Contacts of the helix formed by residues 268 - 273 (chain D) in PDB entry 1JPM
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 LYS 268 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D ILE* 5.2 4.0 - - - +
244D ASP* 3.2 30.2 + - - -
245D GLU* 4.5 6.1 + - - -
266D ASN* 3.7 14.1 - - - +
267D ILE* 1.3 86.2 - - - +
269D LEU* 1.3 66.0 + - - +
270D MET* 4.4 2.7 - - + +
271D LYS* 3.1 36.8 + - + +
272D ALA* 3.1 14.0 + - - +
294D VAL* 5.2 1.1 - - - -
295D GLY* 3.8 8.5 - - - +
296D SER* 3.8 38.3 + - - +
297D MET* 3.9 28.4 - - + +
321D ASP* 5.9 2.0 - - - -
1001D MG 3.9 5.0 - - - -
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Residues in contact with LEU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ALA* 3.3 4.0 - - + +
105D MET* 3.9 31.6 - - + -
267D ILE* 5.4 0.7 - - + -
268D LYS* 1.3 71.4 - - - +
270D MET* 1.3 58.5 + - + +
273D GLY 2.9 10.4 + - - -
274D GLY* 2.8 53.5 + - - +
275D ILE* 4.0 19.1 - - + -
278D ALA* 3.9 16.6 - - + -
294D VAL* 5.7 2.0 - - + +
295D GLY 5.1 1.8 + - - -
296D SER* 5.9 0.6 - - - +
303D GLY 4.7 0.2 - - - +
306D ALA* 4.0 8.7 - - + -
307D ALA* 3.8 37.2 - - + +
310D PHE* 4.5 11.7 - - + -
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Residues in contact with MET 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLU 3.3 23.1 - - - +
48D ALA* 3.9 2.2 - - - -
49D PRO* 3.8 17.9 - - + +
51D THR* 5.5 0.4 - - - +
55D THR* 4.3 6.0 - - + +
97D MET* 3.1 30.5 - - - +
98D SER* 3.7 38.2 + - - +
101D ALA* 3.3 26.9 - - + -
105D MET* 3.3 17.9 - - + -
268D LYS* 3.2 1.7 - - + +
269D LEU* 1.3 78.4 - - + +
271D LYS* 1.3 56.9 + - - +
297D MET* 3.8 36.3 - - + -
299D GLU* 3.8 15.3 - - - +
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Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 5.0 2.9 - - + -
55D THR* 4.9 0.9 - - + -
97D MET* 3.2 22.2 - - - +
244D ASP* 2.7 46.4 + - - +
245D GLU* 4.9 0.9 - - + -
247D VAL 2.8 16.2 + - - +
248D PHE* 3.5 60.5 - - + +
266D ASN 2.9 20.2 + - - -
267D ILE* 4.8 0.4 - - - +
268D LYS* 3.1 31.3 + - + +
270D MET* 1.3 78.4 - - - +
272D ALA* 1.3 56.3 + - - +
273D GLY 3.2 0.4 - - - -
297D MET* 3.9 21.3 - - + -
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Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLN* 4.0 7.8 + - - +
97D MET* 3.6 10.9 - - - +
248D PHE 3.2 16.6 + - - +
249D THR* 5.1 1.8 - - - +
250D PRO* 5.5 1.7 - - - +
267D ILE* 5.1 0.7 - - + -
268D LYS 3.1 12.4 + - - +
269D LEU 4.2 0.2 - - - +
271D LYS* 1.3 78.1 - - - +
273D GLY* 1.3 62.5 + - - +
274D GLY 3.4 7.6 + - - +
277D GLY* 4.1 15.8 + - - -
278D ALA* 3.7 30.1 - - + +
281D ILE* 4.2 5.4 - - + -
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Residues in contact with GLY 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLN* 2.8 25.0 + - - -
97D MET* 3.2 31.9 - - - -
100D LYS* 3.4 9.9 - - - +
101D ALA* 3.3 16.2 + - - -
104D GLU* 3.6 1.6 - - - +
269D LEU 2.9 4.2 + - - -
270D MET 3.8 1.4 + - - -
271D LYS 3.2 4.9 + - - -
272D ALA* 1.3 78.1 - - - +
274D GLY* 1.3 58.1 + - - +
276D SER* 5.8 0.2 - - - -
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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