Contacts of the helix formed by residues 362 - 371 (chain B) in PDB entry 5JJA
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 ASN 362 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ARG* 4.4 7.5 + - - +
320B PHE* 3.8 14.5 - - - -
321B VAL* 3.6 15.0 - - - +
324B MET* 3.6 36.2 - - + +
358B LEU* 2.9 26.2 + - - +
359B ILE 3.0 5.6 + - - +
361B ASP* 1.3 90.1 + - - +
363B ALA* 1.3 64.3 + - - +
364B ALA 3.3 2.5 - - - -
365B LYS* 3.3 16.9 + - + +
366B ILE* 3.3 15.7 + - + +
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Residues in contact with ALA 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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165A LEU* 4.1 19.1 - - + -
169A GLU* 4.1 19.1 - - - +
203A GLN* 5.1 0.2 - - - +
210A ARG* 5.3 0.8 - - - +
359B ILE* 3.1 8.5 + - - +
360B SER 3.9 15.0 + - - +
361B ASP 3.8 0.8 - - - -
362B ASN* 1.3 77.3 - - - +
364B ALA* 1.3 58.6 + - - +
366B ILE* 4.6 2.0 - - - +
367B LEU* 2.9 49.2 + - + +
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Residues in contact with ALA 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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169A GLU* 4.6 9.1 + - - +
210A ARG* 6.4 2.0 - - - -
362B ASN 3.3 1.0 + - - -
363B ALA* 1.3 79.2 - - - +
365B LYS* 1.3 62.0 + - + +
367B LEU* 5.4 0.4 - - - -
368B PRO* 3.2 23.4 - - - +
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Residues in contact with LYS 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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324B MET* 4.1 26.9 - - + -
325B GLU* 3.9 25.7 - - + +
362B ASN* 3.3 10.1 + - + +
363B ALA 3.2 0.8 - - - -
364B ALA* 1.3 84.0 - - + +
366B ILE* 1.3 63.1 + - + +
367B LEU 3.7 0.2 - - - -
368B PRO* 3.9 4.1 - - - +
369B ILE* 3.3 25.7 - - - +
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Residues in contact with ILE 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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320B PHE* 3.9 17.0 - - + -
324B MET* 4.0 13.0 - - + +
325B GLU* 6.4 0.4 - - + -
328B PHE* 3.8 54.5 - - + -
350B TRP* 5.3 1.8 - - + -
359B ILE* 3.9 33.9 - - + -
362B ASN* 3.3 22.6 + - + +
363B ALA 3.3 2.1 + - - +
365B LYS* 1.3 82.1 - - + +
367B LEU* 1.3 65.8 + - - +
368B PRO 3.4 0.4 - - - -
369B ILE* 3.1 17.5 + - + +
370B MET* 3.1 18.6 + - + +
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Residues in contact with LEU 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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162A LYS* 6.0 0.7 - - + -
165A LEU* 4.2 18.8 - - + -
166A GLN* 4.1 21.8 - - + -
169A GLU* 4.0 26.9 - - + +
350B TRP* 4.6 9.9 - - + -
359B ILE* 5.5 2.0 - - + -
363B ALA* 2.9 32.1 + - + +
364B ALA* 5.4 0.4 - - - -
366B ILE* 1.3 78.3 - - + +
368B PRO* 1.4 59.9 - - + +
370B MET* 3.3 1.7 + - - -
371B PHE* 2.8 55.2 + - + +
375B TYR* 3.7 28.2 - - + +
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Residues in contact with PRO 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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363B ALA 4.0 0.2 - - - +
364B ALA* 3.2 25.6 - - - +
365B LYS 3.9 4.9 - - - +
366B ILE 3.5 3.1 - - - -
367B LEU* 1.4 95.0 - - + +
369B ILE* 1.3 61.1 + - + +
371B PHE 4.5 0.4 - - - +
372B PRO* 3.5 24.4 - - - +
375B TYR* 4.0 30.0 - - + +
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Residues in contact with ILE 369 (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 MET 5.3 0.2 - - - +
325B GLU* 4.2 33.9 - - + +
328B PHE* 3.6 37.0 - - + +
329B ARG* 3.6 28.9 - - + +
332B ALA* 3.8 11.1 - - + +
365B LYS 3.3 22.2 - - - +
366B ILE* 3.1 11.3 + - + +
368B PRO* 1.3 82.6 - - + +
370B MET* 1.3 60.2 + - - +
372B PRO* 3.6 9.7 - - - +
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Residues in contact with MET 370 (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 PHE* 3.6 38.1 - - + +
331B LEU* 3.9 22.9 - - + -
332B ALA* 4.0 14.4 - - - +
335B VAL* 4.1 22.4 - - + -
350B TRP* 4.1 25.4 - - + +
366B ILE* 3.1 27.8 + - + +
367B LEU* 5.0 0.2 - - - -
369B ILE* 1.3 77.0 - - - +
371B PHE* 1.3 91.3 + - + +
372B PRO* 3.4 6.5 - - - +
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Residues in contact with PHE 371 (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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162A LYS* 3.7 30.7 - - + -
166A GLN* 4.1 17.9 - - - -
335B VAL* 6.3 2.5 - - + -
350B TRP* 3.8 30.1 - + - -
367B LEU* 2.8 29.5 + - + +
368B PRO 3.8 3.6 - - - -
370B MET* 1.3 94.6 - - + +
372B PRO* 1.4 60.1 - - - +
373B SER* 3.2 4.5 - - - +
374B LEU* 3.1 22.9 + - + -
375B TYR* 3.0 36.1 + + + +
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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