Contacts of the strand formed by residues 174 - 186 (chain B) in PDB entry 2H11
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 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B LYS* 3.4 20.7 + - - -
146B PHE 3.8 6.1 - - - +
148B MET 5.5 0.7 - - - -
149B ILE* 3.4 33.7 - - + +
170B MET 3.3 17.0 - - - +
171B PHE* 3.2 34.3 + - + +
173B LEU* 1.3 79.6 - - - +
175B GLY* 1.3 70.0 + - - +
178B PHE* 4.0 45.3 - - + -
179B GLN 5.6 0.2 - - - +
180B TYR* 4.2 16.4 - - + -
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LYS* 4.4 14.8 - - - -
146B PHE 3.1 20.0 + - - +
147B ASP* 5.9 0.2 - - - -
173B LEU 4.0 0.2 + - - -
174B LEU* 1.3 78.3 - - - +
176B LYS* 1.3 66.7 + - - -
177B LYS 3.3 7.5 + - - -
178B PHE* 3.3 16.5 - - - +
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B GLY* 1.3 72.7 - - - +
177B LYS* 1.3 65.4 + - + +
178B PHE* 4.1 2.1 - - - -
244B GLU* 3.7 21.1 - - - +
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Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ASP* 4.3 12.6 - - - +
175B GLY* 3.9 8.0 - - - +
176B LYS* 1.3 83.4 - - + +
178B PHE* 1.3 65.1 + - - +
244B GLU* 3.2 26.7 - - + +
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Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B PHE 4.4 2.2 - - - +
147B ASP 3.3 14.4 - - - +
171B PHE* 5.7 0.2 - + - -
174B LEU* 4.0 42.4 - - + -
175B GLY 3.3 21.5 - - - +
176B LYS 4.1 3.4 - - - -
177B LYS* 1.3 75.1 - - - +
179B GLN* 1.3 68.3 + - - +
180B TYR* 4.1 9.9 - - + -
211B ILE* 4.5 12.8 - - + -
212B CYS* 3.8 24.9 - - - -
242B LEU 3.8 11.0 - - - -
243B THR* 3.4 31.7 - - - +
244B GLU* 2.9 42.1 + - + +
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Residues in contact with GLN 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 3.2 34.0 + - - +
60B LYS* 3.7 28.6 + - - +
63B LEU* 4.9 1.0 - - - +
147B ASP 3.1 8.6 + - - +
148B MET* 3.1 42.0 - - + +
149B ILE 3.0 22.7 + - - -
174B LEU* 5.8 0.2 - - - -
178B PHE* 1.3 80.6 - - - +
180B TYR* 1.3 63.1 + - - +
181B LEU* 3.8 3.1 - - + -
241B LEU* 4.0 16.1 - - + +
242B LEU 3.6 4.7 - - - -
243B THR* 4.3 9.8 - - + +
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ILE* 3.9 30.3 - - + -
151B ASP* 2.5 44.6 + - + -
166B TYR* 3.7 5.0 + - - -
170B MET* 3.6 36.5 - - + +
171B PHE* 5.9 0.9 - + - -
174B LEU* 4.2 14.4 - - + -
178B PHE* 4.1 10.3 - + + -
179B GLN* 1.3 72.6 - - - +
181B LEU* 1.3 67.1 + - - +
182B LEU* 3.7 17.1 + - + +
208B PHE* 4.1 22.3 - + - -
212B CYS* 6.1 0.7 - - - -
240B TYR 3.7 1.0 - - - +
241B LEU* 3.6 1.7 - - - -
242B LEU* 2.8 59.7 + - + +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 4.4 4.9 - - + -
56B PHE* 3.5 53.6 - - + -
79B PHE* 5.1 2.2 - - + -
148B MET* 4.1 22.9 - - + -
149B ILE 2.9 15.9 + - - +
150B TRP* 3.7 28.7 - - + -
151B ASP* 2.8 31.0 + - - +
179B GLN* 4.7 5.8 - - + +
180B TYR* 1.3 71.9 - - - +
182B LEU* 1.3 59.2 + - - +
239B LEU* 4.7 2.9 - - + -
240B TYR 3.5 8.3 - - - +
241B LEU* 3.6 24.0 - - + -
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ASP* 3.5 31.4 - - - +
155B LEU* 3.7 21.8 - - + -
180B TYR* 3.7 13.7 + - + +
181B LEU* 1.3 75.4 - - - +
183B CYS* 1.3 75.2 + - - +
184B VAL* 3.9 7.6 - - + -
204B ILE* 3.5 37.7 - - + -
208B PHE* 4.3 11.0 - - + -
238B LYS 3.5 1.2 - - - +
239B LEU* 3.4 3.4 - - - +
240B TYR* 2.7 52.4 + - + +
242B LEU* 4.6 8.5 - - + -
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Residues in contact with CYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B HIS* 3.7 18.6 - - - -
150B TRP* 3.3 38.1 - - - -
151B ASP* 2.8 14.2 + - - +
152B ARG* 3.7 23.6 - - + -
153B GLY 4.6 2.3 + - - -
156B VAL* 4.1 8.7 + - - +
182B LEU* 1.3 74.5 - - - +
184B VAL* 1.3 68.9 + - - +
185B LEU* 6.0 0.2 - - - -
237B GLU* 4.3 8.7 - - + +
238B LYS 3.3 6.5 - - - +
239B LEU* 3.7 16.6 - - - -
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 4.4 1.3 - - + -
156B VAL* 3.9 17.9 - - + -
182B LEU* 3.9 23.5 - - + -
183B CYS* 1.3 79.1 - - - +
185B LEU* 1.3 67.4 + - - +
186B SER* 6.4 0.2 - - - -
199B VAL* 4.1 24.0 - - + +
204B ILE* 4.1 15.5 - - + -
237B GLU* 3.5 5.1 - - - +
238B LYS* 2.9 44.3 + - + +
240B TYR* 3.8 27.4 - - + -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B VAL* 4.2 11.3 - - + +
184B VAL* 1.3 84.6 - - - +
186B SER* 1.3 61.4 + - - +
187B TYR* 4.1 11.0 - - + -
196B PRO* 3.4 35.7 - - + -
197B PHE 4.8 3.3 - - - +
198B TYR* 3.6 19.4 - - - -
199B VAL 4.3 7.6 + - - +
222B ALA* 5.1 2.0 - - + -
227B HIS* 5.9 0.2 - - - +
230B TRP* 4.1 15.5 - - + -
235B LEU* 4.1 22.7 - - + -
236B PHE 3.5 9.6 - - - +
237B GLU* 4.2 22.7 - - + +
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B VAL* 6.4 0.2 - - - -
185B LEU* 1.3 73.8 - - - +
187B TYR* 1.3 64.2 + - - +
198B TYR* 4.0 14.1 + - - -
219B LYS* 5.3 3.7 + - - -
234B CYS* 4.7 1.2 - - - -
235B LEU* 3.6 3.9 - - - +
236B PHE* 2.7 49.8 + - - +
238B LYS* 4.7 22.3 + - - -
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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