Contacts of the helix formed by residues 235 - 244 (chain A) in PDB entry 1NBF
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A THR* 2.8 22.5 + - - +
232A LEU* 3.1 19.4 + - - +
233A PHE 4.1 0.7 - - - -
234A PHE* 1.3 74.2 - - - +
236A ASN* 1.3 64.1 + - - +
237A GLN 3.3 1.3 - - - -
238A LEU* 2.8 31.3 + - + +
239A ARG 3.2 8.5 + - - -
323A LEU* 4.5 3.6 - - + -
324A PHE* 4.1 19.4 - - + -
401A VAL* 4.2 24.8 - - + +
403A HIS* 5.6 0.9 + - - -
451A HIS* 5.0 4.0 + - - -
517A VAL* 5.8 2.3 - - - +
519A ILE* 6.0 0.9 - - + -
527A VAL* 4.1 7.9 - - + -
528A LEU* 4.7 4.9 - - - -
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Residues in contact with ASN 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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233A PHE 4.3 0.2 - - - -
234A PHE* 3.1 16.8 + - - +
235A THR* 1.3 72.5 - - - +
237A GLN* 1.3 64.5 + - - +
239A ARG* 3.0 44.8 + - - +
240A LYS* 3.0 18.1 + - - +
471A PRO 5.0 3.0 + - - +
527A VAL 3.2 12.4 + - - +
528A LEU* 3.4 19.5 + - - +
529A GLN 2.8 30.6 + - - +
530A ALA* 4.2 5.1 - - - +
531A VAL* 3.9 8.8 - - + +
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Residues in contact with GLN 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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235A THR 3.1 0.4 + - - -
236A ASN* 1.3 73.8 - - - +
238A LEU* 1.3 59.7 + - - +
240A LYS* 3.7 18.2 + - - +
241A ALA* 3.3 20.1 + - - +
319A THR* 4.8 3.8 - - + +
322A LYS* 3.5 22.0 + - - +
323A LEU* 3.5 29.4 - - + +
400A PRO* 5.8 0.2 - - - +
526A GLU* 3.3 33.0 + - - +
527A VAL* 2.9 47.1 + - + +
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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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232A LEU* 4.0 36.6 - - + +
235A THR* 2.8 14.2 + - + +
237A GLN* 1.3 75.4 - - - +
239A ARG* 1.3 60.6 + - - +
241A ALA* 3.1 5.1 + - - +
242A VAL* 2.9 40.7 + - + +
264A PHE* 5.5 2.9 - - + -
304A LEU* 4.7 3.8 - - + -
307A VAL* 5.6 0.7 - - + -
311A MET* 4.8 2.9 - - + -
319A THR* 4.3 11.4 - - + -
320A ILE* 3.9 31.0 - - + -
323A LEU* 3.8 18.2 - - + +
324A PHE* 4.0 21.1 - - + -
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Residues in contact with ARG 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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232A LEU 4.6 1.2 + - - +
233A PHE* 2.9 62.9 + - + +
234A PHE* 4.1 7.9 - - - -
235A THR 3.2 2.7 + - - +
236A ASN* 3.0 29.8 + - - +
238A LEU* 1.3 78.4 - - - +
240A LYS* 1.3 57.7 + - - +
242A VAL* 3.1 4.2 + - - +
243A TYR* 2.9 41.1 + - + -
264A PHE* 3.5 35.2 - - + -
268A GLN* 2.9 41.4 - - - +
531A VAL* 3.8 21.9 + - - +
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Residues in contact with LYS 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 ASN 3.0 14.6 + - - +
237A GLN* 3.8 23.6 - - - +
239A ARG* 1.3 75.7 - - - +
241A ALA* 1.3 63.4 + - - +
243A TYR* 3.2 12.3 + - - +
244A MET* 3.1 28.7 + - + +
526A GLU 5.3 1.0 + - - -
529A GLN* 3.2 42.2 + - - +
530A ALA 4.7 1.6 - - - +
531A VAL* 3.6 24.9 - - + -
535A ASP* 3.9 32.3 + - + +
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Residues in contact with ALA 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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237A GLN 3.3 8.4 + - - +
238A LEU* 3.1 9.5 + - - +
240A LYS* 1.3 79.8 - - - +
242A VAL* 1.3 61.3 + - - +
244A MET* 3.2 17.2 + - - +
245A MET 3.4 5.2 + - - -
311A MET* 3.7 11.3 - - + +
316A VAL* 3.5 22.8 - - + +
319A THR* 3.5 36.3 - - + +
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Residues in contact with VAL 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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238A LEU* 2.9 26.2 + - + +
239A ARG 3.1 7.2 + - - +
241A ALA* 1.3 72.4 - - - +
243A TYR* 1.3 64.1 + - - +
244A MET 3.0 1.8 - - - -
245A MET* 3.1 24.0 + - - +
257A PRO* 4.4 2.2 - - + +
260A LEU* 4.1 17.7 - - + -
261A GLN* 3.0 45.1 - - + +
264A PHE* 4.1 22.4 - - + -
307A VAL* 4.7 9.6 - - + -
311A MET* 4.1 13.0 - - + -
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Residues in contact with TYR 243 (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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239A ARG* 2.9 35.0 + - + -
240A LYS* 3.2 12.5 + - - +
242A VAL* 1.3 76.5 - - - +
244A MET* 1.3 60.2 + - - +
245A MET 4.0 1.6 - - - +
261A GLN* 3.5 27.2 - - - +
264A PHE* 3.1 40.5 + + + +
265A TYR* 3.3 10.0 + - + -
268A GLN* 2.7 34.2 + - - -
531A VAL* 4.1 7.6 - - + -
535A ASP 4.2 6.1 - - - +
536A ILE* 3.5 29.1 - - + +
537A PRO* 3.5 29.8 - - + +
540A LEU* 3.8 19.5 - - + +
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Residues in contact with MET 244 (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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240A LYS* 3.1 18.4 + - + +
241A ALA* 3.3 10.5 - - - +
242A VAL 3.0 1.0 - - - -
243A TYR* 1.3 75.5 - - - +
245A MET* 1.3 64.9 + - - +
246A PRO* 3.5 4.3 - - - +
315A CYS* 4.0 16.9 - - - -
316A VAL* 3.5 20.0 - - + -
535A ASP* 4.2 14.1 - - - +
537A PRO* 3.9 21.4 - - - +
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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