Contacts of the helix formed by residues 355 - 364 (chain B) in PDB entry 2QNJ
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 ASP 355 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B GLU* 3.8 8.1 - - - -
121B VAL 5.0 2.2 - - - -
348B SER* 2.8 27.3 + - - -
353B LYS* 3.1 12.5 + - + +
354B TYR* 1.3 75.0 - - - +
356B GLU* 1.3 63.8 + - + +
357B ILE* 3.3 7.2 + - - +
358B THR* 2.9 26.3 + - - -
359B ALA* 2.9 28.8 + - - +
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Residues in contact with GLU 356 (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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55B ASN* 3.4 24.5 + - - +
75B HIS* 5.0 0.4 + - + -
120B GLU* 3.3 25.3 + - - +
340B TYR* 2.6 34.6 + - + +
355B ASP* 1.3 74.8 - - + +
357B ILE* 1.3 65.2 + - + +
359B ALA* 3.8 0.7 - - - +
360B THR* 2.6 37.4 + - - -
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Residues in contact with ILE 357 (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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335B MET* 3.5 25.9 - - + +
340B TYR* 3.6 40.6 - - + -
344B GLU* 3.9 30.7 - - + +
345B ILE* 3.8 17.0 - - + +
348B SER* 3.6 26.7 - - - +
349B LEU* 4.6 1.6 - - + -
355B ASP* 3.2 9.4 - - - +
356B GLU* 1.3 79.3 - - + +
358B THR* 1.3 70.9 + - - +
360B THR* 3.1 11.7 + - - -
361B TYR* 3.2 9.0 + - - +
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Residues in contact with THR 358 (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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119B PHE 5.2 1.1 - - - +
348B SER 3.1 20.4 + - - -
349B LEU* 3.9 14.8 - - + +
352B MET* 3.1 37.5 - - + -
353B LYS 2.6 25.1 + - - +
354B TYR* 4.5 3.4 - - + -
355B ASP* 2.9 11.6 + - - -
357B ILE* 1.3 78.7 - - - +
359B ALA* 1.3 63.9 + - - +
361B TYR* 3.0 3.9 + - + +
362B LEU* 2.9 32.2 + - + +
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Residues in contact with ALA 359 (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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56B TYR* 3.7 8.3 - - - +
75B HIS* 5.3 0.2 - - + -
119B PHE* 3.3 25.2 + - - +
120B GLU* 3.3 30.1 - - + +
355B ASP 2.9 12.4 + - - +
356B GLU 3.8 2.7 - - - +
358B THR* 1.3 76.3 - - - +
360B THR* 1.3 64.3 + - - +
362B LEU* 3.1 6.0 + - - +
363B LEU* 2.9 31.7 + - + +
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Residues in contact with THR 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 3.1 23.9 + - - +
77B LEU* 3.5 10.7 - - + +
78B THR* 4.2 7.3 + - - +
335B MET* 3.8 15.7 - - + -
338B MET* 3.7 35.4 - - + -
340B TYR* 5.0 2.2 - - + -
356B GLU 2.6 22.3 + - - -
357B ILE* 3.6 5.4 - - - -
359B ALA* 1.3 76.9 - - - +
361B TYR* 1.3 64.6 + - - +
363B LEU* 3.2 5.0 + - - +
364B LEU* 3.0 28.2 + - + +
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Residues in contact with TYR 361 (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* 4.6 11.2 - - + -
325B ASP 2.5 31.9 + - - -
326B ILE* 3.5 10.2 - - + -
328B ASP* 3.2 31.7 + - - +
331B ARG* 2.7 67.6 + - + -
332B ILE* 4.5 5.6 - - + -
335B MET* 3.8 19.0 - - - -
349B LEU* 3.8 34.5 - - + -
357B ILE 3.2 8.1 + - - +
358B THR* 3.0 9.6 + - + +
360B THR* 1.3 79.0 - - - +
362B LEU* 1.3 71.2 + - + +
364B LEU* 2.9 13.9 + - - +
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Residues in contact with LEU 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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111B ASN* 6.2 1.8 - - - +
118B LEU 4.3 11.0 - - - +
119B PHE* 4.0 34.8 - - + +
324B LEU* 4.0 35.4 - - + -
331B ARG* 4.5 2.3 + - - +
352B MET* 4.7 2.7 - - + -
354B TYR* 4.6 9.2 - - + +
358B THR* 2.9 30.3 + - + +
359B ALA 3.7 6.7 - - - +
361B TYR* 1.3 82.4 - - + +
363B LEU* 1.3 57.6 + - - +
365B GLY* 3.0 19.9 - - - -
367B LYS* 3.9 12.2 + - + +
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Residues in contact with LEU 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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56B TYR* 3.9 21.8 - - + +
75B HIS* 3.8 27.6 - - + -
78B THR* 4.1 7.4 - - + -
80B ARG* 2.7 44.9 + - + +
82B VAL* 4.0 12.3 - - + -
119B PHE* 3.6 43.3 - - + -
359B ALA* 2.9 20.7 + - + +
360B THR 3.5 4.7 - - - +
362B LEU* 1.3 73.1 - - - +
364B LEU* 1.3 50.0 + - - +
365B GLY* 3.1 7.0 - - - -
366B ARG 2.7 20.4 - - - +
367B LYS 4.3 3.4 - - - +
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 3.6 19.7 - - - +
80B ARG* 3.7 21.1 + - - +
331B ARG* 3.6 48.4 - - + +
334B ILE* 4.1 33.8 - - + +
335B MET* 4.4 5.4 - - + -
338B MET* 4.5 3.6 - - + -
360B THR* 3.0 29.0 + - + +
361B TYR 2.9 10.6 + - - +
363B LEU* 1.3 78.3 - - - +
365B GLY* 1.3 46.3 + - - -
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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