Contacts of the helix formed by residues 251 - 266 (chain B) in PDB entry 1OIZ
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 SER 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B PRO* 3.9 3.4 - - - -
243B LEU* 3.9 12.1 - - - +
244B GLU* 2.7 26.8 + - - -
249B GLU 4.1 0.2 + - - -
250B PHE* 1.3 75.9 - - - +
252B MET* 1.3 62.9 + - - +
253B GLU* 2.9 21.6 + - - +
254B ASP* 3.0 34.9 + - - +
255B ILE* 3.3 8.5 + - - +
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Residues in contact with MET 252 (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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101B HIS 4.6 0.2 - - - -
102B GLY 3.8 15.5 - - - +
104B LEU* 5.0 0.2 - - - -
116B ILE* 3.8 36.6 - - + +
118B ARG* 3.7 34.1 - - + +
242B PRO* 3.4 24.7 - - + +
244B GLU* 2.7 27.1 + - + +
245B TYR* 4.4 4.0 - - + -
251B SER* 1.3 71.4 + - - +
253B GLU* 1.3 58.1 + - - +
255B ILE* 3.2 31.4 + - + +
256B CYS* 2.8 47.7 + - - -
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Residues in contact with GLU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA 5.5 0.3 - - - +
99B GLY* 4.9 4.0 - - - -
118B ARG* 2.9 41.6 + - - -
121B HIS* 5.0 4.4 + - - -
244B GLU* 4.4 7.2 - - - +
251B SER* 2.9 16.4 + - - +
252B MET* 1.3 78.8 - - - +
254B ASP* 1.3 59.0 + - - +
256B CYS* 3.4 4.5 + - - +
257B GLN* 3.0 29.0 + - - +
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Residues in contact with ASP 254 (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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105B ARG* 4.0 19.7 + - - +
250B PHE* 4.0 8.3 - - - +
251B SER* 3.0 32.8 + - - +
253B GLU* 1.3 75.7 - - - +
255B ILE* 1.3 59.4 + - + +
257B GLN* 3.2 5.8 + - - +
258B GLU* 2.9 39.9 + - - +
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Residues in contact with ILE 255 (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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103B VAL 3.4 33.2 - - - +
104B LEU* 4.3 9.2 - - + +
105B ARG* 3.7 36.3 - - + +
242B PRO* 4.8 0.7 - - + -
250B PHE* 3.7 33.2 - - + -
251B SER 3.6 11.4 - - - +
252B MET* 3.2 37.4 + - + +
254B ASP* 1.3 76.9 - - - +
256B CYS* 1.3 61.4 + - - +
258B GLU* 3.4 6.2 + - - +
259B TRP* 3.0 23.4 + - - +
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Residues in contact with CYS 256 (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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96B LEU 4.9 3.4 - - - +
99B GLY* 3.6 36.3 - - - -
101B HIS 3.8 22.0 - - - +
102B GLY* 4.4 0.2 - - - -
118B ARG* 3.6 11.2 - - - +
252B MET* 2.8 42.7 + - - +
253B GLU* 3.7 7.2 - - - +
255B ILE* 1.3 72.9 - - - +
257B GLN* 1.3 57.0 + - - +
259B TRP* 3.3 2.6 + - - +
260B THR* 2.9 33.4 + - - -
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Residues in contact with GLN 257 (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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253B GLU 3.0 16.8 + - - +
254B ASP* 3.2 6.7 + - - +
256B CYS* 1.3 76.0 - - - +
258B GLU* 1.3 59.2 + - + +
260B THR* 3.2 14.5 + - - +
261B ASN* 2.9 70.0 + - - +
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Residues in contact with GLU 258 (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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105B ARG* 2.9 53.4 + - - +
254B ASP* 2.9 26.0 + - - +
255B ILE* 3.7 8.3 - - - +
257B GLN* 1.3 77.0 - - + +
259B TRP* 1.3 58.5 + - - +
