Contacts of the strand formed by residues 181 - 191 (chain C) in PDB entry 1P5Q
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 LYS 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C TYR* 3.2 5.3 - - - -
178C TYR* 2.7 43.7 + - + +
179C LYS* 3.0 4.4 + - + +
180C ASP* 1.3 73.7 - - - +
182C LEU* 1.3 76.9 + - - +
183C PHE* 3.5 6.1 + - + +
236C GLN* 3.0 38.1 + - - +
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Residues in contact with LEU 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C GLU* 4.0 12.3 - - + +
176C GLY 3.3 12.8 - - - +
177C TYR* 3.3 37.7 - - + +
180C ASP 4.0 0.4 + - - -
181C LYS* 1.3 87.9 - - - +
183C PHE* 1.3 60.1 - - - +
184C ASP 3.8 18.4 - - - +
185C GLN* 4.2 24.2 - - + +
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Residues in contact with PHE 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C GLY* 3.0 40.4 + - - -
177C TYR 3.3 2.9 - - - -
178C TYR* 3.6 15.0 - - + -
181C LYS* 3.5 5.6 + - + +
182C LEU* 1.3 74.7 - - - +
184C ASP* 1.3 72.5 + - + +
227C PHE* 4.8 2.2 - + - -
235C PHE* 3.2 69.0 - + + +
236C GLN* 6.0 1.3 - - + -
237C ILE* 3.9 11.9 - - + -
243C LEU* 3.2 34.5 - - + -
245C TYR* 3.8 19.5 - + - -
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Residues in contact with ASP 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C LEU* 3.9 13.7 - - - +
175C GLU* 3.3 4.3 - - - -
176C GLY* 2.8 32.7 + - - +
182C LEU* 3.8 4.5 - - - +
183C PHE* 1.3 102.3 - - + +
185C GLN* 1.3 64.2 + - - +
186C ARG* 2.9 47.9 + - - +
199C ASP 4.4 0.2 - - - +
200C LEU* 4.3 5.5 - - - +
235C PHE* 3.6 18.8 - - + -
245C TYR* 4.8 3.2 - - + -
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Residues in contact with GLN 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C LEU 3.5 8.5 - - - +
175C GLU* 4.4 15.0 + - + +
182C LEU* 4.2 24.1 - - + +
184C ASP* 1.3 76.3 + - - +
186C ARG* 1.3 75.9 + - - +
187C GLU* 6.4 0.2 - - - +
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Residues in contact with ARG 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C VAL 4.1 0.5 - - - +
173C ALA* 3.5 0.3 - - - -
174C LEU* 2.7 49.2 + - + +
184C ASP* 2.9 36.3 + - - +
185C GLN* 1.3 87.5 - - - +
187C GLU* 1.3 63.1 + - - +
188C LEU* 3.6 30.8 + - + +
198C LEU* 3.0 32.7 + - - +
199C ASP* 4.2 9.2 + - - +
200C LEU* 3.7 12.2 - - - +
235C PHE* 4.5 2.8 - - - -
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Residues in contact with GLU 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C VAL 3.3 8.3 - - - +
173C ALA* 3.9 16.2 - - + +
185C GLN* 6.4 0.2 - - - +
186C ARG* 1.3 74.1 - - - +
188C LEU* 1.3 61.3 + - - +
250C LYS* 2.8 33.4 + - + +
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C GLU* 3.6 5.5 - - - +
172C VAL* 2.8 56.7 + - + +
174C LEU* 4.5 13.2 - - + -
186C ARG* 3.6 38.1 - - + +
187C GLU* 1.3 77.9 - - - +
189C ARG* 1.3 67.4 + - - +
190C PHE* 3.9 16.6 - - + -
198C LEU* 4.2 25.6 - - + -
200C LEU* 4.9 4.0 - - + -
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Residues in contact with ARG 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ILE* 4.0 19.5 - - + -
170C VAL 3.4 15.9 - - - +
171C GLU* 2.9 38.1 + - + -
188C LEU* 1.3 80.5 - - - +
190C PHE* 1.3 63.0 + - - +
198C LEU* 5.0 2.1 - - - +
251C SER* 5.8 0.2 - - - -
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Residues in contact with PHE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ALA 3.6 0.2 - - - +
169C ILE* 3.6 6.5 - - - -
170C VAL* 2.9 47.5 + - + +
172C VAL* 4.0 15.7 - - + -
188C LEU* 3.9 16.8 - - + -
189C ARG* 1.3 75.2 - - - +
191C GLU* 1.3 71.0 + - - +
192C ILE* 3.8 19.4 + - + -
194C GLU* 3.5 6.3 - - - +
195C GLY* 4.2 12.1 - - - -
198C LEU* 3.4 25.6 - - + -
200C LEU* 3.7 24.7 - - + -
205C GLU* 3.5 26.9 - - + -
208C ILE* 3.9 19.5 - - + -
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Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C GLY* 3.4 30.2 - - - +
168C ALA 3.2 4.3 - - - -
169C ILE* 3.4 22.3 - - + +
190C PHE* 1.3 76.1 - - - +
192C ILE* 1.3 69.0 + - - +
193C GLY* 2.8 4.7 + - - -
194C GLU* 2.8 41.2 + - + +
276C ARG* 4.2 10.7 + - - -
280C TYR* 4.7 6.2 + - - +
291C LEU* 5.2 8.6 - - + +
292C GLN* 3.4 22.7 + - - -
295C LYS* 3.1 28.6 - - - -
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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