Contacts of the strand formed by residues 193 - 196 (chain A) in PDB entry 3CPU
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 GLY 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ILE 4.2 0.5 - - - +
94A TYR* 3.5 17.1 - - - -
95A VAL 3.2 19.8 + - - -
191A VAL* 3.5 4.9 + - - +
192A ALA* 1.3 81.6 - - - +
194A PHE* 1.3 78.6 + - - -
228A PRO* 4.1 1.9 - - - +
229A PHE 2.9 16.4 - - - -
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Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 4.5 1.0 - - - -
95A VAL* 3.3 26.5 - - + +
97A ALA* 4.2 7.0 - - + -
183A MET* 3.6 52.3 - - + -
186A LEU* 3.8 26.2 - - + -
187A ILE* 3.8 22.7 - - + -
191A VAL* 3.8 15.3 - - + -
193A GLY* 1.3 83.7 - - - -
195A ARG* 1.3 61.8 + - - +
196A LEU* 3.8 13.3 + - + -
214A LEU* 4.9 0.4 - - + -
228A PRO* 4.2 8.3 - - + -
229A PHE 2.7 11.1 + - - +
230A ILE* 3.6 19.8 - - + +
231A TYR* 3.1 33.4 + - - +
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Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 3.6 19.5 - - - +
62A TYR* 4.1 2.6 - - - -
95A VAL 2.9 11.7 + - - +
96A ASP* 2.8 38.0 + - - +
97A ALA* 2.9 28.4 + - - +
194A PHE* 1.3 74.2 - - - +
196A LEU* 1.3 63.2 + - - +
197A ASP* 2.8 30.6 + - - +
231A TYR* 3.3 39.7 + - + +
233A GLU* 3.2 43.7 + - + +
254A THR* 5.9 0.9 - - + -
298A ASN* 4.9 0.6 - - - +
299A HIS* 3.8 19.6 - - - -
498A CL 3.3 21.8 - - - +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ALA* 4.0 8.5 - - + -
99A ILE* 4.1 24.0 - - + -
183A MET* 4.3 9.9 - - + -
194A PHE* 4.1 17.5 - - + +
195A ARG* 1.3 76.0 - - - +
197A ASP* 1.3 61.1 + - - +
199A SER* 2.9 21.3 + - - +
202A MET* 4.6 5.6 - - + -
207A ILE* 3.7 32.1 - - + -
211A LEU* 4.6 7.2 - - + -
230A ILE* 4.1 21.8 - - + -
231A TYR 2.9 11.1 + - - -
232A GLN* 3.9 16.4 - - + -
233A GLU* 2.9 28.9 + - - -
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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