Contacts of the helix formed by residues 392 - 401 (chain B) in PDB entry 2JB3
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 ALA 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LEU* 4.5 4.0 - - + -
326B ILE* 5.1 1.6 - - + -
350B ILE* 3.8 16.5 - - + +
369B ALA* 4.0 20.0 - - + +
370B TYR* 3.8 23.6 - - + -
380B PHE* 4.4 0.6 - - - -
388B ARG 2.9 19.8 + - - +
389B LEU* 3.2 7.8 + - - +
391B LYS* 1.3 71.1 + - - +
393B ILE* 1.3 56.4 + - - +
396B GLY* 2.9 27.5 + - - -
404B TYR* 3.7 6.5 + - - -
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Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE* 4.2 9.0 - - + -
389B LEU* 2.9 47.5 + - + +
390B ALA* 3.9 7.0 - - - +
392B ALA* 1.3 75.4 - - - +
394B ALA* 1.3 66.0 + - - +
397B SER* 2.9 22.5 + - - -
404B TYR* 3.7 10.3 - - + +
405B THR* 3.7 34.3 - - + +
408B ILE* 3.5 26.9 - - + -
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Residues in contact with ALA 394 (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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390B ALA 3.1 17.5 + - - +
391B LYS* 3.3 5.8 - - + +
393B ILE* 1.3 77.2 - - - +
395B GLU* 1.3 63.8 + - + +
397B SER* 2.7 24.7 + - - -
398B GLU* 3.3 18.4 + - - +
405B THR* 6.1 0.2 - - - -
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Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LYS* 3.6 12.2 - - + +
349B ASP* 3.3 14.3 + - - +
350B ILE* 3.0 47.2 + - + +
391B LYS* 3.1 48.4 - - + +
394B ALA* 1.3 76.9 - - + +
396B GLY* 1.3 65.6 + - - +
398B GLU* 3.1 32.2 + - - +
399B ILE* 3.6 11.1 + - - +
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Residues in contact with GLY 396 (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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350B ILE* 3.9 2.5 - - - +
353B ILE* 3.9 19.1 - - - -
392B ALA 2.9 19.4 + - - -
395B GLU* 1.3 75.8 - - - +
397B SER* 1.3 57.3 + - - +
399B ILE* 3.1 3.3 + - - +
400B HIS* 2.9 26.5 + - - +
404B TYR* 3.6 25.4 - - - -
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Residues in contact with SER 397 (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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393B ILE 2.9 16.2 + - - -
394B ALA* 2.7 21.7 + - - -
396B GLY* 1.3 76.3 - - - +
398B GLU* 1.3 59.6 + - - +
399B ILE 3.1 0.2 - - - -
401B GLY* 2.9 45.4 + - - -
402B GLU* 4.3 10.6 + - - +
404B TYR* 3.7 3.1 - - - -
405B THR* 3.8 20.3 - - - +
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Residues in contact with GLU 398 (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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115B ASN* 3.5 12.9 + - - -
124B GLY 4.1 6.7 - - - +
126B SER* 4.3 0.5 + - - -
348B LYS* 2.8 42.3 + - - +
394B ALA* 3.5 19.5 - - - +
395B GLU* 3.1 18.3 + - - +
397B SER* 1.3 82.7 + - - +
399B ILE* 1.3 57.9 + - - +
401B GLY 4.8 0.2 - - - -
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Residues in contact with ILE 399 (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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113B PHE* 3.4 25.7 - - + +
115B ASN* 4.0 11.0 - - + +
126B SER* 2.7 30.9 + - - +
344B SER* 4.3 7.4 - - - -
345B ASN 4.9 2.7 - - - +
346B THR* 3.5 38.8 - - + +
348B LYS* 4.0 10.5 - - + -
350B ILE* 3.8 17.5 - - + -
353B ILE* 4.2 6.1 - - + -
395B GLU 3.8 7.9 - - - +
396B GLY 3.1 6.1 + - - +
398B GLU* 1.3 82.7 - - - +
400B HIS* 1.3 80.7 + - + +
401B GLY 3.6 1.1 + - - -
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Residues in contact with HIS 400 (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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113B PHE* 3.4 26.2 - + - -
332B TRP* 3.9 14.2 - + + -
337B ASP* 3.1 17.6 + - - -
339B ILE* 3.6 22.4 - - + -
344B SER* 2.8 26.1 + - - -
353B ILE* 3.9 19.3 - - + -
355B PHE* 3.6 16.4 - + - -
396B GLY 2.9 9.6 + - - +
399B ILE* 1.3 91.3 - - + +
401B GLY* 1.3 62.9 + - - +
403B LYS* 3.1 30.0 + - - +
404B TYR* 4.0 13.5 - - + -
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Residues in contact with GLY 401 (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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397B SER* 2.9 26.2 + - - -
399B ILE 3.6 1.4 + - - -
400B HIS* 1.3 77.7 - - - +
402B GLU* 1.3 67.6 + - - -
403B LYS* 3.2 3.6 - - - -
404B TYR* 3.2 21.1 + - - +
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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