Contacts of the helix formed by residues 242 - 257 (chain A) in PDB entry 1PXV
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 TRP 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A GLN* 3.6 0.2 - - - +
240A ASN* 2.9 33.1 + - + +
241A SER* 1.3 75.3 - - - +
243A ALA* 1.3 54.3 + - - +
244A ALA* 3.2 2.7 - - - -
245A GLY 2.7 25.3 + - - -
246A PHE* 2.8 21.0 + + + -
263A ALA* 4.3 6.5 - - + -
264A HIS* 3.7 49.8 - + + -
267A MET* 3.4 33.6 - - + +
276A GLU* 5.5 0.2 - - - -
279A LEU* 2.8 36.1 + - + -
280A PRO* 3.4 37.5 - - + +
282A CYS 3.4 16.8 - - - -
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLN* 3.4 17.3 - - - +
241A SER 3.3 5.1 + - - -
242A TRP* 1.3 75.3 - - - +
244A ALA* 1.3 55.9 + - - +
246A PHE* 3.3 5.4 + - - +
247A SER* 2.9 32.4 + - - -
340A HIS* 3.2 39.7 - - + +
341A ALA* 3.5 15.0 - - - +
361A PRO* 3.8 2.1 - - + +
98C GLY* 4.1 7.6 - - - -
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Residues in contact with ALA 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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242A TRP 3.0 1.4 + - - -
243A ALA* 1.3 76.6 - - - +
245A GLY* 1.3 58.8 + - - +
248A MET* 2.8 39.8 + - + +
284A THR* 3.5 27.8 - - + +
289A MET* 3.5 30.3 - - + -
323A MET* 4.0 4.5 - - - -
341A ALA* 3.7 12.2 - - + +
97C ILE 4.6 4.9 + - - +
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Residues in contact with GLY 245 (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 TRP 2.7 10.0 + - - -
244A ALA* 1.3 80.2 - - - +
246A PHE* 1.3 59.8 + - - -
248A MET* 4.3 1.7 - - - +
249A ALA* 3.0 26.5 + - - +
263A ALA* 3.7 12.0 - - - -
266A ILE* 3.7 20.0 - - - +
267A MET* 4.1 20.5 - - - -
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Residues in contact with PHE 246 (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 GLU* 3.5 49.5 - - + +
236A GLN 3.5 20.4 - - - -
237A GLN* 3.4 34.1 - - + -
240A ASN* 3.4 26.5 - - - -
242A TRP* 2.8 33.5 + + + -
243A ALA 3.6 2.7 - - - +
245A GLY* 1.3 76.2 - - - +
247A SER* 1.3 61.6 + - - +
249A ALA* 3.3 2.3 + - - +
250A ALA* 3.1 24.8 + - - +
263A ALA* 3.5 16.3 - - + +
359A TRP* 3.7 9.5 - + + -
361A PRO* 3.6 21.3 - - + -
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ALA 2.9 17.9 + - - -
246A PHE* 1.3 74.1 - - - +
248A MET* 1.3 65.6 + - - +
250A ALA* 3.3 3.1 + - - +
251A LEU* 3.0 30.1 + - - +
323A MET* 3.7 16.6 - - - -
341A ALA 3.4 2.1 + - - -
342A LEU* 3.2 42.9 - - - -
343A ALA* 3.6 8.9 + - - +
359A TRP* 4.5 2.7 - - - -
361A PRO* 3.6 5.4 - - - +
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Residues in contact with MET 248 (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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244A ALA* 2.8 40.1 + - + +
245A GLY 4.3 0.4 - - - +
247A SER* 1.3 72.0 - - - +
249A ALA* 1.3 58.1 + - - +
251A LEU* 3.3 6.4 + - - -
252A LEU* 2.9 38.6 + - + +
266A ILE* 4.1 32.1 - - + -
270A LEU* 4.7 2.7 - - + -
284A THR* 4.7 7.6 - - + -
289A MET* 3.9 19.5 - - - +
292A TYR* 4.0 15.7 - - + -
323A MET* 3.6 20.4 - - + -
393A TYR* 3.6 36.3 - - + -
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Residues in contact with ALA 249 (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 GLU* 4.0 5.2 - - - +
245A GLY 3.0 20.3 + - - +
246A PHE 3.7 4.5 - - - +
247A SER 3.2 0.2 - - - -
248A MET* 1.3 75.6 - - - +
250A ALA* 1.3 58.4 + - - +
253A ASN* 2.9 37.1 + - - +
261A TYR* 3.7 7.7 - - - +
262A ASN* 3.7 37.9 - - - +
263A ALA 3.9 1.3 - - - +
266A ILE* 3.7 8.7 - - + +
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Residues in contact with ALA 250 (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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231A PHE* 3.7 28.2 - - + -
