Contacts of the helix formed by residues 277 - 285 (chain B) in PDB entry 1JPP
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 GLY 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241B VAL* 4.1 2.8 - - - +
273B VAL 3.4 0.8 + - - -
274B ARG 3.3 12.4 + - - -
275B LEU 2.9 6.4 - - - -
276B ALA* 1.3 83.5 - - - +
278B GLY* 1.3 63.1 + - - +
279B LEU* 3.3 4.2 + - - -
280B GLN* 4.4 4.6 + - - +
281B LYS* 4.0 18.7 + - - +
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 4.2 14.1 - - - -
273B VAL* 3.2 18.5 + - - -
274B ARG* 4.9 1.2 - - - +
276B ALA 3.8 0.4 - - - -
277B GLY* 1.3 76.3 - - - +
279B LEU* 1.3 59.2 + - - +
281B LYS* 3.9 3.5 - - - +
282B MET* 3.1 53.4 + - - +
304B LEU* 5.7 0.4 - - - -
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Residues in contact with LEU 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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274B ARG* 5.3 14.8 - - + +
277B GLY* 3.3 2.3 - - - -
278B GLY* 1.3 74.3 - - - +
280B GLN* 1.3 67.9 + - - +
281B LYS 3.1 1.3 - - - -
282B MET* 3.5 3.4 + - + +
283B VAL* 3.2 29.5 + - - +
301B LEU* 4.3 14.3 - - + +
304B LEU* 4.5 27.4 - - + -
305B ALA 6.0 0.2 - - - +
311B SER* 4.1 26.7 - - - +
314B ILE* 3.9 42.0 - - + -
315B ILE* 4.2 25.1 - - + -
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Residues in contact with GLN 280 (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 GLY 4.4 5.6 + - - +
278B GLY 3.7 0.2 - - - -
279B LEU* 1.3 77.8 - - - +
281B LYS* 1.3 79.8 + - - +
283B VAL* 3.5 5.2 + - - +
284B ALA* 3.1 31.2 + - - +
314B ILE* 4.8 4.9 - - + +
318B SER* 4.6 22.4 - - - +
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Residues in contact with LYS 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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241B VAL* 3.6 37.7 - - + +
242B LYS* 5.0 9.0 - - - +
244B LEU* 4.1 20.2 - - + +
245B GLY* 5.1 10.2 - - - +
277B GLY 4.0 11.9 + - - +
278B GLY* 3.9 8.2 - - - +
279B LEU 3.1 0.8 - - - -
280B GLN* 1.3 89.7 + - + +
282B MET* 1.3 66.8 + - - +
284B ALA* 3.0 16.8 + - - +
285B LEU* 3.3 17.7 + - - +
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Residues in contact with MET 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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241B VAL* 6.0 0.2 - - + -
244B LEU* 4.6 15.9 - - + -
256B ILE* 4.5 13.5 - - + -
259B LEU* 4.8 9.9 - - + -
263B LEU* 5.6 2.9 - - + -
273B VAL* 4.0 19.1 - - + -
278B GLY* 3.1 37.0 + - - +
279B LEU* 3.5 3.3 + - - +
281B LYS* 1.3 77.5 - - - +
283B VAL* 1.3 61.2 + - - +
285B LEU* 3.2 21.4 + - + +
286B LEU* 3.7 6.3 + - - +
297B THR* 3.7 27.6 - - + +
300B CYS* 3.9 31.6 - - + -
301B LEU* 4.2 14.8 - - + -
304B LEU* 4.3 13.9 - - + -
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Residues in contact with VAL 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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279B LEU 3.2 19.1 + - - +
280B GLN* 3.9 5.4 - - - +
281B LYS 3.2 0.8 - - - -
282B MET* 1.3 77.1 - - - +
284B ALA* 1.3 61.1 + - - +
285B LEU 3.2 0.2 - - - -
286B LEU* 3.3 34.8 + - + +
301B LEU* 4.1 21.3 - - + -
315B ILE* 4.4 24.9 - - + +
318B SER* 4.3 24.2 - - - +
319B GLY 4.6 2.2 - - - +
320B GLY* 4.3 15.5 - - - +
323B ALA* 5.6 1.9 - - + +
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Residues in contact with ALA 284 (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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280B GLN* 3.1 27.8 + - - +
281B LYS* 3.0 13.3 + - - +
283B VAL* 1.3 77.1 - - - +
285B LEU* 1.3 59.1 + - + +
287B ASN* 2.9 24.1 + - - +
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Residues in contact with LEU 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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244B LEU* 4.0 44.6 - - + +
252B LEU* 4.2 21.5 - - + -
256B ILE* 5.3 2.2 - - + -
281B LYS 3.3 13.2 + - - +
282B MET* 3.2 15.4 + - - +
283B VAL 3.2 0.4 - - - -
284B ALA* 1.3 75.1 - - + +
286B LEU* 1.3 58.1 + - - +
287B ASN* 2.8 14.8 + - - +
288B LYS* 3.1 33.3 + - - +
293B PHE* 3.8 26.3 - - + -
294B LEU* 4.0 5.5 - - - +
297B THR* 4.8 8.7 - - + +
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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