Contacts of the strand formed by residues 230 - 237 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A LYS* 3.5 41.1 - - + +
223A THR 3.2 13.9 - - - +
224A THR* 3.2 23.6 - - + +
228A GLY 3.3 4.4 + - - +
229A GLU* 1.3 74.6 - - - +
231A VAL* 1.3 68.3 + - - +
232A PRO* 4.5 0.4 - - + +
317D PRO* 3.4 18.8 - - + +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 3.4 16.1 - - - -
223A THR* 3.3 7.5 + - + +
229A GLU* 5.3 9.4 - - + +
230A VAL* 1.3 81.6 - - - +
232A PRO* 1.3 76.4 - - + +
233A LEU 3.5 1.3 - - - +
234A HIS* 3.4 40.4 + - + +
192D ARG* 5.0 14.4 - - - +
256D ILE* 5.2 13.5 - - + -
315D PHE 5.7 2.7 - - - +
317D PRO* 4.7 7.6 - - + -
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Residues in contact with PRO 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ARG 3.2 2.6 - - - +
222A LYS* 3.0 49.0 + - + +
230A VAL 4.7 0.2 - - - -
231A VAL* 1.3 84.6 - - + +
233A LEU* 1.3 66.4 + - + +
280A ASP* 5.4 0.3 - - - +
317D PRO* 3.6 22.0 - - + -
319D VAL* 3.3 46.9 - - + +
320D ALA* 5.1 3.1 - - - +
321D GLU 5.9 0.9 - - - +
326D TYR* 6.4 0.7 - - + -
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.4 43.1 - - + -
44A VAL* 4.7 2.7 - - + -
220A VAL* 5.2 10.5 - - + -
221A ARG* 4.0 4.3 - - - +
231A VAL* 4.3 3.8 - - - +
232A PRO* 1.3 83.4 - - + +
234A HIS* 1.3 64.2 + - - +
235A GLN* 3.6 15.8 + - + +
282A GLU* 5.7 0.4 - - - +
253D ALA* 4.7 9.6 - - + -
255D LEU* 5.8 2.8 - - - +
319D VAL* 4.2 17.6 - - + +
326D TYR* 3.6 49.8 - - + +
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Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A VAL 5.6 0.2 - - - -
220A VAL* 3.0 29.1 - - - +
221A ARG* 2.8 22.7 + - + +
223A THR* 3.3 29.5 - - + +
231A VAL* 3.4 29.6 + - + +
232A PRO 3.5 1.0 - - - -
233A LEU* 1.3 74.7 - - - +
235A GLN* 1.3 75.5 + - - +
236A VAL* 3.3 30.9 - - + +
192D ARG* 4.5 22.1 + - - -
258D TYR* 5.2 8.9 + + - -
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.8 28.5 - - - -
218A GLN* 3.1 26.9 + - - +
219A VAL 3.6 4.0 - - - -
220A VAL* 3.6 13.7 - - + -
233A LEU* 3.6 14.1 + - + +
234A HIS* 1.3 91.9 + - - +
236A VAL* 1.3 66.4 + - - +
237A ASP* 4.2 1.6 + - - -
250D PHE* 3.5 14.1 + - - +
253D ALA* 4.8 10.3 + - - +
255D LEU* 3.2 32.5 - - + +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A GLN* 3.4 3.5 - - - +
219A VAL* 2.9 46.0 + - + +
234A HIS* 3.3 32.3 - - + +
235A GLN* 1.3 71.0 - - - +
237A ASP* 1.3 69.1 + - - +
238A ILE 3.0 5.1 + - - +
266A PRO* 3.7 31.4 - - + -
243D GLY* 4.7 12.3 - - - +
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Residues in contact with ASP 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A HIS* 5.5 12.5 - - + +
217A MET 3.8 6.7 - - - +
218A GLN* 3.0 34.6 + - - +
235A GLN 4.3 0.8 + - - -
236A VAL* 1.3 72.4 - - - +
238A ILE* 1.3 60.6 + - - +
239A PRO* 3.5 4.5 - - - +
242D ASN* 2.7 41.4 + - - +
243D GLY* 3.8 5.5 - - - +
244D VAL* 3.3 33.0 + - + +
248D SER 3.6 9.8 - - - +
249D ILE* 5.0 3.7 - - - +
250D PHE 5.6 0.2 + - - -
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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