Contacts of the strand formed by residues 192 - 196 (chain C) in PDB entry 2PGW
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 ARG 192 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLU* 5.7 0.9 - - - +
2200B GOL 4.2 20.6 - - - +
164C ARG* 3.7 27.2 + - - +
165C VAL* 3.6 19.0 - - - +
166C PHE* 3.0 31.6 + - - -
190C ASP 3.7 1.1 + - - +
191C ALA* 1.3 76.1 - - - +
193C LEU* 1.3 59.2 + - - +
194C ARG* 3.3 9.9 - - - +
217C ASP* 5.8 0.4 - - - -
219C GLU* 2.9 42.8 + - + +
322C ASP* 2.6 44.0 + - - -
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Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C PHE* 3.6 24.2 - - + +
168C LEU* 4.2 12.8 - - + -
181C THR* 4.4 12.3 - - + +
184C VAL* 3.9 26.0 - - + -
185C ARG* 3.8 30.4 - - + +
188C ILE* 4.1 6.5 - - + -
191C ALA 3.5 1.2 + - - -
192C ARG* 1.3 74.4 - - - +
194C ARG* 1.3 68.9 + - - +
195C LEU* 4.1 11.4 - - + -
216C TYR 4.6 2.5 - - - +
217C ASP 4.3 3.2 + - - +
218C ILE* 3.6 24.2 - - + +
219C GLU* 2.8 33.5 + - - +
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Residues in contact with ARG 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B HIS* 4.3 1.4 + - - -
140C PHE* 5.6 0.2 - - - -
165C VAL* 3.4 21.6 - - + +
166C PHE 2.8 13.8 + - - +
167C TYR* 3.5 16.1 - - + -
168C LEU* 2.9 26.5 + - - +
192C ARG* 3.3 11.1 - - - +
193C LEU* 1.3 75.0 - - - +
195C LEU* 1.3 65.3 + - - +
219C GLU* 2.7 46.1 + - + +
220C PHE* 3.2 52.9 - - + -
296C CYS* 4.2 3.2 - - - -
321C ASP* 2.7 43.4 + - - -
322C ASP* 4.3 0.2 + - - -
323C GLY* 3.4 17.6 + - - -
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Residues in contact with LEU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C TYR* 5.1 2.0 - - - -
168C LEU* 3.2 37.2 - - + +
170C VAL* 4.1 17.5 - - + -
181C THR* 4.1 2.5 - - - +
193C LEU* 4.1 14.4 - - + -
194C ARG* 1.3 81.6 - - - +
196C ASP* 1.3 55.4 + - - +
197C ALA 3.9 0.4 - - - -
213C LEU* 3.8 35.7 - - + -
218C ILE* 3.6 33.9 - - + -
220C PHE* 3.0 7.2 + - - +
221C ILE* 3.1 16.2 - - + -
222C GLU* 2.7 33.4 + - - +
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Residues in contact with ASP 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C PHE* 6.0 0.2 - - - -
167C TYR* 3.1 42.5 + - + +
168C LEU 2.9 11.4 + - - +
169C LYS* 3.7 13.4 - - - +
170C VAL* 2.9 27.7 + - - +
194C ARG 4.3 0.2 + - - -
195C LEU* 1.3 70.7 - - - +
197C ALA* 1.3 61.8 + - - +
198C ASN* 2.9 34.6 + - - +
222C GLU* 3.5 16.2 - - - +
223C GLN* 5.0 1.6 - - - +
247C ASP* 4.9 4.3 - - - +
248C GLN* 5.1 1.9 + - - -
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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