Contacts of the strand formed by residues 269 - 277 (chain B) in PDB entry 2P0R
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 GLN 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B SER* 3.4 6.1 - - - -
266B PHE* 3.1 31.8 + - + +
267B ARG 3.3 9.0 + - - +
268B GLY* 1.3 79.1 - - - +
270B ARG* 1.3 66.9 + - - +
271B ILE* 4.1 10.5 - - + +
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Residues in contact with ARG 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLN* 3.4 38.7 + - + +
264B VAL* 3.3 14.3 - - - +
265B SER* 4.0 19.1 + - - +
269B GLN* 1.3 75.2 - - - +
271B ILE* 1.3 63.4 + - - +
272B GLU* 3.8 3.1 + - - +
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Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLN* 4.4 1.3 - - - -
264B VAL* 2.7 45.5 + - + +
266B PHE* 4.6 12.3 - - + +
269B GLN* 4.1 11.1 - - + +
270B ARG* 1.3 73.4 - - - +
272B GLU* 1.3 72.0 + - - +
273B LEU* 3.4 5.5 + - + -
289B TRP* 3.2 36.1 - - + +
320B ALA* 4.1 20.4 - - + -
321B PHE 5.9 0.2 - - - +
322B LYS* 5.8 6.5 - - + +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B TYR* 3.6 41.6 - - + +
262B ASP 4.1 3.8 - - - -
263B GLN* 3.5 28.8 + - + +
270B ARG 3.8 3.1 + - - +
271B ILE* 1.3 76.3 - - - +
273B LEU* 1.3 54.5 + - - +
320B ALA* 3.7 5.0 - - - -
321B PHE* 2.8 47.9 + - + +
325B LYS* 5.5 1.7 + - - -
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B TYR* 3.6 10.1 + - - -
261B ILE* 3.8 0.2 - - - -
262B ASP 2.7 43.8 + - - +
264B VAL* 3.8 16.6 - - + -
271B ILE* 3.4 12.0 + - + +
272B GLU* 1.3 75.5 - - - +
274B ILE* 1.3 59.7 + - - +
289B TRP* 3.5 53.2 - - + +
296B TRP* 4.6 5.8 - - + -
307B LEU* 4.1 19.1 - - + -
318B TRP* 3.7 18.6 - - + -
319B MET* 3.2 19.3 - - - +
320B ALA* 3.6 7.4 - - - -
321B PHE 4.7 0.4 - - - -
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B TYR* 5.4 0.2 - - + -
220B LEU* 4.6 8.5 - - + -
258B VAL* 4.0 21.3 - - + -
260B GLY 3.7 9.0 - - - +
261B ILE* 4.0 9.4 - - + +
273B LEU* 1.3 74.4 - - - +
275B ARG* 1.3 64.0 + - - +
276B ILE* 4.4 2.0 - - + -
317B PHE 4.1 0.2 - - - +
318B TRP* 3.4 5.5 - - - -
319B MET* 2.8 48.9 + - + +
321B PHE* 4.1 21.1 - - + +
324B PHE* 3.5 66.4 - - + -
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Residues in contact with ARG 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG* 3.3 22.4 - - - +
108B LEU* 5.4 1.2 - - - +
258B VAL* 3.5 2.8 - - - +
259B THR* 2.9 57.0 + - - +
260B GLY* 2.6 26.9 + - - +
274B ILE* 1.3 73.0 - - - +
276B ILE* 1.3 73.2 + - - +
307B LEU 3.4 23.6 + - - -
308B CYS* 4.5 9.5 - - - +
316B GLU* 3.8 22.4 + - + -
317B PHE 3.4 14.4 - - - +
318B TRP* 3.6 33.5 - - + +
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Residues in contact with ILE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B CYS* 3.4 11.2 - - - -
256B TYR* 3.4 37.0 - - + -
257B SER 3.3 2.9 - - - +
258B VAL* 3.2 37.5 - - + -
259B THR* 4.3 2.7 - - - -
274B ILE* 4.4 4.9 - - + -
275B ARG* 1.3 81.0 - - - +
277B ARG* 1.3 65.6 + - - +
316B GLU* 3.2 3.5 - - - +
317B PHE* 2.9 52.5 + - + +
319B MET* 4.4 10.1 - - + -
324B PHE* 3.4 24.7 - - + -
328B PHE* 4.3 3.6 - - + -
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Residues in contact with ARG 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG* 2.9 57.6 + - - +
87B THR* 4.1 9.3 + - - +
89B ILE* 3.1 33.5 + - - +
90B CYS* 4.8 1.8 - - - -
104B ALA* 4.4 9.8 - - - +
256B TYR* 3.5 8.2 - - - -
257B SER* 2.8 38.6 + - - +
259B THR* 4.2 7.0 - - + -
276B ILE* 1.3 77.5 - - - +
278B ASN* 1.3 83.6 + - - +
279B PRO* 3.6 10.6 - - - +
281B GLY* 3.7 15.2 - - - -
314B ASP 3.9 8.9 + - - -
315B GLY 3.4 5.2 - - - -
316B GLU* 3.7 24.2 - - + +
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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