Contacts of the helix formed by residues 278 - 291 (chain B) in PDB entry 2C1H
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 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B PHE* 3.8 26.5 - - + -
206B TYR* 3.7 13.5 - - + -
253B LYS* 3.6 14.8 - - - -
254B PRO* 3.8 17.3 - - + -
276B TYR* 3.2 6.8 + - + +
277B HIS* 1.3 75.7 - - - +
279B SER* 1.3 67.3 + - - +
280B GLY 4.4 0.7 - - - +
281B GLU* 3.2 36.1 + - + +
282B TYR* 3.1 18.4 + - - +
1330B DSB 3.5 30.3 - - + +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B MET* 3.7 17.5 - - - -
205B PHE 3.6 1.4 + - - -
206B TYR 3.9 0.2 - - - -
208B PRO* 3.4 15.6 - - - +
209B PHE* 2.8 32.0 + - - +
278B VAL* 1.3 71.1 - - - +
280B GLY* 1.3 54.5 + - - +
282B TYR* 3.2 7.5 + - - +
283B ALA* 2.7 36.2 + - - +
318B TYR* 3.5 8.2 - - - -
1330B DSB 2.8 26.8 + - - -
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Residues in contact with GLY 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 4.5 9.0 - - - +
205B PHE* 2.9 33.0 + - - -
208B PRO* 4.1 11.9 - - - -
278B VAL 3.3 0.4 - - - -
279B SER* 1.3 72.7 + - - +
281B GLU* 1.3 58.6 + - - +
283B ALA* 3.3 1.6 + - - +
284B MET* 2.9 40.6 + - - +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A MET* 4.3 1.3 - - - +
205B PHE* 4.1 17.6 - - + -
254B PRO* 3.8 4.3 - - - +
255B GLY 3.2 11.1 + - - -
256B LEU* 3.0 48.8 + - + +
257B ALA* 4.1 3.5 + - - +
277B HIS* 3.0 33.5 + - + -
278B VAL* 3.2 33.3 + - + +
280B GLY* 1.3 74.1 - - - +
282B TYR* 1.3 61.7 - - - +
284B MET* 3.3 14.1 + - + +
285B VAL* 3.2 29.1 + - - +
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Residues in contact with TYR 282 (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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55B MET* 4.1 24.2 - - + -
56B PRO 2.7 29.0 + - - -
57B GLY* 3.6 16.5 - - - -
58B SER* 3.9 16.5 + - - -
277B HIS* 4.7 10.7 - + - +
278B VAL 3.1 12.3 + - - +
279B SER* 3.2 10.5 + - - +
281B GLU* 1.3 76.8 - - - +
283B ALA* 1.3 59.4 + - - +
285B VAL* 3.5 1.8 + - - -
286B LYS* 3.1 41.3 + - + +
300B MET* 3.9 30.3 - - + +
318B TYR* 3.6 43.4 + + + -
319B TYR* 4.0 10.0 - + + -
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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
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288A ALA* 4.1 4.7 - - + +
293A TRP* 3.6 15.6 - - + -
294A ILE* 5.5 1.1 - - + -
54B SER 3.5 24.9 - - - +
56B PRO* 5.3 0.4 - - - -
208B PRO* 3.9 11.9 - - + -
279B SER 2.7 19.9 + - - +
280B GLY* 3.8 3.8 - - - +
282B TYR* 1.3 74.7 - - + +
284B MET* 1.3 58.7 + - - +
286B LYS* 3.7 6.4 - - - +
287B ALA* 2.9 33.6 + - - +
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Residues in contact with MET 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 5.1 11.7 - - + -
281A GLU* 4.4 3.1 - - - +
284A MET* 3.2 64.9 - - + +
285A VAL* 3.7 28.7 - - + +
288A ALA* 4.1 9.9 - - + -
294A ILE* 4.4 7.2 - - + -
299A VAL* 4.3 13.9 - - + -
