Contacts of the helix formed by residues 278 - 292 (chain B) in PDB entry 1PJS
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 PRO 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B CYS 3.5 8.3 - - - +
277B VAL* 1.3 86.7 - - - +
279B GLN* 1.3 65.4 + - - +
280B GLU* 3.4 6.1 - - + +
281B GLU* 3.2 54.9 + - + +
282B ILE* 3.3 8.5 + - - +
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Residues in contact with GLN 279 (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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277B VAL 3.5 2.3 + - - -
278B PRO* 1.3 69.5 - - - +
280B GLU* 1.3 61.1 + - - +
282B ILE* 3.0 20.4 + - - +
283B ASN* 2.8 57.8 + - - +
300B LYS* 5.2 2.0 + - - -
309B ARG* 5.1 4.5 + - - +
312B GLU* 3.5 29.7 - - + +
313B GLU* 2.6 33.3 + - - +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PRO* 3.4 6.0 - - + +
279B GLN* 1.3 77.3 - - - +
281B GLU* 1.3 82.1 + - + +
283B ASN* 3.3 14.1 + - - +
284B GLN* 2.8 61.5 + - - +
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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
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277B VAL* 4.1 10.7 - - + +
278B PRO* 3.2 38.7 + - + +
279B GLN 3.1 0.8 - - - -
280B GLU* 1.3 94.3 - - + +
282B ILE* 1.3 57.1 + - - +
284B GLN* 3.7 4.6 - - - +
285B ILE* 2.6 41.6 + - + +
288B ARG* 4.7 1.8 + - - +
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Residues in contact with ILE 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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246B VAL* 4.6 3.6 - - + -
268B VAL* 3.9 34.5 - - + +
276B CYS* 5.9 0.4 - - - -
277B VAL* 3.5 38.1 - - + +
278B PRO 3.6 3.6 - - - +
279B GLN* 3.0 22.3 + - - +
281B GLU* 1.3 76.3 - - - +
283B ASN* 1.3 64.2 + - - +
285B ILE* 3.4 9.3 + - - +
286B LEU* 3.2 23.3 + - + +
298B ARG* 4.2 24.0 - - - +
313B GLU* 4.0 19.7 - - - +
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Residues in contact with ASN 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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347A ARG* 5.6 2.8 - - - +
279B GLN* 2.8 53.4 + - - +
280B GLU* 3.4 16.3 - - - +
282B ILE* 1.3 76.0 - - - +
284B GLN* 1.3 69.5 + - - +
286B LEU* 3.3 12.6 + - - +
287B LEU* 3.1 22.3 + - - +
312B GLU* 4.0 18.3 + - - +
313B GLU* 3.3 19.4 + - - +
316B THR* 4.4 15.9 + - + +
317B LEU* 5.1 2.8 - - - +
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Residues in contact with GLN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLU* 2.8 54.9 + - - +
281B GLU* 3.7 6.7 - - - +
282B ILE 3.3 0.4 - - - -
283B ASN* 1.3 78.2 - - - +
285B ILE* 1.3 53.8 + - - +
287B LEU* 3.3 16.0 + - - +
288B ARG* 2.6 58.1 + - - +
316B THR* 5.0 12.7 - - - +
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Residues in contact with ILE 285 (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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246B VAL* 5.7 8.3 - - + -
266B VAL* 4.7 12.8 - - + -
268B VAL* 4.5 16.6 - - + -
277B VAL* 5.3 5.2 - - + -
281B GLU* 2.6 31.7 + - + +
282B ILE* 3.5 14.8 - - + +
284B GLN* 1.3 72.5 - - - +
286B LEU* 1.3 59.1 - - + +
288B ARG* 3.2 30.3 - - - +
289B GLU* 2.8 54.5 + - - +
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Residues in contact with LEU 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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218B VAL* 3.5 22.4 - - + +
220B LEU* 4.9 0.7 - - + -
246B VAL* 3.7 31.0 - - + -
282B ILE* 3.2 18.0 + - + +
283B ASN 3.5 6.3 - - - +
284B GLN 3.2 0.6 - - - -
285B ILE* 1.3 76.5 - - + +
287B LEU* 1.3 62.4 + - - +
290B ALA* 3.3 24.8 + - - +
296B VAL* 3.8 18.6 - - + +
298B ARG* 3.8 24.2 - - + -
313B GLU* 3.6 49.8 - - + +
317B LEU* 5.1 1.6 - - + -
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Residues in contact with LEU 287 (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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283B ASN 3.1 12.7 + - - +
284B GLN* 3.7 17.7 - - - +
286B LEU* 1.3 79.4 - - - +
288B ARG* 1.3 59.0 + - - +
290B ALA* 3.3 4.1 + - - +
291B GLN* 2.8 69.6 + - + +
316B THR* 3.0 38.8 - - + +
317B LEU* 3.9 16.2 - - + -
320B ALA* 4.1 14.4 - - + -
322B ILE* 4.6 3.8 - - + +
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Residues in contact with ARG 288 (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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281B GLU* 4.7 1.6 + - - +
284B GLN* 2.6 39.9 + - - +
285B ILE* 3.2 40.9 - - + +
287B LEU* 1.3 73.7 - - - +
289B GLU* 1.3 66.0 + - - +
291B GLN* 3.1 32.3 + - - +
292B LYS* 3.1 26.5 + - - +
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Residues in contact with GLU 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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244B ILE* 3.8 24.6 - - + +
266B VAL* 5.3 2.9 - - - +
285B ILE* 2.8 42.6 + - - +
288B ARG* 1.3 78.6 + - - +
290B ALA* 1.3 59.1 + - - +
292B LYS* 3.4 32.0 + - + +
294B LYS* 3.1 57.8 + - + +
296B VAL* 4.0 14.4 - - + -
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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
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206B ARG* 4.6 1.6 + - - -
216B GLY* 3.4 9.2 - - - -
217B GLU 3.9 7.2 - - - +
218B VAL* 3.7 19.5 - - + -
286B LEU 3.3 20.5 + - - +
287B LEU 3.7 2.0 - - - +
288B ARG 3.2 0.8 - - - -
289B GLU* 1.3 72.7 - - - +
291B GLN* 1.3 58.7 + - - +
292B LYS 3.0 2.0 - - - -
293B GLY* 2.8 24.3 + - - -
294B LYS 3.6 10.5 - - - -
296B VAL* 3.7 4.7 - - + +
322B ILE* 3.7 24.4 - - + +
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Residues in contact with GLN 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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214B HIS* 4.8 5.0 + - - -
287B LEU* 2.8 41.2 + - + +
288B ARG* 3.2 24.9 - - - +
290B ALA* 1.3 77.9 - - - +
292B LYS* 1.3 55.3 + - + +
293B GLY* 3.0 4.6 + - - -
320B ALA* 4.1 10.1 - - + +
322B ILE* 3.8 16.1 - - + +
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Residues in contact with LYS 292 (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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214B HIS* 3.6 23.8 + - - -
288B ARG* 3.1 25.9 + - + +
289B GLU* 3.6 34.5 + - + +
290B ALA 3.0 1.0 - - - -
291B GLN* 1.3 76.0 - - + +
293B GLY* 1.3 58.9 + - - +
294B LYS* 3.5 16.2 + - + +
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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