Contacts of the helix formed by residues 232 - 244 (chain A) in PDB entry 1OFD
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A ILE 3.4 0.2 - - - -
231A ASN* 1.3 91.6 - - - +
233A LEU* 1.3 63.9 + - - +
234A LEU 3.4 2.5 - - - -
235A GLY* 3.0 8.0 + - - -
236A ASN* 2.7 44.4 + - - -
325A PRO 3.6 0.9 + - - -
327A ASP* 3.2 17.7 + - + -
720A ILE* 3.6 24.7 - - + -
725A SER* 3.7 34.8 - - - +
729A ALA* 4.2 9.3 - - + +
731A ILE* 4.8 1.1 - - - -
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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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230A ILE* 3.8 20.6 - - + +
231A ASN 3.6 1.8 - - - -
232A THR* 1.3 76.9 - - - +
234A LEU* 1.3 57.2 + - - +
236A ASN* 3.7 6.6 - - + +
237A ILE* 2.8 61.7 + - + +
266A GLN 5.8 1.1 - - - +
268A ASN 4.4 7.6 - - - +
270A ASP* 3.7 42.8 - - + +
273A ASN* 4.4 2.9 - - + -
326A TRP* 4.1 23.1 - - + -
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Residues in contact with LEU 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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232A THR 3.4 0.8 - - - -
233A LEU* 1.3 78.0 - - - +
235A GLY* 1.3 58.7 + - - +
237A ILE* 3.6 5.9 + - - +
238A ASN* 3.0 46.6 + - - +
266A GLN* 4.3 16.8 + - - +
728A GLY 3.6 15.5 - - - +
729A ALA* 5.6 0.2 - - + -
730A GLN* 3.8 41.5 - - + +
731A ILE* 6.4 0.2 - - + -
747A ALA 4.7 1.1 - - - +
748A GLY* 4.1 25.1 - - - +
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Residues in contact with GLY 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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232A THR 3.0 7.8 + - - -
234A LEU* 1.3 78.4 - - - +
236A ASN* 1.3 59.4 + - - +
238A ASN* 3.1 2.8 + - - +
239A TRP* 2.9 40.1 + - - -
324A GLU* 5.9 0.2 - - - -
725A SER 5.2 2.2 - - - -
728A GLY* 3.6 32.3 - - - -
729A ALA* 3.6 6.1 - - - +
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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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230A ILE* 3.4 11.9 - - - +
232A THR* 2.7 44.1 + - - +
233A LEU* 3.7 4.0 - - - +
235A GLY* 1.3 74.0 - - - +
237A ILE* 1.3 62.6 + - - +
239A TRP* 4.0 1.7 - - - +
240A MET* 3.0 26.2 + - - +
324A GLU* 3.0 26.1 - - - +
325A PRO 3.1 15.6 - - - +
326A TRP* 3.3 48.9 + - + +
725A SER 5.2 0.5 - - - +
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Residues in contact with ILE 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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233A LEU* 2.8 48.0 + - + +
234A LEU* 3.7 4.5 - - - +
236A ASN* 1.3 75.9 - - - +
238A ASN* 1.3 58.3 + - - +
240A MET* 3.3 1.0 + - - +
241A ALA* 2.9 35.0 + - + +
264A VAL* 3.1 35.0 - - + +
265A ASN* 4.4 1.8 - - - +
266A GLN* 3.4 57.0 - - + +
273A ASN* 3.8 11.7 - - + +
326A TRP* 5.2 0.9 - - + -
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Residues in contact with ASN 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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234A LEU* 3.0 39.4 + - - +
235A GLY* 3.1 5.4 + - - +
237A ILE* 1.3 75.9 - - - +
239A TRP* 1.3 67.3 + - + +
241A ALA* 3.9 4.9 - - - +
242A ALA* 3.1 23.7 + - - +
266A GLN* 3.5 24.5 + - - +