205B PHE* 4.5 13.7 - - + -
256B LEU* 6.3 0.4 - - + -
280B GLY 2.9 26.6 + - - +
281B GLU* 3.4 12.1 - - + +
282B TYR 3.2 0.4 - - - -
283B ALA* 1.3 75.7 - - - +
285B VAL* 1.3 64.6 + - - +
287B ALA* 4.3 0.2 - - - -
288B ALA* 3.3 16.8 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A MET* 3.7 18.2 - - + -
256B LEU* 5.8 2.2 - - + -
277B HIS* 5.5 4.0 - - + -
281B GLU 3.2 15.8 + - - +
282B TYR 3.9 1.1 - - - +
283B ALA 3.4 0.2 - - - -
284B MET* 1.3 75.5 - - - +
286B LYS* 1.3 58.9 + - - +
289B ALA* 3.0 29.3 + - - +
294B ILE* 3.3 20.5 - - + +
296B GLU* 4.1 12.1 - - + +
299B VAL* 3.9 19.1 - - + -
300B MET* 3.7 44.2 - - + +
303B SER* 5.4 3.1 - - - +
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Residues in contact with LYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A TRP* 4.7 2.2 - - + -
56B PRO* 3.2 55.0 + - + +
57B GLY* 4.6 4.6 - - - -
282B TYR* 3.1 28.5 + - + +
283B ALA* 3.7 8.3 - - - +
284B MET 3.3 0.2 - - - -
285B VAL* 1.3 78.7 - - - +
287B ALA* 1.3 61.0 + - - +
289B ALA* 4.0 4.5 - - - +
290B ALA* 3.3 22.3 + - - +
296B GLU* 3.1 31.8 + - - +
300B MET* 4.2 14.1 - - + +
319B TYR* 5.1 5.9 - - - -
322B GLU* 5.8 4.0 - - - +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ALA* 3.6 31.8 - - - +
288A ALA* 3.6 9.2 - - + +
291A LYS* 4.3 6.7 - - + -
293A TRP* 3.8 16.8 - - + -
283B ALA 2.9 17.5 + - - +
284B MET 4.3 0.9 - - - +
286B LYS* 1.3 74.5 - - - +
288B ALA* 1.3 64.7 + - - +
290B ALA* 3.5 11.2 + - - +
291B LYS* 3.5 20.3 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ALA 3.9 21.5 - - - +
284A MET* 3.9 7.4 - - + -
287A ALA* 3.6 8.0 - - - +
284B MET 3.3 18.2 + - - +
287B ALA* 1.3 76.5 - - - +
289B ALA* 1.3 62.6 + - - +
291B LYS* 3.4 7.8 + - - +
293B TRP* 3.1 31.7 + - + +
294B ILE* 3.7 23.9 + - + -
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Residues in contact with ALA 289 (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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285B VAL 3.0 18.6 + - - +
286B LYS 4.0 4.5 - - - +
288B ALA* 1.3 75.2 - - - +
290B ALA* 1.3 59.3 + - - +
291B LYS 3.1 0.4 - - - -
292B GLY* 3.0 18.2 + - - -
294B ILE* 3.5 23.7 - - + +
296B GLU* 3.7 32.8 - - + +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LYS* 6.6 0.2 - - + -
286B LYS 3.3 15.8 + - - +
287B ALA* 3.7 9.6 - - - +
288B ALA 3.3 0.4 - - - -
289B ALA* 1.3 77.6 - - - +
291B LYS* 1.3 63.2 + - + +
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Residues in contact with LYS 291 (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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287A ALA* 4.5 4.3 - - + -
290A ALA* 6.4 1.6 - - + -
287B ALA 3.5 15.0 + - - +
288B ALA 3.4 7.3 + - - +
289B ALA 3.1 0.4 - - - -
290B ALA* 1.3 81.6 - - + +
292B GLY* 1.3 61.0 + - - +
293B TRP* 3.4 54.1 + - + +
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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