Contacts of the helix formed by residues 268 - 277 (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 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B PHE* 3.8 15.3 - - - -
266B GLN 3.0 3.2 + - - -
267B GLU* 1.3 73.7 - - - +
269B ALA* 1.3 66.0 + - - +
270B LYS 3.2 3.7 + - - -
271B MET* 3.4 29.8 + - - +
272B ALA* 3.4 10.6 + - - +
672B GOL 3.1 16.6 + - - -
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Residues in contact with ALA 269 (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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232B PHE* 3.8 5.2 - - - -
237B ILE* 4.1 21.5 - - + -
262B LEU* 3.3 35.9 - - + +
263B LEU* 4.2 10.5 - - + +
266B GLN* 3.6 12.3 + - + +
267B GLU 3.8 0.8 - - - -
268B GLY* 1.3 77.0 - - - +
270B LYS* 1.3 57.1 + - - +
272B ALA* 3.3 1.7 + - - +
273B VAL* 2.8 35.3 + - - +
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Residues in contact with LYS 270 (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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263B LEU* 4.5 15.7 - - + +
268B GLY 3.2 1.2 + - - -
269B ALA* 1.3 74.7 - - - +
271B MET* 1.3 69.1 + - + +
273B VAL* 3.4 1.4 + - - +
274B ARG* 3.2 55.4 + - - +
303B ILE* 3.4 41.1 + - + +
304B LEU* 4.3 14.8 - - + -
306B TYR* 4.8 10.5 + - - +
672B GOL 3.1 30.9 + - - +
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Residues in contact with MET 271 (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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268B GLY* 3.4 27.4 + - - +
270B LYS* 1.3 79.8 - - + +
272B ALA* 1.3 62.0 + - - +
274B ARG* 3.3 21.7 + - - +
275B LEU* 3.3 16.3 + - - +
672B GOL 4.3 11.7 - - - +
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PHE* 4.7 8.5 - - + -
237B ILE* 3.9 24.3 - - + +
238B PRO* 5.9 3.4 - - + +
268B GLY 3.4 9.0 + - - +
269B ALA* 3.3 8.3 + - - +
270B LYS 3.1 0.4 - - - -
271B MET* 1.3 75.2 - - - +
273B VAL* 1.3 63.5 + - - +
274B ARG 2.9 4.7 - - - -
275B LEU* 3.0 21.1 + - - +
276B ALA* 3.2 11.6 + - - +
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Residues in contact with VAL 273 (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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237B ILE* 3.8 27.4 - - + -
241B VAL* 5.1 4.9 - - + -
259B LEU* 4.0 15.7 - - + -
262B LEU* 6.1 0.7 - - + -
263B LEU* 3.7 21.5 - - + -
269B ALA* 2.8 23.6 + - + +
270B LYS 4.0 3.4 - - - +
272B ALA* 1.3 72.4 - - - +
274B ARG* 1.3 58.5 + - - +
276B ALA* 3.8 3.6 + - - +
277B GLY 3.4 3.6 + - - -
278B GLY* 3.2 23.7 + - - -
282B MET* 4.0 26.7 - - + -
304B LEU* 4.2 17.0 - - + -
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Residues in contact with ARG 274 (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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270B LYS* 3.2 44.1 + - - +
271B MET* 3.4 16.3 - - - +
272B ALA 2.9 1.0 - - - -
273B VAL* 1.3 78.1 - - - +
275B LEU* 1.3 64.6 + - + +
277B GLY* 3.3 11.1 + - - +
278B GLY 4.9 1.6 - - - +
279B LEU* 5.3 13.4 - - + +
303B ILE 4.7 0.4 + - - -
304B LEU* 2.6 53.6 + - + +
306B TYR 5.0 2.4 + - - -
308B ASN* 4.1 22.5 + - - +
311B SER* 3.4 21.1 + - - -
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Residues in contact with LEU 275 (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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271B MET 3.3 11.5 + - - +
272B ALA* 3.0 12.0 + - - +
274B ARG* 1.3 74.5 - - - +
276B ALA* 1.3 64.2 + - - +
277B GLY* 2.9 7.0 + - - -
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Residues in contact with ALA 276 (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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237B ILE* 4.8 1.3 - - + -
238B PRO* 4.1 22.6 - - + +
241B VAL* 3.5 37.1 - - + +
272B ALA 3.2 8.5 + - - +
273B VAL* 3.9 7.2 - - - +
275B LEU* 1.3 78.9 - - - +
277B GLY* 1.3 62.2 + - - +
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Residues in contact with GLY 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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