Contacts of the helix formed by residues 261 - 278 (chain A) in PDB entry 4LOX
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 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLY 3.7 3.2 - - - +
4A GLU* 3.6 31.4 - - - -
50A LYS* 3.2 39.6 + - - +
51A ASP* 2.7 19.2 + - - -
53A PHE* 3.6 1.2 - - - -
260A GLY* 1.3 66.1 - - - -
262A LYS* 1.3 58.1 + - - +
263A TYR 3.0 5.8 - - - -
264A GLY* 2.8 24.5 + - - -
265A ASP* 3.6 6.9 + - - +
301A ARG* 4.2 14.0 + - - -
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Residues in contact with LYS 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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50A LYS* 5.5 0.6 - - - +
51A ASP* 5.3 1.0 + - - -
176A VAL 3.8 14.6 - - - +
177A SER* 3.3 26.7 - - - +
180A GLY 2.9 26.1 + - - +
181A SER* 4.3 0.6 - - - +
182A PHE* 4.2 21.5 - - + +
258A ILE* 3.7 15.3 - - + -
259A ILE 4.4 5.4 - - - +
260A GLY 3.1 0.6 - - - -
261A SER* 1.3 79.0 + - - +
263A TYR* 1.3 56.3 + - - +
264A GLY 3.3 0.2 - - - -
265A ASP* 3.0 19.2 + - + +
266A TYR* 2.9 26.9 + - - +
298A ASN* 5.4 1.1 + - - +
16E C 3.9 15.8 + - - -
17E A 3.1 26.5 + - - -
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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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3A GLY 3.8 17.9 - - - +
4A GLU 4.1 3.1 - - - -
5A ASN* 3.8 19.5 - - + +
254A HIS* 5.7 2.4 + - - -
257A LYS* 3.6 42.8 - - + -
258A ILE* 3.5 38.7 - - + +
260A GLY 3.1 16.0 + - - +
261A SER 2.9 0.4 + - - -
262A LYS* 1.3 76.9 - - - +
264A GLY* 1.3 55.0 + - - +
266A TYR* 3.3 22.0 + + - +
267A MET* 3.0 53.3 + - + +
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Residues in contact with GLY 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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3A GLY* 3.0 22.9 + - - -
261A SER 2.8 8.9 + - - -
263A TYR* 1.3 72.4 - - - +
265A ASP* 1.3 62.9 + - - +
267A MET* 3.3 16.8 + - - +
268A ASP* 3.0 22.3 + - - +
301A ARG* 3.1 22.2 + - - -
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 5.8 1.7 + - - -
182A PHE* 4.9 4.9 - - + -
261A SER* 3.6 2.3 + - - +
262A LYS* 3.0 29.2 + - + +
264A GLY* 1.3 74.8 - - - +
266A TYR* 1.3 58.6 + - - +
268A ASP* 3.3 1.0 + - - -
269A TRP* 2.9 29.0 + - - +
297A MET* 3.7 11.2 - - + +
298A ASN* 2.6 55.3 + - - +
301A ARG* 2.8 32.4 + - - +
17E A 4.8 2.8 + - - -
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Residues in contact with TYR 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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182A PHE* 3.8 42.4 - + + -
249A ILE 4.9 0.2 - - - -
250A ILE* 2.7 36.0 + - + +
253A PHE* 3.7 25.8 - - + -
254A HIS* 3.0 25.6 + - + +
258A ILE* 4.6 5.6 - - + -
262A LYS 2.9 11.9 + - - +
263A TYR* 3.5 30.7 - + - +
265A ASP* 1.3 77.2 - - - +
267A MET* 1.3 64.1 + - + +
269A TRP* 3.2 8.8 + + - +
270A CYS* 2.9 59.4 + - - -
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Residues in contact with MET 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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3A GLY* 3.0 43.7 - - - +
263A TYR* 3.0 40.7 + - + +
264A GLY* 3.3 13.4 + - - +
266A TYR* 1.3 82.9 - - + +
268A ASP* 1.3 67.6 + - - +
270A CYS* 3.4 8.3 + - - +
271A LYS* 3.1 34.0 + - - +
301A ARG* 6.0 0.2 - - - +
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Residues in contact with ASP 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 GLY 3.0 15.8 + - - +
265A ASP 3.8 3.8 - - - +
267A MET* 1.3 76.8 - - - +
269A TRP* 1.3 65.2 + - - +
271A LYS* 3.1 37.1 + - - +
272A ILE* 3.2 17.3 + - - +
293A LEU* 4.0 19.5 - - + +
296A GLY 4.4 4.0 - - - +
297A MET* 4.1 24.2 - - + +
301A ARG* 2.9 25.1 + - - -
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Residues in contact with TRP 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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182A PHE* 3.6 42.6 - + + -
183A LYS 2.9 30.5 + - - +
200A LEU* 3.6 21.6 - - + +
201A VAL 3.6 22.2 - - - -
202A PHE* 3.9 10.1 - - + -
245A ILE* 3.7 25.8 - - + -
249A ILE* 3.8 22.4 - - + -
250A ILE* 3.5 35.7 - - + -
265A ASP 2.9 14.2 + - - +
