Contacts of the strand formed by residues 182 - 187 (chain H) in PDB entry 5PRC
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 TYR 182 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134H ILE* 4.0 19.3 - - + -
171H LEU* 3.5 4.5 - - - +
172H TRP* 2.8 32.3 + - + +
181H ARG* 1.3 96.9 + - + +
183H LEU* 1.3 68.9 + - - +
195H LEU* 3.9 32.3 - - + -
196H ILE 3.1 7.4 - - - +
197H PRO* 3.4 43.3 - - + -
198H LEU* 4.2 4.9 - - - +
230H ILE* 4.8 5.6 - - + -
235H GLU* 2.7 47.6 + - + +
238H VAL* 4.1 12.3 - - + -
239H SER* 3.9 8.6 + - - -
231M ARG* 4.4 2.3 + - - -
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Residues in contact with LEU 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H PRO* 3.7 29.6 - - + -
157H VAL* 5.9 0.2 - - + -
168H VAL* 4.3 11.9 - - + -
170H ASP 3.6 3.4 - - - +
171H LEU* 3.8 16.2 - - + -
172H TRP* 5.0 0.2 - - - -
182H TYR* 1.3 81.9 - - - +
184H GLU* 1.3 62.3 + - - +
185H LEU* 5.6 0.2 - - + -
194H ALA 3.7 0.3 - - - +
195H LEU* 3.1 6.8 - - - -
196H ILE* 2.8 42.7 + - + +
198H LEU* 3.8 25.3 - - + +
201H CYS* 3.9 22.4 - - + -
203H VAL* 5.0 1.6 - - + -
208H ILE* 4.0 28.9 - - + -
10M ILE* 5.0 1.1 - - + -
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Residues in contact with GLU 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H ARG* 2.7 30.4 + - - -
168H VAL* 3.2 7.2 - - - +
169H THR* 2.6 41.2 + - - +
170H ASP* 2.9 15.8 + - + +
172H TRP* 2.8 26.8 + - - +
182H TYR 4.3 0.2 + - - -
183H LEU* 1.3 73.9 - - - +
185H LEU* 1.3 58.7 + - - +
193H THR* 3.2 28.7 + - - +
194H ALA 3.3 5.2 - - - +
195H LEU* 3.4 19.0 - - + +
227H ARG* 3.2 21.0 + - - +
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Residues in contact with LEU 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H VAL* 4.1 17.7 - - + -
165H ALA 4.4 2.0 - - - +
166H GLY* 4.1 20.6 - - - +
167H THR 3.1 18.2 - - - +
168H VAL* 4.4 0.4 - - + -
169H THR* 3.9 3.6 - - - -
183H LEU* 5.6 0.4 - - + -
184H GLU* 1.3 75.5 - - - +
186H SER* 1.3 62.1 + - - +
187H VAL* 3.5 9.1 + - + -
193H THR* 3.1 9.1 - - - -
194H ALA* 2.9 51.2 + - + +
196H ILE* 4.0 23.1 - - + -
218H PHE* 3.4 42.4 - - + -
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Residues in contact with SER 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H GLY* 2.9 25.3 - - - -
167H THR* 2.9 18.4 + - - -
169H THR* 3.3 17.1 - - - +
185H LEU* 1.3 69.2 - - - +
187H VAL* 1.3 69.1 + - - +
188H ALA* 4.6 0.2 - - - -
190H SER 4.6 4.2 + - - -
191H ALA* 5.7 1.0 - - - -
192H ARG 3.9 8.0 + - - -
193H THR* 4.4 4.0 - - - -
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Residues in contact with VAL 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H ALA 3.7 11.0 - - - +
166H GLY* 4.3 0.4 - - - -
185H LEU* 4.3 7.0 - - + +
186H SER* 1.3 76.5 + - - +
188H ALA* 1.3 71.3 + - - +
189H GLY 3.5 0.3 + - - -
190H SER* 3.1 37.2 - - - +
192H ARG* 3.2 44.4 + - + +
194H ALA* 4.1 17.9 - - + +
215H SER 5.7 1.3 - - - +
218H PHE* 4.1 24.5 - - + +
219H ALA* 4.6 6.5 - - + +
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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