Contacts of the strand formed by residues 198 - 203 (chain C) in PDB entry 1PL8
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 GLN 198 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C HIS 3.3 3.5 + - - +
174C LYS* 3.4 27.8 - - + +
175C VAL 2.8 26.2 + - - +
197C ALA* 1.3 87.8 - - + +
199C VAL* 1.3 64.7 + - - +
218C ASP* 3.2 16.7 - - + +
219C LEU* 3.9 17.7 - - + +
238C GLN 5.1 1.6 + - - -
239C LEU* 3.9 37.5 + - + +
312D SER* 4.8 6.1 - - - -
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Residues in contact with VAL 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C VAL* 3.2 8.5 - - + +
177C VAL* 3.8 27.8 - - + -
188C LEU* 3.4 28.0 - - + -
191C ALA* 3.9 14.8 - - + -
192C LYS* 4.1 16.8 - - + -
196C ALA* 3.9 21.5 - - + -
198C GLN* 1.3 79.9 - - - +
200C VAL* 1.3 63.6 + - - +
201C VAL* 4.1 4.9 + - + -
217C ALA* 4.0 1.0 - - - -
218C ASP* 2.9 31.6 + - - +
219C LEU 3.2 7.8 + - - +
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Residues in contact with VAL 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C VAL 2.8 10.8 + - - +
176C LEU* 3.4 16.8 - - + +
177C VAL* 2.7 32.9 + - - +
199C VAL* 1.3 74.6 - - - +
201C VAL* 1.3 63.6 + - - +
219C LEU* 3.2 21.3 - - + +
220C VAL* 4.5 1.8 - - - +
221C LEU* 4.9 6.5 - - + -
235C VAL* 4.7 9.2 - - + +
238C GLN* 3.8 23.3 - - + +
239C LEU* 3.3 47.6 - - + -
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Residues in contact with VAL 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C VAL* 3.2 12.3 - - + +
179C GLY 3.8 16.6 - - - +
180C ALA* 3.9 15.7 - - + -
185C MET* 4.1 7.4 - - + -
188C LEU* 4.3 13.5 - - + -
199C VAL* 4.1 15.0 - - + -
200C VAL* 1.3 79.6 - - - +
202C THR* 1.3 74.2 + - - +
209C LEU* 3.5 10.4 - - + +
212C ALA* 4.4 5.2 - - + -
217C ALA* 4.0 21.3 - - + -
219C LEU 2.9 8.0 + - - +
220C VAL* 3.2 4.8 - - + -
221C LEU 2.8 23.2 + - - -
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Residues in contact with THR 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU* 3.8 21.8 - - + -
177C VAL 3.0 4.2 + - - -
178C CYS* 3.2 25.6 - - - +
179C GLY* 2.8 25.0 + - - -
180C ALA 3.5 0.2 + - - -
200C VAL* 5.1 0.9 - - + -
201C VAL* 1.3 80.2 - - - +
203C ASP* 1.3 67.7 + - - +
209C LEU* 3.8 1.1 - - - -
221C LEU* 3.1 25.1 - - + -
223C ILE* 3.9 17.7 - - + -
231C ILE* 4.9 4.7 - - + -
235C VAL* 4.7 10.3 - - + -
255C SER* 5.0 0.3 + - - -
400C NAD 3.9 6.1 - - - -
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Residues in contact with ASP 203 (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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180C ALA* 2.6 29.1 + - + +
202C THR* 1.3 78.5 - - - +
204C LEU* 1.3 70.4 + - - +
205C SER* 2.7 19.0 + - - +
208C ARG* 4.3 4.0 - - - -
209C LEU* 3.6 19.4 - - + +
221C LEU 3.2 4.0 + - - -
222C GLN* 3.3 8.3 - - - -
223C ILE* 2.7 27.7 + - - +
400C NAD 2.5 53.7 + - - -
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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