Contacts of the helix formed by residues 258 - 274 (chain A) in PDB entry 1OFY
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 ASN 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A THR* 3.2 15.7 - - - +
247A LYS 3.5 16.4 + - - +
248A GLU* 3.9 4.9 - - - +
249A ILE* 3.3 36.3 - - + +
250A ASP 6.2 0.2 - - - +
256A ARG 3.7 1.6 + - - -
257A PRO* 1.3 74.5 - - - +
259A LEU* 1.3 61.4 + - - +
260A MET* 3.5 15.6 + - - +
261A ALA* 3.0 25.0 + - - +
262A ALA* 2.8 23.2 + - - +
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Residues in contact with LEU 259 (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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185A ALA* 4.0 18.4 - - + -
186A LEU* 3.8 25.6 - - + -
241A CYS* 3.7 28.0 - - + -
242A GLY* 3.8 22.0 - - - +
245A HIS* 3.4 18.6 + - + +
246A THR 2.8 15.0 + - - +
247A LYS* 4.2 7.7 - - + +
258A ASN* 1.3 73.7 - - - +
260A MET* 1.3 63.4 + - - +
262A ALA* 3.5 6.6 - - + +
263A TYR* 3.1 42.5 + - + +
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Residues in contact with MET 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 3.6 21.1 - - + +
247A LYS 5.3 1.4 + - - +
258A ASN* 3.3 16.3 + - - +
259A LEU* 1.3 77.1 - - - +
261A ALA* 1.3 70.2 - - + +
263A TYR* 3.4 5.5 + - - +
264A HIS* 3.0 43.2 + - + +
1301A HEC 3.8 45.0 - - + -
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Residues in contact with ALA 261 (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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257A PRO* 4.0 15.5 - - + -
258A ASN* 3.0 22.3 + - - +
260A MET* 1.3 80.3 - - + +
262A ALA* 1.3 60.6 + - - +
264A HIS* 4.3 7.0 - - - -
265A LEU* 2.7 43.9 + - + +
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Residues in contact with ALA 262 (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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245A HIS* 4.0 22.9 - - + +
257A PRO* 3.8 4.2 - - - +
258A ASN 2.8 17.2 + - - +
259A LEU* 3.5 9.6 - - + +
261A ALA* 1.3 77.1 - - - +
263A TYR* 1.3 64.1 + - - +
266A GLN* 3.1 26.7 + - - +
1299A HEC 3.6 37.5 - - + +
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Residues in contact with TYR 263 (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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183A ILE* 3.5 21.8 - - + +
185A ALA* 4.3 7.6 - - - +
186A LEU* 4.3 3.4 - - + -
241A CYS* 3.8 14.8 - - + -
242A GLY 5.1 0.3 + - - -
259A LEU* 3.1 54.6 + - + +
260A MET* 3.9 4.3 - - - +
262A ALA* 1.3 79.7 - - - +
264A HIS* 1.3 65.2 + - - +
267A CYS* 2.9 32.0 + - - -
1298A HEC 2.4 41.3 + - + -
1299A HEC 4.2 13.0 - - + -
1300A HEC 4.8 2.2 - - + -
1301A HEC 3.5 56.3 - + + -
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Residues in contact with HIS 264 (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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260A MET* 3.0 36.4 + - + +
261A ALA* 3.3 6.6 + - - +
263A TYR* 1.3 76.7 - - - +
265A LEU* 1.3 58.1 + - + +
267A CYS* 4.9 1.6 - - - -
268A MET* 2.8 55.6 + - + +
1301A HEC 2.0 92.2 + + + -
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 4.6 2.3 - - - +
257A PRO* 4.0 26.0 - - + -
261A ALA* 2.7 30.3 + - + +
264A HIS* 1.3 73.9 - - + +
266A GLN* 1.3 56.6 + - - +
268A MET* 5.0 1.6 - - - -
269A GLY* 2.9 26.9 + - - -
1299A HEC 3.6 18.4 - - + -
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Residues in contact with GLN 266 (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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117A ILE* 3.7 27.4 + - + +
227A THR 4.3 1.8 + - - -
228A CYS* 3.0 53.2 + - - +
230A HIS* 3.8 10.1 + - - -
262A ALA 3.1 18.8 + - - +
263A TYR 4.0 1.1 - - - +
265A LEU* 1.3 75.8 - - - +
267A CYS* 1.3 67.0 + - - +
