Contacts of the helix formed by residues 243 - 253 (chain B) in PDB entry 2R6C
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 SER 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B SER* 4.1 0.2 + - - -
241B GLU 3.9 1.6 + - - -
242B MET* 1.3 79.0 - - - +
244B ALA* 1.3 65.2 + - - +
245B GLN* 4.4 4.2 - - - +
246B GLN* 3.1 32.2 + - - +
247B LEU* 3.3 21.3 + - - +
292B ASP* 4.2 9.4 - - - -
376E MET* 5.1 0.6 - - - +
377E MET* 5.5 13.9 - - - -
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Residues in contact with ALA 244 (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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239B SER* 4.6 0.4 - - - -
243B SER* 1.3 74.6 - - - +
245B GLN* 1.3 75.4 + - + +
246B GLN 3.6 0.2 - - - -
247B LEU* 3.8 7.8 - - - +
248B VAL* 3.2 25.1 + - - +
290B ILE* 4.0 24.5 - - + +
292B ASP* 3.5 35.0 + - + +
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Residues in contact with GLN 245 (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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243B SER* 3.3 3.7 + - - +
244B ALA* 1.3 99.4 - - + +
246B GLN* 1.3 61.2 + - - +
247B LEU 3.2 1.1 - - - -
248B VAL* 3.8 15.0 + - + +
249B MET* 3.4 22.0 + - - +
292B ASP* 4.9 3.6 + - - -
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Residues in contact with GLN 246 (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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242B MET* 3.7 15.2 - - - +
243B SER* 3.1 27.4 + - - +
245B GLN* 1.3 75.3 - - - +
247B LEU* 1.3 61.2 + - - +
249B MET* 3.9 15.7 - - + +
250B ARG* 3.3 51.2 + - - +
376E MET* 3.0 54.3 - - - +
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Residues in contact with LEU 247 (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 THR* 5.9 2.0 - - + -
221B LEU* 3.9 33.1 - - + +
237B ILE* 4.1 9.2 - - + -
239B SER* 3.5 31.4 - - - -
242B MET* 3.7 16.6 - - + -
243B SER 3.3 15.3 + - - +
244B ALA 3.8 5.4 - - - +
245B GLN 3.2 0.2 - - - -
246B GLN* 1.3 78.2 - - - +
248B VAL* 1.3 65.7 + - - +
250B ARG* 3.2 13.9 + - - +
251B MET* 3.3 33.9 + - + +
290B ILE* 4.0 25.8 - - + -
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Residues in contact with VAL 248 (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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244B ALA 3.2 19.2 + - - +
245B GLN* 3.8 15.0 - - + +
246B GLN 3.5 0.4 - - - -
247B LEU* 1.3 78.6 - - - +
249B MET* 1.3 51.5 + - - +
251B MET* 3.0 14.2 + - + +
252B LEU* 2.7 51.3 + - + +
283B LEU* 4.6 10.8 - - + -
290B ILE* 3.9 20.4 - - + -
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Residues in contact with MET 249 (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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245B GLN 3.4 17.7 - - - +
246B GLN* 3.9 24.0 - - + +
248B VAL* 1.3 76.7 - - + +
250B ARG* 1.3 68.2 + - + +
252B LEU* 3.8 12.6 - - + -
253B CYS* 2.5 42.5 + - - -
263B LEU* 4.3 25.1 - - + -
264B ARG* 4.2 35.4 - - + +
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Residues in contact with ARG 250 (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 THR* 6.2 0.2 - - - -
218B ALA* 6.4 0.7 - - - -
221B LEU* 4.2 14.5 - - + +
222B ASN* 5.3 2.3 + - - -
242B MET* 3.7 25.1 - - - +
246B GLN* 3.3 46.9 + - - +
247B LEU 3.2 12.0 + - - +
248B VAL 3.2 0.6 - - - -
249B MET* 1.3 89.2 - - + +
251B MET* 1.3 56.2 - - - +
253B CYS* 4.6 3.6 - - - -
254B ALA* 3.5 16.6 + - - +
264B ARG* 4.4 22.7 - - - +
436B ASN* 3.3 35.5 + - - +
376E MET* 5.2 4.8 - - - +
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Residues in contact with MET 251 (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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221B LEU* 5.0 17.3 - - + +
225B GLN* 3.1 47.0 + - + +
237B ILE* 5.0 4.9 - - + -
247B LEU* 3.3 31.6 + - + +
248B VAL* 3.0 18.3 + - + +
250B ARG* 1.3 75.6 - - - +
252B LEU* 1.3 63.9 + - - +
253B CYS 3.4 0.2 - - - -
254B ALA* 3.7 2.7 - - + -
255B GLU* 3.3 9.0 + - - +
283B LEU* 4.0 21.6 - - + +
288B ILE* 3.7 47.8 - - + -
290B ILE* 4.5 7.4 - - + -
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Residues in contact with LEU 252 (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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248B VAL* 2.7 30.7 + - + +
249B MET* 3.5 11.9 - - + +
251B MET* 1.3 75.4 - - - +
253B CYS* 1.3 65.1 + - - +
255B GLU* 3.0 15.7 + - + +
258B ILE* 3.3 18.9 - - - +
263B LEU* 5.0 5.2 - - + -
276B LEU* 3.8 23.8 - - + -
279B ALA* 3.8 15.5 - - + +
280B MET* 3.7 40.8 - - + +
283B LEU* 3.9 17.5 - - + -
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Residues in contact with CYS 253 (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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249B MET* 2.5 31.3 + - - +
250B ARG* 4.4 5.6 - - - +
252B LEU* 1.3 73.6 - - - +
254B ALA* 1.3 61.2 + - - +
255B GLU 3.0 11.4 + - - +
257B ASN* 3.9 2.3 - - - -
258B ILE* 3.5 25.4 + - - +
259B ASN* 3.5 34.5 - - + -
263B LEU* 4.0 19.1 - - - -
264B ARG* 5.3 6.5 - - - -
434B GLU 5.2 0.7 - - - +
435B TYR* 3.3 18.6 - - - +
436B ASN* 4.8 4.0 - - + -
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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