Contacts of the helix formed by residues 277 - 291 (chain B) in PDB entry 2P1N
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 VAL 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B TYR* 3.1 13.7 + - - +
246B THR* 3.4 26.9 - - - +
247B ALA 4.7 5.2 - - - +
249B VAL* 5.9 3.6 - - + -
275B ASP 4.1 1.6 - - - +
276B ALA* 1.3 69.0 - - - +
278B PRO* 1.3 75.2 - - + +
279B ALA* 4.3 6.1 - - + +
280B TYR* 2.8 53.0 + - + +
281B LEU* 3.7 6.9 + - - +
301B VAL* 4.8 0.9 - - - -
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Residues in contact with PRO 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ALA 3.7 2.7 - - - +
277B VAL* 1.3 82.7 - - + +
279B ALA* 1.3 61.8 + - - +
280B TYR 3.0 1.9 + - - -
281B LEU* 3.3 25.7 + - + +
282B PRO* 3.5 10.2 - - - +
301B VAL* 3.6 22.9 - - + -
305B ASP* 3.5 30.2 - - - +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B VAL* 4.2 35.7 - - + -
254B TYR* 3.9 13.3 - - - -
277B VAL* 2.9 7.0 + - + +
278B PRO* 1.3 76.3 - - - +
280B TYR* 1.3 63.6 + - + +
282B PRO* 3.6 11.0 - - - +
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 3.8 12.8 - - + -
245B TYR* 2.9 33.3 + - + +
247B ALA* 3.5 20.6 - - + -
248B GLU 2.5 31.2 + - - -
249B VAL* 4.2 9.0 - - + -
250B ARG 3.1 17.4 + - - -
253B VAL* 3.6 20.5 - - + +
254B TYR* 3.9 38.6 - + + -
257B LEU* 4.1 14.1 - - + -
277B VAL* 2.8 36.4 + - + +
279B ALA* 1.3 75.7 - - + +
281B LEU* 1.3 63.6 + - - -
282B PRO* 3.1 4.1 - - - -
283B ALA* 3.3 13.7 + - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TYR* 3.9 19.1 - - + -
273B PHE* 4.2 22.9 - - + -
276B ALA* 4.5 6.1 - - + -
277B VAL 3.7 5.8 + - - +
278B PRO* 3.3 14.1 + - + +
280B TYR* 1.3 75.4 - - - +
282B PRO* 1.3 67.1 - - + +
284B VAL* 2.7 32.6 + - + +
285B TYR* 3.8 9.7 - - + +
296B LEU* 4.9 4.9 - - + -
301B VAL* 4.1 35.7 - - + -
305B ASP* 4.5 14.4 - - + +
306B LEU* 6.1 0.7 - - + -
309B LEU* 4.6 22.4 - - + -
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Residues in contact with PRO 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 3.4 18.0 + - + +
278B PRO 3.5 13.5 - - - +
279B ALA* 3.6 10.3 - - - +
280B TYR 3.1 6.5 - - - -
281B LEU* 1.3 93.3 - - + +
283B ALA* 1.3 52.0 + - - +
284B VAL 2.8 0.7 - - - -
285B TYR* 2.8 69.7 + - + +
286B SER 4.8 0.2 + - - -
308B LYS* 5.7 5.4 - - - +
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TYR* 4.2 2.0 - - - +
254B TYR* 3.3 27.2 + - + -
257B LEU* 3.8 25.6 - - + -
258B SER* 3.9 25.1 - - - +
261B LEU* 3.7 17.7 - - + +
280B TYR 3.3 15.6 + - - +
281B LEU 2.9 0.2 + - - -
282B PRO* 1.3 76.7 - - - +
284B VAL* 1.3 59.5 + - - +
285B TYR 3.3 1.0 + - - -
286B SER* 4.6 6.1 + - - -
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TYR* 3.8 16.6 - - + +
261B LEU* 4.1 20.0 - - + -
270B LEU* 3.4 35.0 - - + -
273B PHE* 4.3 13.7 - - + -
281B LEU* 2.7 17.0 + - + +
283B ALA* 1.3 80.6 - - - +
285B TYR* 1.3 63.0 + - - +
286B SER 3.5 0.9 - - - -
287B VAL* 3.2 21.7 + - + +
288B CYS* 3.8 4.7 - - - -
309B LEU* 3.9 27.4 - - + -