232A LYS 4.7 12.9 + - - +
233A ILE* 5.8 0.7 - - - -
234A ARG 6.1 0.4 - - - +
246A PHE 3.1 15.5 + - - +
247A SER 3.9 2.9 - - - +
249A ALA* 1.3 77.5 - - - +
251A LEU* 1.3 58.1 + - - +
253A ASN* 3.5 7.5 + - - +
254A ALA* 3.0 27.9 + - - +
343A ALA* 5.1 0.2 - - + -
359A TRP* 3.8 19.5 - - + -
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Residues in contact with LEU 251 (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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228A LEU* 3.9 17.7 - - + -
231A PHE* 4.5 3.8 - - + -
247A SER 3.0 23.4 + - - +
248A MET* 3.8 3.6 - - - +
250A ALA* 1.3 75.2 - - - +
252A LEU* 1.3 61.0 + - - +
254A ALA* 3.3 3.7 + - - +
255A THR* 2.9 35.1 + - - +
321A GLY* 4.0 6.3 - - - -
322A ILE 3.5 32.8 - - - +
323A MET* 3.9 14.6 - - + +
343A ALA* 4.0 12.6 - - + -
344A VAL 3.5 24.7 - - - +
393A TYR* 3.9 23.1 - - + -
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Residues in contact with LEU 252 (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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248A MET* 2.9 23.8 + - + +
251A LEU* 1.3 71.9 - - - +
253A ASN* 1.3 61.1 + - - +
255A THR* 3.9 2.9 - - - +
256A LYS* 2.8 42.3 + - + +
261A TYR* 3.8 29.2 - - + -
266A ILE* 4.8 0.2 - - + -
292A TYR* 3.7 32.1 - - + -
293A GLY* 5.5 1.1 - - - +
296A GLN* 4.3 13.5 - - + -
298A ARG* 3.9 19.7 - - + +
393A TYR* 3.5 36.1 - - + +
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Residues in contact with ASN 253 (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 ASN* 4.8 1.7 - - - +
232A LYS 5.9 0.2 - - - +
234A ARG* 3.6 24.8 - - - +
249A ALA* 2.9 26.5 + - - +
250A ALA* 3.8 6.7 - - - +
252A LEU* 1.3 74.7 - - - +
254A ALA* 1.3 58.2 + - - +
257A ASN* 3.0 8.0 + - - -
258A THR* 2.9 48.7 + - - +
259A ASP* 3.7 8.2 + - - +
260A THR 3.3 5.2 + - - -
261A TYR* 3.0 50.5 + - - -
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Residues in contact with ALA 254 (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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228A LEU* 4.2 10.8 - - + -
229A LYS 3.4 25.7 - - - +
230A ASN* 3.6 19.3 + - - +
231A PHE* 3.8 27.4 - - + +
234A ARG* 5.3 0.2 - - - +
250A ALA 3.0 17.9 + - - +
251A LEU 3.5 4.3 - - - +
252A LEU 3.2 0.2 - - - -
253A ASN* 1.3 77.5 - - - +
255A THR* 1.3 62.9 + - - +
257A ASN 3.2 8.7 + - - -
319A ASN* 4.1 1.2 + - - -
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Residues in contact with THR 255 (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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228A LEU* 4.4 9.2 - - + -
251A LEU 2.9 23.2 + - - +
252A LEU* 3.7 4.3 + - - -
254A ALA* 1.3 74.7 - - - +
256A LYS* 1.3 60.9 + - - +
257A ASN* 5.0 1.0 - - - +
298A ARG* 2.9 21.0 + - - -
319A ASN* 3.4 36.6 + - - +
321A GLY* 4.0 8.3 - - - +
393A TYR* 2.6 38.0 + - - +
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Residues in contact with LYS 256 (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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252A LEU* 2.8 25.4 + - + +
255A THR* 1.3 77.9 + - - +
257A ASN* 1.3 70.1 + - - +
258A THR* 3.9 16.7 - - + -
261A TYR* 3.8 23.8 - - + -
296A GLN* 2.7 31.6 + - - -
297A GLY* 4.7 2.4 - - - -
298A ARG* 3.4 32.4 - - - +
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Residues in contact with ASN 257 (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 ASN* 3.2 38.2 + - - +
253A ASN 3.0 9.5 + - - -
254A ALA 3.2 7.2 + - - +
255A THR 3.2 1.3 - - - +
256A LYS* 1.3 82.0 - - - +
258A THR* 1.3 60.1 + - - +
230B ASN* 5.5 2.6 - - - +
257B ASN* 5.0 9.7 + - - +
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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