Contacts of the strand formed by residues 242 - 250 (chain B) in PDB entry 2C10
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 HIS 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B GLY* 4.1 5.2 - - - -
229B LEU 3.8 3.4 - - - -
230B TYR* 3.4 41.1 + + + -
240B LEU 3.7 1.4 + - - -
241B HIS* 1.3 77.1 - - - +
243B VAL* 1.3 60.8 + - - +
244B GLY* 3.0 29.8 + - - -
245B LEU 3.6 14.4 - - - -
246B GLU* 3.0 44.2 + - + +
291B ILE* 3.9 16.3 - - - +
376B SER* 5.8 0.4 - - - -
378B ALA* 5.5 0.4 - - - +
497B SER* 3.5 15.5 - - - +
498B ALA* 3.8 11.2 - - + -
499B PHE* 3.7 26.7 + - + +
514B HIS* 5.5 0.7 - - - +
515B THR* 5.9 2.3 - - - +
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Residues in contact with VAL 243 (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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195B LEU* 5.7 0.4 - - + -
199B CYS* 4.0 21.0 - - - -
208B LEU* 3.7 25.4 - - + -
229B LEU* 3.1 34.6 + - + +
231B TYR* 3.7 42.0 - - + +
242B HIS* 1.3 72.2 - - - +
244B GLY* 1.3 58.5 - - - +
245B LEU* 4.0 16.2 - - + +
266B TYR* 4.0 7.4 + - + -
267B GLN* 4.0 7.8 + - - -
291B ILE* 3.3 24.3 - - + +
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Residues in contact with GLY 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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242B HIS* 3.0 19.2 + - - -
243B VAL* 1.3 78.5 - - - +
245B LEU* 1.3 59.8 + - - +
246B GLU* 4.2 1.1 + - - -
265B PHE* 3.5 7.0 - - - +
266B TYR* 3.2 7.5 - - - -
267B GLN* 2.8 29.1 + - - -
499B PHE* 3.5 25.4 - - - -
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Residues in contact with LEU 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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188B LEU* 3.9 28.5 - - + -
191B ALA* 6.3 0.4 - - + -
194B LEU* 5.6 0.4 - - + -
195B LEU* 4.3 19.3 - - + -
208B LEU* 5.8 0.7 - - + -
229B LEU* 3.1 42.5 + - + +
242B HIS* 3.6 1.9 - - - -
243B VAL* 3.4 13.8 - - + +
244B GLY* 1.3 78.3 - - - +
246B GLU* 1.3 66.6 + - - +
247B LEU* 4.5 5.6 - - + -
264B VAL* 3.8 22.2 - - + -
265B PHE 3.4 12.3 - - - +
266B TYR* 3.7 20.9 - - + -
274B LEU* 4.5 7.0 - - + -
277B LEU* 4.0 11.4 - - + -
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Residues in contact with GLU 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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226B TRP* 3.6 15.4 - - + -
227B PHE 3.2 10.1 - - - +
228B GLY* 4.1 5.2 - - - -
242B HIS* 3.0 30.2 + - + +
244B GLY 5.1 0.4 - - - -
245B LEU* 1.3 79.2 - - - +
247B LEU* 1.3 70.4 + - - +
264B VAL* 3.7 0.3 - - - +
265B PHE* 3.0 38.9 + - + +
376B SER* 3.2 27.3 + - - -
377B PRO* 3.3 8.5 - - - +
378B ALA* 3.1 39.5 + - + +
379B ALA 4.9 0.3 + - - -
498B ALA* 4.7 3.5 - - - +
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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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183B ILE* 3.7 38.1 - - + -
187B GLU* 5.5 0.2 - - + -
188B LEU* 4.3 8.5 - - + -
225B THR 3.3 4.0 - - - +
226B TRP* 3.4 4.7 - - - -
227B PHE* 2.7 41.5 + - + +
229B LEU* 3.7 18.8 - - + -
245B LEU* 4.5 5.2 - - + -
246B GLU* 1.3 81.5 - - - +
248B LEU* 1.3 58.9 + - - +
249B VAL* 3.3 10.8 + - + +
261B ILE* 4.3 13.2 - - + -
263B LYS 3.8 1.6 - - - -
264B VAL* 3.9 29.8 - - + -
274B LEU* 4.1 20.0 - - + -
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Residues in contact with LEU 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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553A TRP* 4.0 19.1 - - + +
217B GLY* 6.1 0.7 - - - -
224B ALA* 3.6 32.8 - - + +
225B THR 3.6 3.1 - - - -
226B TRP* 3.3 54.0 - - + +
247B LEU* 1.3 68.3 - - - +
249B VAL* 1.3 59.1 + - - +
261B ILE* 3.3 7.4 - - - +
262B GLN* 2.9 59.4 + - + +
263B LYS* 3.0 21.6 + - + +
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Residues in contact with VAL 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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179B ILE* 4.3 12.3 - - + -
182B MET* 4.3 15.0 - - - -
183B ILE* 4.2 16.8 - - + -
224B ALA* 3.0 4.4 - - - -
225B THR 2.8 41.6 + - - +
227B PHE* 3.9 23.8 - - + -
247B LEU* 4.0 7.0 - - + +
248B LEU* 1.3 72.5 - - - +
250B ASN* 1.3 69.4 + - - +
251B HIS* 3.3 18.4 - - + -
259B TRP* 5.1 0.7 - - + -
260B THR 3.6 9.6 - - - +
261B ILE* 3.8 21.1 - - + -
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Residues in contact with ASN 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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223B ARG 3.6 8.6 + - - +
224B ALA* 4.0 4.9 - - + +
248B LEU 3.9 1.6 + - - -
249B VAL* 1.3 71.0 - - - +
251B HIS* 1.3 61.0 + - - +
252B LYS* 3.3 26.0 + - - +
253B ALA 5.8 0.2 - - - -
259B TRP* 3.5 10.0 - - - +
260B THR* 3.0 44.8 + - - +
262B GLN* 3.2 35.2 - - + +
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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