Contacts of the strand formed by residues 174 - 178 (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 LYS 174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C GLY 3.8 9.9 - - - +
173C HIS* 1.3 74.3 - - - +
175C VAL* 1.3 60.2 + - - +
197C ALA* 4.0 6.5 - - - -
198C GLN* 3.4 37.4 - - + +
239C LEU* 4.1 17.6 + - + -
241C CYS* 3.8 28.5 - - - -
243C PRO* 3.2 16.7 - - + +
244C GLU* 2.8 39.5 + - - +
245C VAL 3.6 3.3 + - - -
264C ARG* 4.4 2.8 - - - +
308D SER* 3.6 31.5 + - - +
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C VAL* 4.1 16.6 - - + -
173C HIS* 4.0 12.8 - - + -
174C LYS* 1.3 79.5 - - - +
176C LEU* 1.3 65.8 + - - +
177C VAL* 4.0 13.0 - - + -
191C ALA* 4.6 5.4 - - + -
196C ALA* 3.9 22.9 - - + -
198C GLN 2.8 12.7 + - - +
199C VAL* 3.2 10.8 - - + +
200C VAL* 2.8 34.8 + - - +
239C LEU* 5.2 0.4 - - - +
243C PRO* 4.2 2.2 - - - -
245C VAL* 3.3 18.4 - - + +
247C ILE* 4.4 16.4 - - + -
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C VAL* 1.3 75.0 - - - +
177C VAL* 1.3 67.1 + - - +
178C CYS* 4.0 12.3 - - - -
200C VAL* 3.4 16.8 - - + +
202C THR* 3.8 27.6 - - + -
231C ILE* 6.0 2.5 - - + -
235C VAL* 4.2 23.1 - - + -
243C PRO* 3.9 12.0 - - + +
245C VAL 3.0 7.5 + - - +
246C THR* 3.2 33.7 - - + +
247C ILE 2.8 26.9 + - - -
258C ALA* 5.3 1.8 - - + +
259C GLY* 4.9 2.7 - - - +
262C ALA* 4.1 23.1 - - + -
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Residues in contact with VAL 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C VAL* 4.3 9.0 - - + -
176C LEU* 1.3 79.5 - - - +
178C CYS* 1.3 61.8 + - - +
179C GLY 3.6 14.5 + - - +
184C GLY* 3.5 28.3 - - - +
187C THR* 4.0 21.3 - - + -
188C LEU* 4.5 7.0 - - - +
191C ALA* 5.5 0.7 - - + -
199C VAL* 3.8 22.9 - - + -
200C VAL 2.7 12.4 + - - +
201C VAL* 3.2 12.2 - - + +
202C THR* 3.0 24.1 + - - -
247C ILE* 3.5 9.2 - - + +
249C CYS* 4.2 5.8 - - - -
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Residues in contact with CYS 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU* 4.0 16.6 - - - -
177C VAL* 1.3 70.1 - - - +
179C GLY* 1.3 59.7 + - - +
202C THR* 3.2 13.9 - - - +
231C ILE* 6.5 0.7 - - - -
246C THR* 3.9 25.4 - - - -
247C ILE 3.0 8.5 + - - -
248C GLU* 3.4 13.7 - - - +
249C CYS* 2.8 32.4 + - - +
250C THR* 3.2 5.6 - - + +
255C SER* 3.1 37.5 - - - +
258C ALA* 5.7 2.7 - - - -
259C GLY* 5.2 1.1 - - - -
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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
------------------------------------------------------------
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