626A HIS* 5.1 3.9 + - + +
627A HIS* 4.2 22.2 - - - -
630A ILE* 4.8 22.7 - - + +
728A GLY* 4.7 4.3 + - - +
730A GLN* 4.5 1.6 - - - +
747A ALA 5.1 1.2 + - - -
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Residues in contact with TRP 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 GLY 2.9 29.7 + - - +
236A ASN 4.1 0.4 - - - +
238A ASN* 1.3 78.3 - - + +
240A MET* 1.3 61.1 + - - +
242A ALA* 3.4 12.7 + - + +
243A ARG* 3.5 20.0 + - - +
323A GLN* 5.9 0.2 - - - +
324A GLU* 3.7 32.9 - - + +
525A ARG* 3.3 31.4 - - - +
626A HIS* 4.0 12.1 - + - -
630A ILE* 6.3 0.7 - - + -
635A ARG* 3.7 43.1 - - + -
636A LEU* 3.9 20.3 - - + +
724A ALA 4.6 3.6 + - - -
725A SER 5.7 0.7 - - - -
727A HIS* 3.3 36.6 - + - -
728A GLY* 3.0 33.6 - - - +
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Residues in contact with MET 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 19.0 + - - +
237A ILE 3.3 2.7 + - - +
239A TRP* 1.3 74.0 - - - +
241A ALA* 1.3 61.4 + - - +
243A ARG* 3.0 45.6 + - - +
244A GLU* 3.6 7.8 + - - +
247A LEU* 6.1 1.1 - - - -
263A ILE* 4.6 10.8 - - + -
264A VAL* 3.7 26.7 - - + -
277A ALA* 4.3 14.8 - - + +
280A LEU* 4.7 17.5 - - + -
281A LEU* 5.9 1.3 - - + -
295A LEU* 4.3 13.7 - - + -
323A GLN* 3.8 26.2 - - - +
326A TRP* 4.4 7.9 - - + +
528A LEU* 3.9 12.8 - - + -
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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 ILE* 2.9 23.4 + - + +
238A ASN* 3.9 5.8 - - - +
240A MET* 1.3 75.9 - - - +
242A ALA* 1.3 57.9 + - - +
244A GLU* 3.0 46.2 + - - +
245A LYS* 4.6 6.9 + - - -
264A VAL* 5.1 6.8 - - + +
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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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238A ASN 3.1 13.9 + - - +
239A TRP* 3.5 12.1 - - + +
240A MET 3.2 0.4 - - - -
241A ALA* 1.3 74.6 - - - +
243A ARG* 1.3 59.3 + - - +
244A GLU 3.6 0.2 + - - -
245A LYS* 4.3 17.4 + - - +
246A GLU* 5.3 3.1 + - - +
630A ILE* 5.3 11.2 - - + +
633A GLY 5.5 2.8 - - - +
635A ARG* 4.6 13.9 - - + +
636A LEU* 3.3 31.4 - - + +
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Residues in contact with ARG 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 TRP* 3.5 17.2 + - - +
240A MET* 3.0 31.0 + - - +
242A ALA* 1.3 77.8 - - - +
244A GLU* 1.3 62.1 + - - +
245A LYS 3.5 0.7 - - - -
246A GLU* 3.3 16.2 + - - +
247A LEU* 3.3 25.8 + - + +
322A LEU 2.5 32.9 + - - -
323A GLN* 3.5 18.2 - - - +
324A GLU* 5.1 0.6 + - - -
525A ARG* 4.3 19.9 + - - +
526A GLY 3.1 25.7 + - - -
528A LEU* 3.6 32.9 - - - +
636A LEU* 3.7 15.6 - - + +
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Residues in contact with GLU 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 MET 3.9 7.4 - - - +
241A ALA* 3.0 35.7 + - - +
242A ALA 3.3 0.2 - - - -
243A ARG* 1.3 77.2 - - - +
245A LYS* 1.3 63.6 + - + +
246A GLU 3.4 0.7 + - - -
247A LEU* 3.4 26.7 + - + +
257A LEU 6.1 0.3 - - - -
258A GLU* 5.7 0.9 - - - +
261A THR* 3.9 14.1 - - - +
262A PRO* 3.5 9.8 - - - +
263A ILE* 2.7 41.3 + - + +
264A VAL* 3.3 12.6 + - - +
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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