269A GLY* 3.3 0.7 + - - -
270A CYS 3.2 17.7 + - - -
1298A HEC 4.6 4.9 - - - +
1299A HEC 3.5 46.9 - - + +
1300A HEC 3.7 11.3 - - + +
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Residues in contact with CYS 267 (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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263A TYR* 2.9 34.1 + - - +
264A HIS* 4.2 2.0 - - - +
266A GLN* 1.3 77.8 - - - +
268A MET* 1.3 63.6 + - - +
270A CYS* 3.5 1.9 + - - +
271A HIS* 3.2 29.3 + - - -
1299A HEC 6.3 0.2 - - - -
1300A HEC 1.8 83.0 - - + -
1301A HEC 3.8 22.2 - - + -
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Residues in contact with MET 268 (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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264A HIS* 2.8 42.7 + - + +
265A LEU* 4.6 1.8 - - - +
267A CYS* 1.3 72.1 - - - +
269A GLY* 1.3 59.7 + - - +
271A HIS* 3.6 5.0 - - - +
272A LYS* 2.8 33.4 + - - +
281A ASP* 3.5 57.7 - - - +
1301A HEC 3.6 48.2 - - + -
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Residues in contact with GLY 269 (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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116A ALA* 3.8 7.7 - - - +
117A ILE* 3.9 12.8 - - - -
265A LEU 2.9 23.7 + - - -
266A GLN 3.8 0.4 - - - -
267A CYS 3.2 0.2 - - - -
268A MET* 1.3 77.4 - - - +
270A CYS* 1.3 62.2 + - - +
272A LYS* 3.5 4.1 + - - +
273A GLY* 2.9 20.1 + - - -
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Residues in contact with CYS 270 (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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113A GLY* 3.5 28.9 - - - +
117A ILE* 3.7 4.7 - - + +
266A GLN 3.2 7.6 + - - +
269A GLY* 1.3 75.1 - - - +
271A HIS* 1.3 64.5 + - - +
273A GLY* 2.8 12.6 + - - -
274A MET* 3.0 17.7 + - - +
1300A HEC 1.8 91.3 - - + -
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Residues in contact with HIS 271 (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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267A CYS 3.2 12.1 + - - +
268A MET* 3.6 6.7 - - - +
270A CYS* 1.3 78.6 - - - +
272A LYS* 1.3 62.2 + - - +
274A MET 3.5 0.5 + - - -
275A ASP 3.2 3.3 + - - -
276A VAL* 2.8 45.5 + - + +
279A PRO* 3.8 21.7 + - + +
281A ASP* 4.8 4.6 + - - +
1300A HEC 1.9 94.7 + + - -
1301A HEC 3.5 22.2 - - + +
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Residues in contact with LYS 272 (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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268A MET 2.8 20.2 + - - +
269A GLY* 3.9 4.0 - - - +
271A HIS* 1.3 74.2 - - - +
273A GLY* 1.3 65.9 + - - +
274A MET 3.1 1.0 + - - -
275A ASP* 3.1 19.2 + - - +
281A ASP* 4.8 15.3 + - - +
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Residues in contact with GLY 273 (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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109A ARG* 5.2 1.0 - - - +
112A ALA* 3.6 34.6 - - - +
116A ALA* 4.3 6.5 - - - -
269A GLY 2.9 12.6 + - - -
270A CYS 2.8 13.3 + - - -
272A LYS* 1.3 77.2 - - - +
274A MET* 1.3 57.6 + - - -
275A ASP* 3.4 5.9 + - - +
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Residues in contact with MET 274 (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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109A ARG* 2.9 53.7 + - + +
110A GLU* 4.6 6.1 - - - +
113A GLY* 3.7 17.5 - - - -
114A CYS 4.9 0.2 - - - -
204A LEU* 3.7 24.7 - - + -
207A ARG* 3.8 28.7 - - - +
270A CYS* 3.0 25.2 + - - +
273A GLY* 1.3 77.4 - - - +
275A ASP* 1.3 67.5 + - - +
276A VAL* 3.4 14.8 + - + +
1300A HEC 3.7 23.1 - - + -
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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