261B ASN* 3.5 10.2 + - - +
262B PHE* 3.0 27.2 + - - +
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Residues in contact with TRP 259 (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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96B LEU* 4.9 4.5 - - + -
101B HIS* 3.7 24.8 - + - +
102B GLY* 3.9 11.2 - - - -
103B VAL* 3.5 37.2 - - + +
113B LYS* 5.7 3.6 - - - -
139B THR* 2.9 34.1 + - + -
142B LEU* 4.4 4.0 - - + -
143B ILE* 3.7 22.2 - - + -
255B ILE 3.0 17.0 + - - +
256B CYS 3.8 2.7 - - - +
258B GLU* 1.3 75.6 - - - +
260B THR* 1.3 58.9 + - - +
262B PHE* 3.1 40.3 + + + +
263B ILE* 2.9 55.6 + - + +
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Residues in contact with THR 260 (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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93B ILE* 4.0 25.8 - - + -
96B LEU* 3.4 42.5 + - + +
97B LYS* 4.7 9.4 - - + -
101B HIS 5.2 1.1 + - - -
256B CYS 2.9 22.8 + - - -
257B GLN* 3.4 18.8 - - - +
259B TRP* 1.3 76.4 - - - +
261B ASN* 1.3 64.5 + - - +
263B ILE* 3.3 2.6 + - - +
264B MET* 3.1 30.5 + - + +
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Residues in contact with ASN 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 GLN* 2.9 54.8 + - - +
258B GLU* 3.5 10.2 - - - +
260B THR* 1.3 72.7 - - - +
262B PHE* 1.3 56.7 + - - +
264B MET* 3.3 9.2 + - - +
265B LYS* 3.0 28.3 + - - +
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Residues in contact with PHE 262 (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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142B LEU* 3.8 33.4 - - + -
258B GLU 3.0 15.8 + - - +
259B TRP* 3.1 43.0 + + + +
261B ASN* 1.3 74.7 - - - +
263B ILE* 1.3 60.7 + - - +
265B LYS* 3.3 18.7 + - + +
266B SER* 2.6 43.7 + - - -
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Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO* 3.5 29.6 - - + -
92B ILE* 5.1 0.4 - - + -
96B LEU* 3.8 24.2 - - + -
138B ILE* 3.7 17.5 - - + -
139B THR* 4.5 1.6 - - - +
142B LEU* 3.2 28.0 - - + -
259B TRP* 2.9 44.9 + - + +
260B THR 3.3 6.7 + - - +
262B PHE* 1.3 74.3 - - - +
264B MET* 1.3 66.1 + - + +
266B SER* 3.3 14.2 + - - -
267B GLU* 3.3 11.6 + - - -
270B LEU* 3.8 11.1 - - + +
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Residues in contact with MET 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO* 3.2 39.9 - - + -
93B ILE* 3.4 32.8 - - + -
260B THR* 3.1 21.0 + - + +
261B ASN* 3.7 8.7 - - - +
262B PHE 3.3 0.2 - - - -
263B ILE* 1.3 78.7 - - + +
265B LYS* 1.3 65.7 + - - +
267B GLU* 3.3 30.9 - - + +
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Residues in contact with LYS 265 (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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261B ASN 3.0 13.1 + - - +
262B PHE* 3.5 24.0 - - + +
264B MET* 1.3 78.4 - - - +
266B SER* 1.3 57.0 + - - +
267B GLU* 3.3 3.9 + - - +
268B ASP* 4.9 3.3 + - - +
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Residues in contact with SER 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 3.8 23.4 - - - +
262B PHE* 2.6 46.3 + - - -
263B ILE 3.3 6.2 + - - -
264B MET 3.2 0.4 - - - -
265B LYS* 1.3 73.9 - - - +
267B GLU* 1.3 58.5 + - - +
268B ASP* 3.3 2.9 - - - -
269B TYR* 3.2 13.7 + - - +
270B LEU* 3.0 27.1 + - - +
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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