Contacts of the helix formed by residues 258 - 274 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B HIS* 4.3 0.4 - - - -
246B THR* 2.9 22.4 - - - +
247B LYS 2.6 21.7 + - - +
248B GLU* 4.2 3.4 - - - +
249B ILE* 3.7 33.9 - - - +
250B ASP 5.8 0.2 - - - +
256B ARG 3.7 1.4 + - - -
257B PRO* 1.3 76.0 - - - +
259B LEU* 1.3 57.5 + - - +
260B MET* 4.1 13.3 - - - +
261B ALA* 2.9 20.3 + - - +
262B ALA* 2.8 24.1 + - - +
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ALA* 4.0 17.3 - - + -
186B LEU* 3.8 25.4 - - + -
241B CYS* 3.8 22.9 - - + -
242B GLY* 3.9 23.3 - - - +
245B HIS* 3.7 20.5 - - + +
246B THR 2.9 13.5 + - - +
247B LYS* 4.3 6.9 + - + +
258B ASN* 1.3 72.5 - - - +
260B MET* 1.3 63.1 + - - +
262B ALA* 3.0 12.1 + - + +
263B TYR* 3.1 51.3 + - + +
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Residues in contact with MET 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 3.4 19.8 - - + +
247B LYS 5.2 1.0 + - - -
258B ASN* 3.3 14.5 + - - +
259B LEU* 1.3 77.7 - - - +
261B ALA* 1.3 66.7 + - + +
263B TYR* 3.5 4.9 + - - +
264B HIS* 2.9 44.6 + - + +
1301B HEC 3.3 53.6 - - + -
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Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B PRO* 3.6 17.3 - - + -
258B ASN* 2.9 23.4 + - - +
260B MET* 1.3 80.4 - - + +
262B ALA* 1.3 58.1 + - - +
264B HIS* 4.4 6.7 - - - +
265B LEU* 2.7 42.5 + - + +
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B HIS* 3.8 20.6 - - + +
257B PRO* 4.0 2.8 - - - +
258B ASN 2.8 12.4 + - - +
259B LEU* 3.0 12.8 + - + +
261B ALA* 1.3 76.8 - - - +
263B TYR* 1.3 57.7 + - - +
266B GLN* 2.8 33.8 + - - +
1299B HEC 3.3 43.2 - - + +
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Residues in contact with TYR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ILE* 3.5 20.9 - - + +
185B ALA* 3.9 12.5 - - + +
186B LEU* 4.2 5.2 - - + -
241B CYS* 4.0 14.4 - - + -
242B GLY 5.2 0.9 + - - -
259B LEU* 3.1 48.9 + - + +
260B MET* 3.8 4.3 - - - +
262B ALA* 1.3 78.2 - - - +
264B HIS* 1.3 63.2 + - - +
266B GLN* 3.1 1.6 + - - -
267B CYS* 2.8 32.1 + - - -
1298B HEC 2.5 39.4 + - + -
1299B HEC 4.3 11.9 - - + -
1300B HEC 5.0 1.8 - - + -
1301B HEC 3.4 57.0 - + + -
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Residues in contact with HIS 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B MET* 2.9 37.5 + - + +
261B ALA* 4.0 5.7 - - - +
263B TYR* 1.3 76.1 - - - +
265B LEU* 1.3 63.7 + - + +
267B CYS* 5.1 1.1 - - - -
268B MET* 3.0 51.5 + - + +
1301B HEC 2.0 96.2 + + + -
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 4.4 2.8 - - - +
257B PRO* 4.0 26.2 - - + -
261B ALA* 2.7 31.0 + - + +
264B HIS* 1.3 75.4 - - + +
266B GLN* 1.3 58.7 + - - +
268B MET* 5.1 0.9 - - - -
269B GLY* 2.8 28.5 + - - +
1299B HEC 3.5 20.6 - - + -
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Residues in contact with GLN 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 3.6 29.6 - - + +
227B THR 4.3 1.4 - - - +
228B CYS* 3.1 50.5 - - - +
230B HIS* 3.8 7.6 + - - -
262B ALA 2.8 18.3 + - - +
263B TYR* 3.7 2.2 - - - +
265B LEU* 1.3 81.3 - - - +
267B CYS* 1.3 66.2 + - - +
