Contacts of the strand formed by residues 193 - 196 (chain A) in PDB entry 2R2N
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 PHE 193 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE* 3.8 25.8 - + - -
128A ILE* 3.9 28.0 - - + -
129A ILE* 3.7 23.1 - - + -
134A ASN 4.5 0.6 + - - -
135A VAL* 3.5 37.9 - - + -
136A LEU* 3.0 28.4 + - - +
137A LEU* 6.0 0.2 - - + -
149A LEU* 4.0 8.1 - - + -
191A PRO* 3.4 1.5 - - - +
192A LYS* 1.3 80.5 - - - +
194A LEU* 1.3 61.6 + - - +
195A TYR* 3.7 24.2 - - + -
225A PHE* 4.1 5.8 - - - -
226A LEU* 3.2 26.7 - - + +
228A ILE* 3.6 20.9 - - + -
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Residues in contact with LEU 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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136A LEU* 3.3 33.7 - - + +
137A LEU* 3.9 5.8 - - - -
138A ASP 5.1 0.4 - - - +
159A VAL* 4.6 10.3 - - + -
166A ILE* 5.1 10.8 - - + -
171A LEU* 3.8 17.7 - - + -
193A PHE* 1.3 75.8 - - - +
195A TYR* 1.3 69.6 + - - +
196A THR* 5.0 9.9 - - + -
216A ILE* 3.5 32.3 - - + -
225A PHE* 3.8 18.6 - - + -
226A LEU 2.9 7.6 + - - +
227A ILE* 3.5 10.4 - - + +
228A ILE 2.8 25.5 + - - +
246A PHE* 6.0 0.2 - - + -
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Residues in contact with TYR 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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121A LEU* 4.3 5.3 - - + +
125A PHE* 3.7 22.4 - + - -
136A LEU 2.9 9.2 + - - +
137A LEU* 3.2 36.1 - - + +
138A ASP* 4.0 1.1 - - - +
141A ALA* 5.1 6.5 - - + -
142A TYR* 4.1 6.5 - - - +
145A THR* 3.5 42.7 - - + +
149A LEU* 5.8 0.4 - - + -
193A PHE* 3.7 20.8 - - + -
194A LEU* 1.3 76.3 - - - +
196A THR* 1.3 72.0 + - - +
197A VAL* 3.5 14.5 - - + +
201A ASN* 6.1 0.4 - - - -
228A ILE* 3.5 21.3 - - + -
230A ASP* 2.7 41.5 + - + -
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Residues in contact with THR 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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138A ASP* 2.7 25.1 + - - -
166A ILE* 3.6 12.4 - - + +
194A LEU* 4.2 9.4 + - + -
195A TYR* 1.3 84.4 - - - +
197A VAL* 1.3 67.3 + - - +
198A PRO* 3.3 9.3 - - + +
208A LEU* 4.1 13.8 - - + +
227A ILE* 5.4 2.9 - - + -
228A ILE 3.1 10.2 + - - +
229A GLU* 3.8 0.6 - - - -
230A ASP 3.1 23.9 + - - -
246A PHE* 4.0 27.8 - - + -
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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