Contacts of the strand formed by residues 191 - 199 (chain D) in PDB entry 1WUR
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 ARG 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D GLU* 2.7 35.3 + - + +
175D GLY 3.4 14.8 - - - +
176D VAL* 4.0 13.0 - - + +
177D HIS* 6.0 0.2 - - - -
189D HIS 4.9 8.5 + - - +
190D SER* 1.3 77.6 + - - +
192D THR* 1.3 62.7 + - - +
99E VAL* 3.8 0.5 - - - -
100E LYS* 3.0 61.4 + - + +
118E LYS* 6.1 0.8 - - - +
216E ARG 5.6 3.8 + - - -
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Residues in contact with THR 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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149D GLN* 2.8 36.0 + - + +
174D GLU* 3.2 2.9 - - - -
175D GLY 2.8 27.1 + - - -
177D HIS* 4.2 3.1 - - - -
180D MET* 5.2 2.8 - - - -
190D SER* 4.9 0.7 + - - -
191D ARG* 1.3 76.1 + - - +
193D VAL* 1.3 70.3 + - - +
194D THR* 4.1 8.7 - - + -
97E VAL* 4.3 4.9 - - + -
98E VAL 3.3 9.2 - - - +
99E VAL* 3.9 14.6 - - + +
132E LEU* 3.5 39.7 - - + +
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Residues in contact with VAL 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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172D VAL* 4.0 23.8 - - + -
173D VAL 3.3 2.9 - - - -
174D GLU* 3.6 33.0 - - + +
192D THR* 1.3 76.3 - - - +
194D THR* 1.3 71.6 + - - +
195D SER* 5.4 2.2 - - - +
96E MET 4.1 1.7 - - - +
97E VAL* 3.6 2.1 - - - -
98E VAL* 2.8 48.7 + - + +
100E LYS* 3.9 18.6 - - - +
214E HIS* 4.1 25.8 - - + +
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Residues in contact with THR 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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149D GLN* 3.0 43.8 + - + +
150D GLU* 3.8 39.9 - - + +
153D ALA* 3.8 3.1 - - - +
172D VAL* 3.5 3.6 - - - +
173D VAL* 2.8 36.2 + - - +
192D THR* 4.1 7.6 - - + -
193D VAL* 1.3 80.1 - - - +
195D SER* 1.3 65.2 + - - +
96E MET 4.3 6.5 - - - -
97E VAL* 4.4 5.6 - - + -
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Residues in contact with SER 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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150D GLU 5.1 1.0 - - - +
153D ALA* 3.9 9.3 - - - +
154D VAL* 4.8 5.9 - - - +
171D VAL 3.0 15.3 - - - -
172D VAL* 4.1 9.4 - - - -
193D VAL* 5.4 2.4 - - - +
194D THR* 1.3 79.5 - - - +
196D ALA* 1.3 63.0 + - - +
197D MET* 4.1 16.5 - - - +
212D LEU* 6.2 0.2 - - - -
93E GLY* 6.1 0.7 - - - -
95E GLU* 3.2 35.2 + - - +
96E MET* 4.0 10.4 + - - +
210E GLU* 5.7 0.7 + - - -
214E HIS* 5.6 4.6 + - - -
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Residues in contact with ALA 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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153D ALA 3.6 23.3 - - - +
154D VAL* 3.7 22.9 - - + -
157D ALA* 3.9 12.2 - - + +
169D VAL 3.9 1.0 - - - +
170D GLY* 3.5 2.9 - - - -
171D VAL* 3.0 29.7 + - - +
195D SER* 1.3 77.5 - - - +
197D MET* 1.3 63.6 + - - +
198D LEU* 4.3 4.0 - - + -
95E GLU* 3.6 6.1 - - - -
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Residues in contact with MET 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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169D VAL 3.6 1.3 - - - -
170D GLY* 3.8 13.0 - - - -
171D VAL 4.5 0.2 - - - +
172D VAL* 4.3 6.1 - - + -
195D SER* 4.1 24.0 - - - +
196D ALA* 1.3 80.1 - - - +
198D LEU* 1.3 70.9 + - - +
201D PHE* 3.7 26.0 - - - +
202D ARG* 3.4 22.7 - - - +
208D ARG* 3.8 32.1 - - + +
211D PHE* 4.0 24.0 - - + -
212D LEU* 4.4 6.7 - - + -
95E GLU* 3.5 33.7 - - - +
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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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154D VAL* 6.5 0.7 - - + -
157D ALA* 3.5 45.5 - - + +
158D GLU* 3.9 15.3 - - + +
161D GLN* 3.6 30.1 - - + +
168D GLY* 3.1 1.6 - - - -
169D VAL* 2.8 34.5 + - + +
196D ALA* 5.2 2.7 - - + -
197D MET* 1.3 84.4 - - - +
199D GLY* 1.3 68.7 + - - +
201D PHE 3.3 6.3 + - - -
202D ARG* 4.3 4.3 - - - +
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Residues in contact with GLY 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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161D GLN* 4.3 6.4 - - - +
167D GLN 3.2 12.8 - - - -
168D GLY* 3.9 0.9 - - - -
198D LEU* 1.3 73.3 - - - +
200D VAL* 1.3 59.0 + - - -
202D ARG* 3.0 6.8 + - - +
203D GLU* 3.0 42.4 + - - +
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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