Contacts of the helix formed by residues 247 - 263 (chain B) in PDB entry 2PID
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 GLN 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASP* 3.0 22.2 + - - -
123B SER* 4.3 0.6 - - - -
225B GLN* 2.9 27.7 + - - +
243B GLY* 4.2 2.7 - - - -
244B GLY 2.7 12.4 + - - +
246B ASP* 1.3 100.6 + - - +
248B LEU* 1.3 64.2 + - - +
249B GLY 3.3 2.7 - - - -
250B ASN* 3.1 13.7 + - - +
251B ILE* 2.9 41.5 + - + +
384B YSA 3.1 56.8 + - + +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASP* 4.5 9.9 - - - +
52B PHE* 3.3 39.7 - - + -
202B GLN* 6.3 2.7 - - + -
244B GLY 4.1 1.0 + - - -
245B SER* 3.3 17.7 + - - +
246B ASP 3.3 1.2 - - - -
247B GLN* 1.3 75.8 - - - +
249B GLY* 1.3 59.0 + - - +
251B ILE* 3.3 3.1 + - - +
252B MET* 2.9 46.3 + - + +
270B THR* 4.5 12.0 - - + +
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Residues in contact with GLY 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ARG* 3.9 27.7 - - - -
202B GLN* 6.0 1.6 - - - -
203B SER* 4.8 8.9 - - - -
222B GLN* 5.6 0.2 - - - -
246B ASP 4.6 3.2 + - - -
247B GLN 3.3 0.6 - - - -
248B LEU* 1.3 79.6 - - - +
250B ASN* 1.3 58.9 + - - +
252B MET* 3.2 7.4 + - - +
253B SER* 3.0 30.1 + - - -
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Residues in contact with ASN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASP* 3.3 13.5 + - - +
122B PRO* 5.9 0.7 - - - +
123B SER* 3.1 25.9 + - - -
221B TYR* 4.2 2.4 - - - -
222B GLN* 3.4 28.2 + - + +
225B GLN* 3.3 38.3 + - + +
226B ALA* 4.7 3.1 + - - -
241B GLN* 5.0 0.3 + - - -
246B ASP 5.3 0.2 + - - -
247B GLN* 3.1 25.2 + - - +
249B GLY* 1.3 76.2 - - - +
251B ILE* 1.3 63.1 + - - +
253B SER* 3.4 9.0 + - - +
254B GLY* 3.3 15.4 + - - -
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Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 4.0 9.4 - - + -
225B GLN* 4.3 0.4 - - - +
229B PHE* 4.3 6.5 - - + -
241B GLN* 3.6 45.1 - - + +
242B LEU 4.1 2.9 - - - -
243B GLY* 3.9 24.7 - - - +
247B GLN* 2.9 34.2 + - + +
248B LEU 3.8 3.6 - - - +
250B ASN* 1.3 73.3 - - - +
252B MET* 1.3 60.8 + - - +
254B GLY* 3.0 4.2 + - - -
255B TYR* 2.9 26.1 + - + +
267B PHE 4.8 0.2 - - - -
268B GLY* 3.7 26.0 - - - +
269B ILE 4.1 6.1 - - - +
270B THR* 4.5 9.0 - - + -
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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
----------------------------------------------------------
52B PHE* 3.9 25.6 - - + -
201B ARG* 3.8 26.2 - - - +
248B LEU* 2.9 38.3 + - + +
249B GLY* 3.4 11.0 - - - +
251B ILE* 1.3 75.1 - - - +
253B SER* 1.3 65.4 + - - +
255B TYR* 3.2 16.7 + - + +
256B GLU* 2.9 44.6 + - - +
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Residues in contact with SER 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 4.8 1.9 - - - -
198B LEU* 4.1 13.5 - - - +
201B ARG* 3.4 20.3 + - - +
222B GLN* 3.1 31.2 + - - +
226B ALA* 3.8 15.4 - - - +
249B GLY 3.0 10.7 + - - -
250B ASN* 3.7 9.6 - - - -
251B ILE 3.2 0.4 - - - -
252B MET* 1.3 75.2 - - - +
254B GLY* 1.3 63.2 + - - +
256B GLU* 3.7 2.7 - - - +
257B PHE* 3.0 25.8 + - - +
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Residues in contact with GLY 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ALA* 3.7 25.1 - - - +
229B PHE* 4.0 18.4 - - - -
241B GLN* 5.5 0.2 - - - -
250B ASN 3.3 6.2 + - - -
251B ILE 3.0 8.6 + - - -
253B SER* 1.3 79.7 - - - +
255B TYR* 1.3 61.7 + - - +
257B PHE* 3.2 1.0 + - - +
258B ILE* 2.9 28.6 + - - +
