Contacts of the strand formed by residues 255 - 260 (chain C) 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 VAL 255 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217C TYR* 3.7 18.8 - - + -
227C ILE* 3.4 19.5 - - + +
229C GLU* 4.1 15.9 - - + +
246C PHE* 3.8 18.6 - - + +
247C LEU* 4.0 27.1 - - + +
250C ASP* 2.9 30.7 + - + +
253C GLY 3.5 0.4 - - - -
254C ARG* 1.3 82.5 - - - +
256C ILE* 1.3 73.3 + - - +
257C ARG 4.3 1.8 - - - +
275C THR 4.2 0.3 - - - +
276C GLY* 3.6 5.7 - - - -
277C PRO* 3.4 18.2 - - - +
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Residues in contact with ILE 256 (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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124C VAL* 4.0 27.8 - - + -
127C MET* 4.2 7.4 - - + -
128C ILE* 4.7 0.2 - - + -
226C LEU* 4.2 17.3 - - + -
227C ILE 2.9 8.1 + - - +
228C ILE* 3.1 20.0 - - + +
229C GLU 2.9 23.7 + - - -
254C ARG 5.5 0.2 - - - -
255C VAL* 1.3 77.7 - - - +
257C ARG* 1.3 61.8 + - - +
274C LEU* 3.6 31.0 - - + -
275C THR 3.5 8.5 - - - +
276C GLY* 4.7 1.1 - - - -
277C PRO* 4.2 7.4 - - + -
280C LEU* 3.7 33.0 - - + -
281C ILE* 5.1 2.5 - - + -
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Residues in contact with ARG 257 (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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91C GLN* 4.1 2.7 - - - +
95C HIS* 3.8 15.9 + - - -
229C GLU* 3.1 41.4 + - - +
231C ASP* 2.7 27.6 + - - +
234C TYR* 3.1 38.2 - - - +
245C THR* 3.5 8.3 - - - +
247C LEU* 3.9 28.9 - - + -
255C VAL* 4.1 1.9 - - + -
256C ILE* 1.3 73.6 - - - +
258C ALA* 1.3 63.4 + - - +
259C ASP* 2.7 40.9 + - - +
273C PHE 4.0 0.3 - - - +
274C LEU* 3.4 7.0 - - - +
275C THR* 2.7 43.4 + - - +
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Residues in contact with ALA 258 (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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117C SER* 4.4 12.6 - - - +
121C LEU* 4.0 29.6 - - + -
228C ILE* 4.7 0.6 - - + +
229C GLU 2.9 11.9 + - - +
230C ASP* 4.1 8.4 - - - +
231C ASP* 3.0 31.5 + - - +
256C ILE 4.1 0.6 + - - -
257C ARG* 1.3 73.6 - - - +
259C ASP* 1.3 62.2 + - - +
273C PHE 3.6 5.4 - - - +
274C LEU* 4.0 15.0 - - + -
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Residues in contact with ASP 259 (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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91C GLN* 3.1 21.7 + - - +
95C HIS* 5.0 0.5 - - - -
117C SER* 3.3 10.9 - - - -
231C ASP 4.4 6.0 - - - +
234C TYR* 4.6 0.5 - - - +
235C PHE* 4.4 14.6 - - + -
257C ARG* 2.7 50.7 + - - +
258C ALA* 1.3 72.2 - - - +
260C SER* 1.3 61.9 + - - +
273C PHE* 2.8 63.9 + - + +
275C THR* 4.5 0.7 + - - -
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Residues in contact with SER 260 (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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117C SER* 3.9 4.7 - - - -
231C ASP 4.8 0.6 + - - -
232C PRO* 3.6 40.4 - - - +
235C PHE* 4.8 10.4 - - - -
259C ASP* 1.3 77.4 - - - +
261C PHE* 1.3 66.3 + - - +
262C SER* 3.0 20.5 + - - -
263C LYS* 4.7 1.5 + - - +
264C ILE* 4.5 6.8 - - - +
272C GLY* 4.4 3.4 - - - -
273C PHE* 5.1 1.3 - - - -
426C PMP 2.5 29.4 + - - -
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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