Contacts of the helix formed by residues 361 - 368 (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 361 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B VAL* 4.2 7.0 - - - -
329B ARG* 5.6 1.0 + - - -
357B ILE 3.4 0.6 + - - -
358B VAL 3.4 5.6 + - - -
359B GLU 3.3 2.6 - - - -
360B ALA* 1.3 79.3 - - - +
362B GLY* 1.3 67.8 + - - +
363B MET 3.1 4.0 + - - -
364B GLN* 3.2 21.1 + - - +
365B ALA* 3.1 22.7 + - - +
395B GLN* 5.4 1.1 - - - -
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Residues in contact with GLY 362 (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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325B VAL* 4.0 22.2 - - - +
357B ILE* 3.1 27.0 + - - -
358B VAL 4.2 0.6 + - - -
360B ALA 3.8 0.2 - - - -
361B GLY* 1.3 77.7 - - - +
363B MET* 1.3 60.5 + - - +
365B ALA* 4.0 1.3 - - - -
366B LEU* 3.2 35.4 + - - +
388B LEU* 5.1 1.3 - - - -
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Residues in contact with MET 363 (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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357B ILE 4.9 0.2 + - - -
358B VAL* 4.1 28.0 - - + +
361B GLY 3.1 1.0 - - - -
362B GLY* 1.3 77.2 - - - +
364B GLN* 1.3 71.0 + - - +
366B LEU 4.1 0.5 - - - -
367B GLY* 3.3 17.8 + - - -
385B LEU* 3.7 39.6 - - + +
388B LEU* 3.9 28.0 - - + -
389B SER* 4.6 5.8 - - - -
392B ALA* 3.8 19.5 - - + -
395B GLN* 5.6 1.1 - - + +
398B MET* 3.9 28.3 - - + -
401B LEU* 4.3 14.9 - - + +
423B ILE* 5.7 2.9 - - + -
427B LEU* 4.3 11.4 - - + -
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Residues in contact with GLN 364 (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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361B GLY* 3.2 21.6 + - - +
363B MET* 1.3 84.9 - - - +
365B ALA* 1.3 62.5 + - - +
367B GLY* 3.4 9.9 + - - +
368B LEU* 3.7 15.1 + - - +
395B GLN* 4.9 10.3 + - - +
396B GLU 4.5 8.3 + - - -
397B GLY 4.4 18.3 + - - +
398B MET* 4.5 14.1 - - - +
401B LEU* 5.8 6.5 - - + -
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Residues in contact with ALA 365 (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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325B VAL* 3.7 31.4 - - + +
328B MET* 4.2 11.3 - - + +
329B ARG* 4.5 14.4 - - + +
361B GLY 3.1 16.1 + - - +
362B GLY* 4.2 3.1 - - - +
364B GLN* 1.3 77.1 - - - +
366B LEU* 1.3 62.4 + - + +
368B LEU* 3.8 23.8 - - - +
369B HIS* 4.0 10.9 - - - -
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Residues in contact with LEU 366 (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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328B MET* 3.4 32.8 - - + -
341B SER* 5.3 2.9 - - - -
344B LEU* 4.4 16.8 - - + -
357B ILE* 5.9 1.6 - - + -
362B GLY* 3.2 24.1 + - - +
363B MET 4.2 2.9 - - - +
365B ALA* 1.3 75.3 - - + +
367B GLY* 1.3 64.2 + - - +
368B LEU 3.2 2.0 - - - -
369B HIS* 3.8 7.9 + - - +
370B LEU* 4.1 7.6 + - - +
381B CYS* 3.7 33.5 - - + +
384B THR* 3.7 31.9 - - + -
385B LEU* 4.2 25.3 - - + +
388B LEU* 4.8 6.7 - - + -
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Residues in contact with GLY 367 (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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363B MET 3.3 9.4 + - - -
364B GLN 3.4 5.3 + - - -
365B ALA 3.4 0.6 - - - -
366B LEU* 1.3 77.2 - - - +
368B LEU* 1.3 63.4 + - - +
369B HIS 3.3 1.4 + - - -
370B LEU* 3.4 35.6 + - - +
385B LEU* 4.9 1.3 - - - +
401B LEU* 3.9 18.8 - - - +
404B THR* 5.3 3.1 + - - +
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Residues in contact with LEU 368 (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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328B MET 4.5 2.9 - - - +
329B ARG* 4.1 28.9 - - + +
364B GLN 3.7 11.4 + - - +
365B ALA* 3.8 19.7 - - - +
366B LEU 3.2 0.2 - - - -
367B GLY* 1.3 77.8 - - - +
369B HIS* 1.3 68.4 + - + +
370B LEU 3.4 2.0 + - - -
371B THR* 4.7 5.9 + - - -
372B ASP* 3.8 6.2 - - - +
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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