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Residues in contact with TYR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 5.6 7.0 - + + -
53B PRO* 3.5 27.0 - - + +
229B PHE* 4.2 3.7 - - + -
251B ILE* 2.9 12.7 + - + +
252B MET* 3.4 24.9 - - + +
254B GLY* 1.3 75.9 - - - +
256B GLU* 1.3 75.2 + - - +
258B ILE* 3.9 1.0 - - - +
259B ASN* 2.9 59.1 + - + +
265B ASP* 4.5 8.7 + - - -
266B VAL* 3.1 50.3 - - + -
267B PHE* 6.1 1.8 - - - -
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B THR* 4.2 19.9 - - + +
201B ARG* 2.9 32.8 + - - +
252B MET* 2.9 39.0 + - - +
253B SER* 3.7 4.3 - - - +
255B TYR* 1.3 86.0 - - + +
257B PHE* 1.3 61.3 + - - +
259B ASN* 3.8 3.7 + - - +
260B LYS* 2.8 35.4 + - - +
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Residues in contact with PHE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 3.7 24.5 - - + -
192B HIS* 3.6 33.0 - - + -
193B PHE* 3.4 47.6 - + + -
226B ALA* 4.2 7.9 - - + -
227B TYR* 4.3 6.5 - + - -
230B TYR* 3.6 42.8 - + + -
253B SER 3.0 18.8 + - - +
254B GLY 3.7 2.2 - - - +
256B GLU* 1.3 76.3 - - - +
258B ILE* 1.3 58.7 + - + +
260B LYS* 3.6 3.8 - - - +
261B LEU* 2.9 51.8 + - + +
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Residues in contact with ILE 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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229B PHE* 3.7 27.8 - - + +
230B TYR* 3.7 45.1 - - + +
233B PHE* 4.2 16.8 - - + -
254B GLY* 2.9 16.8 + - - +
255B TYR 3.9 2.2 - - - +
257B PHE* 1.3 76.1 - - + +
259B ASN* 1.3 57.7 + - - +
261B LEU* 3.3 2.6 + - - -
262B THR* 2.7 52.5 + - + +
264B GLU* 4.4 5.6 - - + +
266B VAL* 3.9 32.5 - - + -
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Residues in contact with ASN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B TYR* 2.9 42.1 + - + +
256B GLU* 3.8 5.5 + - - +
258B ILE* 1.3 75.1 - - - +
260B LYS* 1.3 63.7 + - - +
263B GLY* 2.6 36.9 + - - +
264B GLU 3.1 24.4 + - - +
265B ASP* 3.7 13.3 - - - +
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Residues in contact with LYS 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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192B HIS* 4.0 41.7 - - + +
194B ARG* 5.7 10.1 - - + +
256B GLU 2.8 23.8 + - - +
257B PHE* 3.6 5.4 - - - +
259B ASN* 1.3 77.3 - - - +
261B LEU* 1.3 63.0 + - - +
263B GLY 4.6 0.7 + - - -
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Residues in contact with LEU 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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188B ALA 5.8 0.2 - - - +
189B VAL* 5.0 3.8 - - + -
192B HIS* 3.2 47.3 - - + +
230B TYR* 4.1 26.5 - - + +
257B PHE* 2.9 48.5 + - + +
258B ILE* 4.0 2.5 - - - +
260B LYS* 1.3 79.3 - - + +
262B THR* 1.3 64.5 + - + +
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Residues in contact with THR 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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230B TYR* 4.2 24.5 - - + +
233B PHE* 4.5 13.9 - - + -
234B GLN* 4.6 7.2 - - - +
258B ILE* 2.7 30.2 + - + +
261B LEU* 1.3 78.2 - - + +
263B GLY* 1.3 57.2 + - - +
264B GLU* 2.9 34.9 + - - +
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Residues in contact with GLY 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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259B ASN* 2.6 32.3 + - - +
260B LYS 4.6 0.4 + - - -
261B LEU 3.8 0.4 - - - -
262B THR* 1.3 73.1 + - - +
264B GLU* 1.3 62.5 + - - +
265B ASP* 4.1 4.5 + - - +
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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