269B GLY* 3.2 5.5 + - - -
270B CYS 3.2 10.9 + - - -
1298B HEC 4.6 7.5 - - - +
1299B HEC 3.2 50.3 - - + +
1300B HEC 3.8 8.8 - - + +
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Residues in contact with CYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B TYR* 2.8 30.8 + - - +
264B HIS 4.5 0.4 - - - +
266B GLN* 1.3 76.2 - - - +
268B MET* 1.3 63.0 + - + +
270B CYS* 3.6 0.9 + - - +
271B HIS* 3.2 30.0 + - - -
1300B HEC 1.8 73.8 - - + +
1301B HEC 3.7 22.2 - - + -
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Residues in contact with MET 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B HIS* 3.0 43.8 + - + +
265B LEU* 4.7 0.7 - - - +
267B CYS* 1.3 73.5 - - - +
269B GLY* 1.3 65.8 + - - +
271B HIS* 3.8 7.9 - - - +
272B LYS* 2.9 26.9 + - - +
281B ASP* 3.0 49.3 - - - +
1301B HEC 3.4 55.0 - - + -
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Residues in contact with GLY 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA* 3.7 7.9 - - - +
117B ILE* 3.9 13.5 - - - -
265B LEU 2.8 22.6 + - - -
266B GLN 3.2 0.6 + - - -
268B MET* 1.3 78.2 - - - +
270B CYS* 1.3 55.8 + - - +
272B LYS* 3.4 5.2 + - - +
273B GLY* 2.9 24.6 + - - -
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Residues in contact with CYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLY* 3.4 30.2 - - - +
117B ILE* 3.7 4.7 - - + +
266B GLN 3.2 6.2 + - - +
269B GLY* 1.3 74.4 - - - +
271B HIS* 1.3 64.4 + - - +
273B GLY* 2.8 11.1 + - - -
274B MET* 3.0 18.1 + - - +
1300B HEC 1.8 91.5 - - + -
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Residues in contact with HIS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B CYS 3.2 12.9 + - - +
268B MET* 3.8 6.9 - - - +
270B CYS* 1.3 79.0 - - - +
272B LYS* 1.3 62.1 + - - +
274B MET 3.7 0.3 + - - -
275B ASP 3.3 1.2 + - - -
276B VAL* 2.6 47.7 + - + +
279B PRO* 3.7 30.0 + - + +
281B ASP* 5.4 2.9 - - - +
1300B HEC 1.9 96.5 + + + -
1301B HEC 3.8 11.5 - - + +
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Residues in contact with LYS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B MET 2.9 17.9 + - - +
269B GLY* 3.8 4.5 - - - +
271B HIS* 1.3 78.8 - - - +
273B GLY* 1.3 62.9 + - - +
275B ASP* 3.4 15.2 + - - +
281B ASP* 4.9 15.5 - - - +
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Residues in contact with GLY 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ARG* 5.2 0.5 - - - -
112B ALA* 3.5 36.0 - - - +
116B ALA* 4.1 6.1 - - - -
269B GLY 2.9 11.8 + - - -
270B CYS 2.8 7.0 + - - -
272B LYS* 1.3 81.4 - - - +
274B MET* 1.3 57.7 + - - +
275B ASP* 3.4 6.2 + - - +
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Residues in contact with MET 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ARG* 3.2 51.3 + - + +
110B GLU* 4.4 6.3 - - - +
113B GLY* 3.7 9.6 - - - -
114B CYS 4.9 0.7 - - - -
204B LEU* 3.8 14.6 - - + -
207B ARG* 3.9 32.5 - - - +
270B CYS* 3.0 39.9 + - - +
273B GLY* 1.3 75.3 - - - +
275B ASP* 1.3 70.8 + - - +
276B VAL* 3.2 13.8 + - + +
1300B HEC 3.7 21.3 - - + -
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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