266A TYR* 3.3 16.6 - + - +
268A ASP* 1.3 77.4 - - - +
270A CYS* 1.3 57.4 + - - +
272A ILE* 3.1 9.9 + - - +
273A ALA* 3.0 25.5 + - - +
297A MET* 3.9 12.0 - - + +
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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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250A ILE* 4.1 21.8 - - + -
266A TYR* 2.9 58.7 + - - -
267A MET* 3.5 10.1 - - - +
269A TRP* 1.3 75.2 - - - +
271A LYS* 1.3 63.8 + - + +
273A ALA* 3.3 10.5 + - - +
274A LEU* 3.0 21.7 + - - +
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Residues in contact with LYS 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 MET* 3.1 22.5 + - - +
268A ASP* 3.1 31.3 + - - +
270A CYS* 1.3 72.6 - - + +
272A ILE* 1.3 66.6 + - - +
274A LEU* 3.3 9.8 + - + +
275A ILE* 3.1 27.5 + - + +
293A LEU* 3.8 26.7 - - + -
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Residues in contact with ILE 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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184A SER* 3.4 30.1 - - - +
198A SER* 4.2 1.3 - - - +
200A LEU* 3.6 18.8 - - + -
268A ASP 3.2 9.7 + - - +
269A TRP* 3.1 11.5 + - - +
271A LYS* 1.3 72.7 - - - +
273A ALA* 1.3 67.7 + - - +
275A ILE* 2.9 10.5 + - - +
276A MET* 2.9 34.7 + - - +
290A ILE* 4.0 28.9 - - + -
293A LEU* 3.9 24.5 - - + -
294A LYS* 4.4 2.9 - - + -
297A MET* 3.9 20.0 - - - -
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Residues in contact with ALA 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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200A LEU* 3.6 19.0 - - + +
242A PHE* 3.3 21.3 - - + -
246A GLN* 3.9 6.5 + - + +
250A ILE* 3.6 29.6 - - + -
269A TRP 3.0 7.3 + - - +
270A CYS 3.5 9.2 - - - +
272A ILE* 1.3 78.6 - - - +
274A LEU* 1.3 50.2 + - - +
276A MET* 3.3 1.1 + - - -
277A GLN* 2.8 32.0 + - - +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A GLN* 5.2 0.7 - - - +
270A CYS 3.0 12.0 + - - +
271A LYS* 3.5 13.0 - - + +
272A ILE 3.1 0.2 - - - -
273A ALA* 1.3 74.1 - - - +
275A ILE* 1.3 68.5 + - + +
277A GLN* 3.1 30.3 + - - +
278A ASN* 3.0 40.4 + - - +
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Residues in contact with ILE 275 (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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271A LYS* 3.1 15.0 + - + +
272A ILE 2.9 7.4 + - - +
274A LEU* 1.3 82.0 - - + +
276A MET* 1.3 60.1 + - - +
278A ASN* 3.3 6.9 + - - +
279A LYS 3.2 2.9 + - - -
280A ASN* 3.0 38.0 + - + -
281A HIS 3.8 17.3 - - - +
286A GLY* 4.2 7.9 - - - +
289A GLU* 3.3 33.4 - - + +
290A ILE* 3.8 23.3 - - + -
293A LEU* 3.8 24.0 - - + -
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Residues in contact with MET 276 (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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198A SER* 3.2 41.7 - - - +
199A ILE* 4.7 0.2 - - - -
200A LEU* 4.0 19.7 - - - +
242A PHE* 3.6 36.4 - - + -
272A ILE* 2.9 25.4 + - - +
273A ALA 3.6 7.4 - - - +
274A LEU 3.2 0.2 - - - -
275A ILE* 1.3 74.7 - - - +
277A GLN* 1.3 63.0 + - - +
279A LYS* 3.0 16.1 + - - +
281A HIS* 3.3 46.9 - - + +
290A ILE* 4.2 2.9 - - + -
3B T 5.3 2.9 - - - +
4B A 6.1 0.4 - - - +
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Residues in contact with GLN 277 (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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242A PHE* 4.2 7.6 - - - -
246A GLN* 2.9 44.6 + - - +
273A ALA 2.8 9.9 + - - +
274A LEU* 3.1 25.1 + - - +
276A MET* 1.3 77.6 - - - +
278A ASN* 1.3 78.9 + - - +
279A LYS* 3.2 18.7 + - - +
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Residues in contact with ASN 278 (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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274A LEU* 3.0 32.2 + - - +
275A ILE* 3.7 4.5 - - - +
277A GLN* 1.3 95.0 + - - +
279A LYS* 1.3 65.2 + - - +
280A ASN* 3.1 33.0 + - - +
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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
------------------------------------------------------------
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