Contacts of the helix formed by residues 341 - 352 (chain A) 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 SER 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A GLY 3.8 2.2 + - - -
340A TYR* 1.3 69.9 - - - +
342A GLN* 1.3 72.0 + - - +
343A GLU* 3.0 16.1 + - - +
344A GLU* 3.0 40.5 + - - +
345A ILE* 3.1 23.0 + - - +
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Residues in contact with GLN 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ILE* 5.1 6.9 - - + +
336A VAL* 4.2 27.5 - - + +
340A TYR 3.5 2.9 + - - +
341A SER* 1.3 79.6 - - - +
343A GLU* 1.3 61.5 + - + +
345A ILE* 3.5 15.0 - - - +
346A GLN* 3.4 22.0 - - - +
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A SER* 3.2 15.0 - - - +
342A GLN* 1.3 79.2 - - + +
344A GLU* 1.3 62.6 + - + +
345A ILE 2.9 1.6 - - - -
346A GLN* 3.0 8.1 + - + +
347A GLU* 2.7 30.0 + - - +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A GLY 4.4 2.1 - - - +
340A TYR* 3.3 24.6 - - + -
341A SER* 3.0 54.1 + - - +
343A GLU* 1.3 78.5 - - + +
345A ILE* 1.3 62.1 + - - +
347A GLU* 3.5 9.8 - - + +
348A SER* 3.1 28.6 + - - -
357A ILE* 3.7 15.2 - - + +
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Residues in contact with ILE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ILE* 4.0 32.3 - - + +
335A MET* 3.9 31.2 - - + -
336A VAL* 4.5 2.9 - - + -
340A TYR* 4.1 14.6 - - + -
341A SER 3.1 22.6 + - - +
342A GLN* 3.5 9.9 - - - +
343A GLU 2.9 0.6 - - - -
344A GLU* 1.3 77.6 - - + +
346A GLN* 1.3 66.7 + - - +
348A SER* 3.3 2.1 + - - -
349A LEU* 2.9 55.2 + - + +
357A ILE* 3.8 20.4 - - + -
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Residues in contact with GLN 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ILE* 2.7 43.6 + - + +
327A SER* 4.9 1.4 + - - +
332A ILE* 4.1 13.4 - - - +
342A GLN 3.4 14.7 + - - +
343A GLU* 3.0 11.2 + - + +
345A ILE* 1.3 79.4 - - - +
347A GLU* 1.3 66.3 + - - +
349A LEU* 4.4 7.0 - - - +
350A SER* 2.8 32.2 + - - -
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A GLU 2.7 20.2 + - - +
344A GLU* 3.5 12.1 - - + +
346A GLN* 1.3 73.9 - - - +
348A SER* 1.3 62.4 + - - +
350A SER* 3.2 11.6 + - - -
351A LYS* 2.8 54.8 + - - +
353A LYS* 3.2 29.5 + - - +
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Residues in contact with SER 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A GLU 3.1 9.7 + - - -
345A ILE 3.9 1.6 - - - -
347A GLU* 1.3 78.2 - - - +
349A LEU* 1.3 54.0 + - - +
352A MET* 2.7 33.1 + - - -
353A LYS* 3.4 22.7 + - - +
355A ASP* 2.8 34.9 + - - -
357A ILE* 3.0 30.2 - - - +
358A THR* 3.7 4.3 + - - -
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A LEU* 5.2 2.2 - - + +
326A ILE* 3.8 44.2 - - + +
345A ILE* 2.9 42.0 + - + +
346A GLN* 4.0 4.9 - - - +
348A SER* 1.3 76.4 - - - +
350A SER* 1.3 67.6 + - - +
352A MET* 3.5 18.7 + - - +
357A ILE* 4.9 1.8 - - + +
358A THR* 4.0 33.9 - - + +
361A TYR* 3.8 42.2 - - + -
362A LEU* 5.9 0.4 - - + -
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Residues in contact with SER 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ILE* 5.0 10.0 - - - +
346A GLN* 2.8 25.0 + - - +
347A GLU* 3.2 5.5 + - - -
349A LEU* 1.3 79.6 - - - +
351A LYS* 1.3 77.3 + - - +
352A MET* 3.2 4.7 + - - +
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLU* 2.8 50.5 + - - +
350A SER* 1.3 84.4 + - - +
352A MET* 1.3 74.9 + - - +
353A LYS* 3.9 19.8 - - + +
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Residues in contact with MET 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A LEU* 3.8 27.8 - - + -
348A SER 2.7 17.9 + - - -
349A LEU* 3.8 8.7 - - - +
350A SER 3.2 8.8 - - - +
351A LYS* 1.3 81.8 - - - +
353A LYS* 1.3 59.8 + - - +
354A TYR* 3.5 50.2 + - + +
358A THR* 3.5 29.8 - - + -
362A LEU* 4.2 10.3 - - + -
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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