D ASP* 2.7 28.2 + - + +
192D GLU* 3.7 6.1 - - - +
194D ALA* 1.3 69.9 - - + +
196D GLY* 1.3 66.3 + - - +
198D LEU* 3.0 17.1 + - + +
199D ARG* 2.9 23.6 + - - +
219D ASP* 3.8 34.5 - - + +
220D GLY* 4.2 5.6 - - - +
223D ALA* 3.6 30.3 - - + -
228D LYS* 5.5 3.1 - - - +
229D LEU* 4.8 3.6 - - + -
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Residues in contact with GLY 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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166D ARG* 3.4 34.2 - - - +
170D LEU* 3.4 19.2 - - - -
192D GLU 2.8 10.5 + - - -
193D MET 3.6 3.4 - - - -
195D LEU* 1.3 77.8 - - - +
197D ALA* 1.3 60.4 + - - +
199D ARG* 3.2 7.3 + - - +
200D ALA 3.0 18.0 + - - -
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Residues in contact with ALA 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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129D LEU* 3.7 16.4 - - + -
169D GLY 4.0 2.0 + - - -
173D MET* 3.7 31.1 - - + +
186D VAL* 4.6 8.3 - - + -
193D MET 2.7 19.8 + - - +
194D ALA* 3.5 7.9 - - - +
196D GLY* 1.3 71.1 - - - +
198D LEU* 1.3 56.9 + - - +
200D ALA* 3.3 2.8 + - - +
201D LEU* 3.0 36.8 + - + +
211D VAL* 4.7 4.0 - - + -
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Residues in contact with LEU 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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194D ALA 2.8 17.0 + - - +
195D LEU* 3.0 25.5 + - + +
197D ALA* 1.3 69.0 - - - +
199D ARG* 1.3 61.2 + - - +
201D LEU* 3.3 8.1 + - + +
202D GLN* 2.9 31.9 + - - +
207D SER* 6.3 4.0 - - - -
209D VAL 5.5 2.2 - - - +
211D VAL* 3.8 25.1 - - + +
223D ALA* 4.7 0.7 - - + -
228D LYS* 3.5 33.7 - - + +
229D LEU* 3.8 34.3 - - + +
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Residues in contact with ARG 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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166D ARG* 6.3 1.1 - - - -
170D LEU* 4.1 22.7 - - + -
195D LEU 2.9 11.1 + - - +
196D GLY* 3.4 11.2 - - - +
198D LEU* 1.3 76.2 - - - +
200D ALA* 1.3 62.7 + - - +
202D GLN* 3.3 28.2 + - - +
203D THR* 3.1 41.0 + - - -
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Residues in contact with ALA 200 (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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170D LEU* 3.4 38.7 - - + +
173D MET* 3.8 14.4 - - + -
174D GLN* 3.9 20.1 + - - +
177D LEU* 4.1 3.9 - - + +
196D GLY 3.0 8.7 + - - +
197D ALA 3.5 8.5 - - - +
198D LEU 3.3 0.2 - - - -
199D ARG* 1.3 76.9 - - - +
201D LEU* 1.3 60.6 + - - +
203D THR* 3.4 4.0 + - - -
204D ALA* 3.3 21.1 + - - +
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Residues in contact with LEU 201 (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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173D MET* 4.4 10.5 - - + -
177D LEU* 3.8 27.4 - - + -
183D VAL* 5.3 0.2 - - + -
186D VAL* 4.5 8.3 - - + -
197D ALA* 3.0 23.8 + - + +
198D LEU* 3.8 6.5 - - + +
200D ALA* 1.3 73.4 - - - +
202D GLN* 1.3 65.1 + - - +
204D ALA 3.3 1.7 + - - -
205D GLY 3.1 4.7 + - - -
206D LYS* 2.8 60.0 + - + +
207D SER* 5.1 1.6 - - - -
209D VAL* 3.7 30.5 - - + +
211D VAL* 3.5 30.3 - - + -
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Residues in contact with GLN 202 (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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198D LEU 2.9 17.7 + - - +
199D ARG* 3.3 31.2 + - - +
201D LEU* 1.3 76.0 - - - +
203D THR* 1.3 62.7 + - - +
205D GLY* 3.1 14.4 + - - -
207D SER* 4.8 19.4 + - - +
228D LYS* 5.9 3.1 - - - +
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Residues in contact with THR 203 (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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170D LEU* 5.7 0.3 - - - +
174D GLN* 4.0 19.7 + - - +
199D ARG* 3.1 26.7 + - - -
200D ALA 3.6 9.4 - - - -
202D GLN* 1.3 79.9 - - - +
204D ALA* 1.3 56.7 + - - +
205D GLY 3.3 0.6 + - - -
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Residues in contact with ALA 204 (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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174D GLN* 6.3 1.3 - - + +
177D LEU* 3.8 28.9 - - + -
200D ALA 3.3 7.7 + - - +
201D LEU 3.3 2.8 + - - +
203D THR* 1.3 76.5 - - + +
205D GLY* 1.3 62.0 + - - +
206D LYS* 4.3 9.2 - - + +
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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