Contacts of the strand formed by residues 230 - 237 (chain B) in PDB entry 6C3P
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 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A PRO* 3.3 23.3 - - + +
222B LYS* 3.5 42.0 - - + +
223B THR 3.2 13.9 - - - +
224B THR* 3.2 23.6 - - + +
228B GLY 3.3 3.1 + - - +
229B GLU* 1.3 75.9 - - - +
231B VAL* 1.3 65.3 + - - +
232B PRO* 4.5 0.6 - - + +
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Residues in contact with VAL 231 (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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192A ARG* 5.2 11.9 - - - +
201A ARG* 6.4 0.4 - - - +
256A ILE* 5.2 14.4 - - + -
315A PHE 5.7 2.5 - - - +
317A PRO* 4.6 9.0 - - + -
222B LYS* 3.4 17.1 - - - -
223B THR* 3.3 7.1 + - + +
229B GLU* 5.3 9.6 - - + +
230B VAL* 1.3 80.9 - - - +
232B PRO* 1.3 75.4 - - + +
233B LEU 5.0 1.1 - - - +
234B HIS* 3.4 41.7 + - + +
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Residues in contact with PRO 232 (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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317A PRO* 3.7 20.9 - - + -
319A VAL* 3.1 52.0 - - + +
320A ALA* 4.9 3.4 - - - +
321A GLU 5.7 0.9 - - - +
326A TYR* 6.2 0.9 - - + -
221B ARG 3.2 2.4 - - - +
222B LYS* 3.0 48.0 + - + +
230B VAL* 4.5 0.7 - - + +
231B VAL* 1.3 83.9 - - + +
233B LEU* 1.3 65.4 + - + +
280B ASP* 5.4 0.3 - - - +
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Residues in contact with LEU 233 (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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253A ALA* 4.7 12.5 - - + +
255A LEU* 5.8 3.1 - - - +
319A VAL* 4.3 17.1 - - + +
326A TYR* 3.6 53.2 - - + +
35B PHE* 3.4 44.2 - - + -
44B VAL* 4.7 0.9 - - + -
220B VAL* 5.2 10.8 - - + -
221B ARG* 4.0 4.0 - - - +
231B VAL* 4.3 2.4 - - - +
232B PRO* 1.3 83.8 - - + +
234B HIS* 1.3 65.9 + - - +
235B GLN* 3.6 15.8 + - + +
282B GLU* 5.7 0.7 - - - +
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Residues in contact with HIS 234 (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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192A ARG* 4.6 21.0 + - - -
258A TYR* 5.3 8.9 + + - -
219B VAL 4.5 0.2 - - - -
220B VAL* 3.0 30.0 - - - +
221B ARG* 2.8 22.1 + - + +
223B THR* 3.3 29.7 - - + +
231B VAL* 3.4 28.3 + - + +
232B PRO 3.5 1.6 - - - -
233B LEU* 1.3 74.5 - - - +
235B GLN* 1.3 76.0 + - - +
236B VAL* 3.3 30.9 - - + +
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Residues in contact with GLN 235 (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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250A PHE* 3.2 18.9 + - - +
253A ALA* 4.7 11.1 + - - +
255A LEU* 3.2 32.1 - - + +
35B PHE* 3.8 29.5 - - - -
218B GLN* 3.1 23.9 + - - +
219B VAL 3.6 4.3 - - - -
220B VAL* 3.6 13.5 - - + -
233B LEU* 3.6 13.2 + - - +
234B HIS* 1.3 92.3 + - - +
236B VAL* 1.3 65.4 + - - +
237B ASP* 4.2 1.0 + - - -
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Residues in contact with VAL 236 (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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243A GLY* 4.8 12.6 - - - +
218B GLN* 3.4 3.3 - - - +
219B VAL* 2.9 47.4 + - + +
234B HIS* 3.3 33.0 - - + +
235B GLN* 1.3 71.4 - - - +
237B ASP* 1.3 68.7 + - - +
238B ILE 3.0 4.9 + - - -
266B PRO* 3.7 32.3 - - + -
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Residues in contact with ASP 237 (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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242A ASN* 2.8 40.6 + - - +
243A GLY* 3.9 5.1 - - - +
244A VAL* 3.2 31.8 + - + +
248A SER 3.4 11.9 - - - +
249A ILE* 4.8 4.5 - - - +
250A PHE 5.4 0.2 + - - -
216B HIS* 5.5 13.8 - - + +
217B MET 3.7 6.6 - - - +
218B GLN* 3.0 34.6 + - - +
235B GLN 4.2 1.4 + - - -
236B VAL* 1.3 71.8 - - - +
238B ILE* 1.3 61.0 + - - +
239B PRO* 3.5 4.3 - - - +
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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