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Residues in contact with TYR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 3.8 10.1 - - + +
282B PRO* 2.8 53.8 + - + +
283B ALA 3.2 0.8 - - - -
284B VAL* 1.3 78.9 - - - +
286B SER* 1.3 54.2 + - - +
288B CYS* 2.7 35.0 + - - +
289B SER 3.9 2.1 + - - -
305B ASP 4.9 1.4 + - - -
308B LYS* 3.8 32.1 + - + +
309B LEU* 3.9 32.6 + - + +
312B GLN* 3.2 37.2 - - + +
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Residues in contact with SER 286 (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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258B SER 5.0 0.2 + - - -
261B LEU* 4.6 0.5 - - - +
262B SER* 3.0 37.9 + - - -
282B PRO 4.8 0.2 + - - -
283B ALA 4.6 6.2 + - - -
285B TYR* 1.3 78.0 - - - +
287B VAL* 1.3 61.6 + - - +
288B CYS 2.9 4.0 + - - -
289B SER* 4.0 9.4 + - - +
290B ARG* 3.8 17.6 + - - -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 3.5 38.8 - - + +
264B CYS 4.4 0.2 - - - +
267B LEU* 3.7 27.6 - - + -
270B LEU* 4.1 11.9 - - + -
284B VAL 3.2 14.5 + - - +
285B TYR 3.0 0.6 - - - -
286B SER* 1.3 80.7 + - - +
288B CYS* 1.3 54.9 + - - +
289B SER 3.6 0.7 - - - -
290B ARG* 2.6 43.9 - - - +
291B LEU* 3.5 33.1 - - + +
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Residues in contact with CYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B VAL* 3.8 13.7 - - - -
285B TYR* 2.7 21.6 + - - +
286B SER 2.9 0.6 - - - -
287B VAL* 1.3 75.4 - - - +
289B SER* 1.3 55.5 + - - +
290B ARG 2.6 16.9 + - - -
291B LEU* 3.4 24.9 + - - +
294B LEU* 5.4 0.4 - - - -
309B LEU* 3.5 26.9 - - - -
312B GLN* 3.0 24.1 - - + +
313B CYS* 3.4 35.4 - - - -
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B TYR 3.9 2.2 + - - -
286B SER 4.0 7.9 + - - -
288B CYS* 1.3 76.6 - - - +
290B ARG* 1.3 77.0 + - - +
312B GLN* 3.3 8.2 + - - +
314B PRO* 4.2 18.2 - - - +
315B LYS* 3.6 20.7 - - - +
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Residues in contact with ARG 290 (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 LEU 4.8 1.4 + - - -
262B SER* 4.9 5.3 + - - +
264B CYS 2.9 26.1 + - - -
265B LYS* 3.5 31.4 + - - +
267B LEU* 3.4 21.8 - - - +
268B ARG* 3.5 38.1 + - - +
286B SER* 3.8 17.4 + - - -
287B VAL* 2.6 38.3 - - - +
288B CYS 2.6 9.9 + - - -
289B SER* 1.3 83.6 + - - +
291B LEU* 1.3 62.7 + - - +
292B THR* 3.5 4.9 + - - +
315B LYS* 4.5 12.0 - - - +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 3.8 9.6 - - + +
268B ARG 3.5 24.5 - - - +
269B CYS 3.9 2.5 - - - +
270B LEU* 4.1 13.7 - - + +
287B VAL* 3.5 32.3 - - + +
288B CYS* 3.4 34.4 + - - +
290B ARG* 1.3 77.1 - - - +
292B THR* 1.3 61.4 + - - +
293B THR 4.4 3.4 - - - +
294B LEU* 4.1 24.0 - - + -
313B CYS* 4.6 3.9 - - - +
315B LYS* 3.4 9.4 + - - +
316B LEU* 3.3 32.7 + - + +
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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
------------------------------------------------------------
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