Contacts of the strand formed by residues 173 - 181 (chain D) in PDB entry 1WOH
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 LEU 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D LEU* 4.2 13.5 - - + -
137D LEU* 3.5 24.2 - - + +
139D VAL* 4.2 10.3 - - + -
166D ALA* 3.9 29.4 - - + -
167D CYS* 4.1 24.9 - - - +
170D LEU* 2.9 28.6 + - + +
171D PRO 4.1 2.8 - - - +
172D ASN* 1.3 76.4 - - - +
174D VAL* 1.3 61.8 + - - +
175D HIS* 3.9 12.1 - - - +
176D ILE* 3.8 28.9 - - + -
197D ARG* 4.6 8.0 + - - -
199D HIS* 5.3 0.9 - - - -
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Residues in contact with VAL 174 (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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136D ASP* 3.8 28.3 - - + +
137D LEU 3.1 3.8 + - - +
138D HIS* 3.6 30.5 - - + +
171D PRO 3.8 13.0 - - - +
172D ASN* 3.1 13.9 + - - +
173D LEU* 1.3 75.0 - - - +
175D HIS* 1.3 64.0 + - + +
197D ARG 4.4 8.3 - - - +
199D HIS* 4.4 8.7 - - - -
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Residues in contact with HIS 175 (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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137D LEU 3.6 1.2 + - - -
138D HIS* 3.3 36.7 + + + +
139D VAL 2.9 23.9 + - - -
173D LEU* 3.5 5.3 + - - +
174D VAL* 1.3 85.9 - - + +
176D ILE* 1.3 72.9 + - - +
177D THR* 3.0 27.7 + - - -
197D ARG 5.3 0.2 - - - -
198D GLY 3.1 26.2 + - - -
199D HIS* 3.9 7.9 - - - -
200D THR* 2.9 27.0 + - - -
217D GLN 6.0 0.7 - - - -
219D PRO* 5.9 1.3 - - + +
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Residues in contact with ILE 176 (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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139D VAL* 3.4 20.9 - - + +
141D GLN* 3.6 23.3 - - - +
148D PHE* 4.4 2.5 - - + -
163D PHE* 3.9 34.1 - - + +
167D CYS* 3.9 13.5 - - - -
173D LEU* 3.8 15.0 - - + -
175D HIS* 1.3 84.1 - - - +
177D THR* 1.3 65.1 - - - +
178D THR* 3.6 9.1 + - - +
199D HIS* 3.4 37.5 + - + +
200D THR 2.8 26.5 + - - +
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Residues in contact with THR 177 (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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139D VAL 2.9 10.9 + - - -
140D VAL* 3.6 4.5 - - - -
141D GLN 2.9 25.3 + - - +
175D HIS* 3.0 24.6 + - - -
176D ILE* 1.3 70.5 - - - +
178D THR* 1.3 61.3 + - - +
179D VAL* 4.0 9.8 + - + +
200D THR* 3.3 13.7 - - + -
202D ILE* 3.9 27.6 - - + -
217D GLN 4.7 7.4 + - - +
218D LEU* 4.3 13.9 - - + -
219D PRO* 4.3 16.4 - - + +
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Residues in contact with THR 178 (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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141D GLN* 2.6 46.9 + - + +
143D ASP* 4.3 4.3 - - + +
145D HIS 4.3 0.4 - - - +
146D LEU* 4.1 18.1 - - + +
176D ILE* 3.6 9.0 - - - +
177D THR* 1.3 69.6 - - - +
179D VAL* 1.3 61.7 + - - +
181D LEU* 3.7 33.0 - - + +
199D HIS* 6.1 0.3 - - - +
200D THR 2.8 12.7 + - - -
201D ILE* 3.9 1.2 - - - +
202D ILE* 2.7 34.9 + - - +
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Residues in contact with VAL 179 (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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140D VAL* 5.4 2.0 - - + -
141D GLN 2.8 9.6 + - - +
142D LEU* 3.5 18.5 - - + +
143D ASP 3.1 23.8 + - - -
177D THR* 4.1 13.0 - - + +
178D THR* 1.3 80.7 - - - +
180D GLY* 1.3 63.4 + - - +
181D LEU 3.6 1.3 - - - -
202D ILE* 3.3 30.3 - - + -
207D VAL* 3.5 27.4 - - + -
214D VAL* 4.1 5.6 - - + -
218D LEU* 4.7 10.1 - - + -
249D LEU* 4.6 3.4 - - + +
257D ILE* 3.6 23.1 - - + -
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Residues in contact with GLY 180 (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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143D ASP 3.1 10.1 - - - +
144D ALA* 3.6 0.2 - - - -
179D VAL* 1.3 78.5 - - - +
181D LEU* 1.3 67.7 + - - +
182D ARG* 2.9 29.1 + - - +
202D ILE 2.9 8.0 + - - -
204D MET* 3.7 25.9 - - - +
232D GLY 5.3 0.2 - - - -
249D LEU* 4.9 7.6 - - - -
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Residues in contact with LEU 181 (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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143D ASP 3.3 9.8 + - - +
144D ALA 3.3 2.2 - - - +
145D HIS* 3.1 42.8 - - - +
146D LEU* 3.3 19.3 - - + +
178D THR* 3.7 17.3 - - + -
180D GLY* 1.3 76.3 - - - +
182D ARG* 1.3 58.9 + - - +
186D PHE* 3.9 25.1 - - + -
201D ILE* 3.3 33.2 - - + -
202D ILE 3.7 6.0 + - - +
203D PRO* 3.4 17.0 - - + +
204D MET* 2.8 24.3 + - - +
205D ASP* 5.5 1.0 - - - +
69F LEU* 4.9 0.7 - - + -
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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