Contacts of the helix formed by residues 320 - 329 (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 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283B VAL* 4.3 11.9 - - - -
286B LEU* 5.3 1.8 - - - -
315B ILE* 3.1 21.4 + - - -
318B SER 3.7 0.6 - - - -
319B GLY* 1.3 76.1 - - - +
321B PRO* 1.3 69.2 - - - +
323B ALA* 2.9 21.2 + - - +
324B LEU* 3.0 25.1 + - - +
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Residues in contact with PRO 321 (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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315B ILE* 4.2 4.3 - - + +
316B LEU* 3.8 38.4 - - + +
319B GLY* 3.8 2.9 - - - -
320B GLY* 1.3 89.8 - - - +
322B GLN* 1.3 58.9 + - - +
323B ALA 3.4 0.3 + - - -
324B LEU* 3.8 7.6 + - + +
325B VAL* 3.0 31.1 + - - +
344B LEU* 5.6 3.6 - - + +
347B LEU* 4.9 13.0 - - + -
353B ASN 5.4 0.9 - - - +
356B ALA* 4.1 27.6 - - + +
357B ILE* 4.3 15.3 - - + +
360B ALA* 4.9 1.8 - - - -
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Residues in contact with GLN 322 (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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319B GLY* 4.0 20.2 + - - +
321B PRO* 1.3 77.4 - - - +
323B ALA* 1.3 69.0 + - - +
325B VAL* 4.1 4.0 - - - +
326B ASN* 3.7 17.3 + - - +
329B ARG* 5.5 1.6 + - - -
356B ALA 5.5 0.7 - - - +
360B ALA* 3.7 26.4 - - + +
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Residues in contact with ALA 323 (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 VAL* 5.6 2.2 - - + +
286B LEU* 4.6 23.7 - - + +
319B GLY 3.7 13.7 - - - +
320B GLY* 2.9 11.3 + - - +
322B GLN* 1.3 89.3 + - - +
324B LEU* 1.3 65.1 + - - +
326B ASN* 3.3 18.6 + - - +
327B ILE* 3.6 9.1 + - - +
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Residues in contact with LEU 324 (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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286B LEU* 4.0 22.7 - - + -
298B THR* 4.6 13.2 - - + -
301B LEU* 5.1 4.7 - - + -
315B ILE* 5.7 3.1 - - + -
320B GLY* 3.0 25.1 + - - +
321B PRO* 4.3 3.8 - - + +
323B ALA* 1.3 72.9 - - - +
325B VAL* 1.3 61.8 + - - +
327B ILE* 2.9 32.9 + - + +
328B MET* 3.3 8.9 + - - +
340B THR* 3.7 26.0 - - + +
343B VAL* 3.6 33.7 - - + -
344B LEU* 4.3 21.5 - - + -
347B LEU* 4.7 7.4 - - + -
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PRO 3.0 24.4 + - - +
322B GLN* 4.1 8.3 - - - +
323B ALA 3.3 0.4 - - - -
324B LEU* 1.3 77.2 - - + +
326B ASN* 1.3 61.4 + - - +
328B MET* 3.2 21.1 + - - +
329B ARG* 3.4 29.7 + - - +
344B LEU* 5.4 9.6 - - + -
357B ILE* 4.6 11.2 - - + -
360B ALA* 4.6 6.5 - - + -
361B GLY* 4.2 5.4 - - - +
362B GLY* 4.0 27.8 - - - +
365B ALA* 3.7 20.3 - - + +
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Residues in contact with ASN 326 (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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322B GLN* 3.7 11.5 + - - +
323B ALA* 3.3 13.5 + - - +
324B LEU 3.1 0.4 - - - -
325B VAL* 1.3 75.9 - - - +
327B ILE* 1.3 68.3 + - - +
329B ARG* 3.4 36.1 + - - +
330B THR* 3.0 39.4 + - - +
331B TYR* 5.8 2.1 - - - -
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Residues in contact with ILE 327 (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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286B LEU* 4.9 20.4 - - + +
294B LEU* 4.7 16.4 - - + -
298B THR* 4.8 7.2 - - + -
323B ALA 3.6 6.7 + - - +
324B LEU* 2.9 22.9 + - + +
326B ASN* 1.3 80.7 - - - +
328B MET* 1.3 65.3 + - - +
330B THR 3.1 12.0 + - - -
331B TYR* 3.2 34.0 + - + +
336B LEU* 4.0 25.8 - - + -
337B LEU* 4.4 6.7 - - + +
340B THR* 4.0 33.7 - - + +
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Residues in contact with MET 328 (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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324B LEU 3.8 11.4 - - - +
325B VAL* 3.2 14.5 + - - +
327B ILE* 1.3 76.1 - - - +
329B ARG* 1.3 56.8 + - - +
330B THR 3.5 1.0 + - - -
331B TYR 4.5 2.3 - - - +
337B LEU* 3.5 43.3 - - + +
340B THR* 4.2 20.6 - - + -
341B SER* 4.3 11.9 - - - -
344B LEU* 4.9 7.2 - - + -
365B ALA* 4.2 18.1 - - + +
366B LEU* 3.4 32.8 - - + -
368B LEU* 4.5 1.4 - - - +
369B HIS* 2.9 39.7 + - + -
377B LEU* 4.9 1.8 - - + -
381B CYS* 4.5 5.6 - - - -
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Residues in contact with ARG 329 (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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322B GLN 5.5 2.0 + - - -
325B VAL* 3.4 30.9 + - - +
326B ASN* 3.5 34.2 - - - +
327B ILE 3.2 0.6 - - - -
328B MET* 1.3 78.2 - - - +
330B THR* 1.3 60.1 + - - +
331B TYR 5.3 0.2 - - - -
360B ALA 5.3 5.1 + - - -
361B GLY* 5.6 1.2 + - - -
365B ALA* 4.5 11.0 - - + +
368B LEU* 4.1 23.1 - - + +
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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