Contacts of the helix formed by residues 231 - 242 (chain A) in PDB entry 6FF7
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 THR 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A PHE* 1.3 76.9 - - - +
232A LEU* 1.3 61.3 + - - +
233A PRO 3.7 3.6 - - - -
234A MET* 3.6 12.1 + - - +
235A MET* 3.0 30.3 + - - +
414A ARG* 5.8 5.4 - - - -
389B ASP* 4.7 19.7 - - - -
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Residues in contact with LEU 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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231A THR* 1.3 72.7 - - - +
233A PRO* 1.4 60.4 - - - +
235A MET* 3.8 4.7 - - - +
236A SER* 2.9 28.6 + - - -
397A ASN* 5.7 1.3 - - + +
400A ASN* 5.5 1.7 - - - +
401A GLY* 5.3 13.0 - - - -
404A LEU* 5.8 3.8 - - + +
414A ARG* 6.1 0.8 - - - +
385B VAL 5.4 3.1 - - - +
386B GLY 4.4 18.6 - - - +
388B VAL* 5.9 8.6 - - + +
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Residues in contact with PRO 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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202A PRO* 5.4 5.6 - - + +
231A THR* 3.7 2.2 - - - -
232A LEU* 1.4 74.8 - - - +
234A MET* 1.3 60.3 + - - +
236A SER* 3.2 7.3 + - - -
237A THR* 3.0 28.9 + - - -
397A ASN* 5.1 16.4 - - + -
400A ASN* 6.1 0.7 - - + -
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Residues in contact with MET 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PRO* 4.3 24.1 - - + +
203A VAL* 5.4 6.6 - - + +
230A PHE* 5.3 4.5 - - + -
231A THR* 3.6 21.1 + - - +
232A LEU 3.4 0.2 - - - -
233A PRO* 1.3 77.4 - - - +
235A MET* 1.3 57.1 + - - +
237A THR* 3.6 7.2 + - - +
238A LEU* 3.3 21.3 + - - +
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Residues in contact with MET 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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138A PRO* 6.3 2.7 - - + -
230A PHE* 5.0 9.8 - - + +
231A THR 3.0 19.5 + - - +
232A LEU* 4.0 4.5 - - - +
234A MET* 1.3 74.2 - - - +
236A SER* 1.3 60.0 + - - +
238A LEU* 3.2 9.9 + - + +
239A TYR* 2.9 27.6 + - - +
404A LEU* 6.2 4.0 - - + -
411A PHE* 5.4 11.4 - - + +
414A ARG* 6.1 4.5 - - - -
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Residues in contact with SER 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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232A LEU 2.9 19.3 + - - -
233A PRO* 3.2 8.3 + - - -
235A MET* 1.3 73.6 - - - +
237A THR* 1.3 60.1 + - - +
239A TYR* 3.3 8.1 + - - +
240A ARG* 2.9 28.6 + - - +
400A ASN* 3.8 32.1 - - - -
404A LEU* 5.7 6.2 - - - +
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Residues in contact with THR 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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199A GLU 4.5 16.2 - - - -
200A ASP* 4.8 11.9 - - - -
202A PRO* 6.2 1.8 - - - -
203A VAL* 5.0 13.2 - - - -
233A PRO 3.0 16.9 + - - -
234A MET* 3.7 7.9 - - - -
235A MET 3.3 0.2 - - - -
236A SER* 1.3 75.5 - - - +
238A LEU* 1.3 57.5 + - - +
240A ARG* 3.8 6.3 - - - +
241A LEU* 2.9 29.8 + - - +
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Residues in contact with LEU 238 (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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138A PRO* 4.4 28.3 - - + +
139A VAL* 5.2 2.5 - - - +
142A SER* 3.6 14.3 - - - -
234A MET 3.3 11.0 + - - +
235A MET* 3.2 14.2 + - - +
237A THR* 1.3 80.1 - - - +
239A TYR* 1.3 56.3 + - - +
241A LEU* 3.3 1.4 + - - -
242A ALA* 3.0 30.7 + - - +
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Residues in contact with TYR 239 (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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235A MET 2.9 16.4 + - - +
236A SER* 3.7 8.5 - - - +
238A LEU* 1.3 76.5 - - - +
240A ARG* 1.3 61.8 + - - +
242A ALA* 3.5 18.3 + - - +
243A ASN* 4.1 3.1 + - - +
404A LEU* 6.0 6.1 - - + -
407A ALA* 6.0 3.1 - - + -
411A PHE* 5.0 15.5 - - + -
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Residues in contact with ARG 240 (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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236A SER 2.9 17.4 + - - +
237A THR* 3.8 7.2 - - - +
238A LEU 3.2 0.2 - - - -
239A TYR* 1.3 79.0 - - - +
241A LEU* 1.3 60.0 + - - +
242A ALA 3.4 0.5 + - - -
243A ASN* 3.8 14.6 + - - +
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Residues in contact with LEU 241 (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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142A SER* 3.6 29.1 - - - +
145A GLY 3.9 3.5 - - - -
146A SER* 3.8 18.3 + - - -
237A THR 2.9 17.0 + - - +
238A LEU* 3.3 3.6 + - - +
240A ARG* 1.3 77.5 - - - +
242A ALA* 1.3 57.9 + - - +
243A ASN 3.3 5.0 + - - +
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Residues in contact with ALA 242 (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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138A PRO 5.2 1.1 - - - +
141A ILE* 4.2 15.5 - - + +
142A SER* 4.0 19.7 - - - +
145A GLY* 4.9 1.8 - - - -
238A LEU 3.0 18.6 + - - +
239A TYR* 3.5 10.7 + - - +
240A ARG 3.2 1.0 - - - -
241A LEU* 1.3 76.8 - - - +
243A ASN* 1.3 63.1 + - - +
245A LEU* 4.4 2.1 + - - +
246A LEU* 3.5 23.6 + - + +
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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