Contacts of the helix formed by residues 346 - 362 (chain A) in PDB entry 4X2Q
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 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TYR* 5.8 4.2 - - - +
168A TRP* 5.8 0.5 + - - -
196A GLN* 3.1 35.2 + - - +
344A GLN* 4.7 0.2 - - - +
345A ILE* 1.3 93.0 - - + +
347A LYS* 1.3 60.7 + - - +
348A LYS* 3.5 22.4 - - + +
349A GLN* 3.6 13.9 - - + +
350A TYR* 2.9 28.1 + - - +
379A PHE* 3.3 14.4 - - - +
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Residues in contact with LYS 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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346A ASP* 1.3 74.3 + - - +
348A LYS* 1.3 61.2 + - - +
350A TYR* 3.9 27.4 - - - -
351A ASN* 2.9 56.5 + - - +
379A PHE* 3.4 29.4 - - + -
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Residues in contact with LYS 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ASP* 3.5 16.3 - - + +
347A LYS* 1.3 80.4 - - - +
349A GLN* 1.3 59.7 + - - +
351A ASN* 4.4 2.9 - - - +
352A LYS* 3.3 36.4 + - + +
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Residues in contact with GLN 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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168A TRP* 3.7 26.8 - - - -
300A GLN* 3.1 22.7 + - - +
344A GLN* 4.2 4.3 - - + -
345A ILE* 3.9 9.2 - - + +
346A ASP* 3.5 19.8 + - + +
347A LYS 3.3 0.4 - - - -
348A LYS* 1.3 78.8 - - - +
350A TYR* 1.3 66.6 + - - +
352A LYS* 3.0 15.5 + - - +
353A ILE* 3.0 26.2 + - + +
401A PHE* 2.8 54.9 + - - +
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Residues in contact with TYR 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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344A GLN* 4.5 3.8 - - - +
346A ASP 2.9 19.8 + - - +
347A LYS* 3.9 30.3 - - - +
348A LYS 3.6 0.2 - - - -
349A GLN* 1.3 77.6 - - - +
351A ASN* 1.3 68.3 + - - +
353A ILE* 3.5 3.3 + - - +
354A LEU* 3.3 44.7 + - + +
373A GLY* 3.4 21.0 - - - -
374A LEU 4.4 0.5 + - - -
375A GLY 4.8 10.0 + - - -
378A GLY 5.3 1.3 - - - -
379A PHE* 3.7 35.0 - + + -
380A PHE 3.4 22.1 + - - -
381A ILE* 3.6 25.8 - - + +
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Residues in contact with ASN 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 LYS* 2.9 43.5 + - - +
348A LYS* 4.4 3.1 - - - +
350A TYR* 1.3 91.1 - - - +
352A LYS* 1.3 59.2 + - - +
354A LEU* 3.5 9.2 + - - +
355A GLU* 3.0 30.7 + - - +
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Residues in contact with LYS 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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348A LYS* 3.3 30.2 + - + +
349A GLN* 3.0 9.0 + - - +
351A ASN* 1.3 78.9 - - - +
353A ILE* 1.3 62.4 + - - +
355A GLU* 3.7 9.8 - - + +
356A LEU* 3.6 20.1 + - - +
401A PHE* 3.8 37.5 - - + -
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Residues in contact with ILE 353 (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 GLN* 3.5 37.5 - - + +
349A GLN* 3.0 28.8 + - + +
350A TYR 3.8 3.6 - - - +
352A LYS* 1.3 75.6 - - - +
354A LEU* 1.3 65.5 + - - +
356A LEU* 3.1 6.4 + - - +
357A ILE* 3.0 33.7 + - + +
381A ILE* 3.8 15.0 - - + -
400A ILE* 4.1 19.7 - - + +
401A PHE* 3.7 28.3 - - + +
402A GLY* 3.9 4.0 - - - -
403A PRO* 4.5 5.2 - - + -
404A VAL* 4.4 7.4 - - + -
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Residues in contact with LEU 354 (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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350A TYR* 3.3 49.6 + - + +
351A ASN* 3.5 10.1 + - - +
353A ILE* 1.3 78.1 - - - +
355A GLU* 1.3 62.7 + - - +
357A ILE* 3.2 11.1 + - + +
358A GLN* 3.1 43.8 + - - +
371A GLY 3.4 24.5 - - - +
372A LYS* 4.0 18.8 - - - -
373A GLY* 4.1 2.9 - - - +
381A ILE* 4.7 8.7 - - + -
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Residues in contact with GLU 355 (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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351A ASN 3.0 19.0 + - - +
352A LYS* 3.7 13.0 - - + +
353A ILE 3.2 0.2 - - - -
354A LEU* 1.3 76.8 - - - +
356A LEU* 1.3 60.8 + - + +
358A GLN* 4.2 4.5 - - - +
359A SER* 3.3 25.1 + - - -
394A ARG* 6.1 0.5 - - - -
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Residues in contact with LEU 356 (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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352A LYS 3.6 11.6 + - - +
353A ILE 3.1 9.4 + - - +
355A GLU* 1.3 80.5 - - + +
357A ILE* 1.3 64.9 + - - +
359A SER* 3.4 13.9 - - - +
360A GLY 3.4 1.2 + - - -
394A ARG* 3.6 36.3 - - + +
395A ILE* 3.3 36.0 - - + +
398A GLU* 4.0 24.0 - - + +
399A GLU 4.7 2.9 - - - +
400A ILE* 3.6 34.1 - - + -
401A PHE* 5.9 6.1 - - + -
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Residues in contact with ILE 357 (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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353A ILE* 3.0 34.8 + - + +
354A LEU* 3.2 18.1 + - + +
356A LEU* 1.3 73.5 - - + +
358A GLN* 1.3 61.3 + - + +
359A SER 3.0 4.0 - - - -
360A GLY 3.1 15.6 + - - -
361A VAL* 3.2 15.6 + - + +
371A GLY* 3.5 41.1 - - - +
381A ILE* 4.4 11.9 - - + -
384A THR* 4.6 3.8 - - + +
386A PHE* 3.5 27.3 - - + -
395A ILE* 5.6 0.2 - - - -
400A ILE* 5.7 1.3 - - + -
404A VAL* 3.8 26.5 - - + -
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Residues in contact with GLN 358 (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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354A LEU* 3.1 28.7 + - - +
355A GLU* 4.2 4.3 + - - +
357A ILE* 1.3 82.9 - - + +
359A SER* 1.3 62.9 + - - +
361A VAL* 3.9 15.0 - - + +
362A ALA* 3.6 19.1 + - - +
371A GLY 4.8 9.4 + - - +
372A LYS* 5.8 3.2 - - - +
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Residues in contact with SER 359 (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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355A GLU* 3.3 24.7 + - - -
356A LEU* 3.4 18.1 - - - +
358A GLN* 1.3 78.1 - - - +
360A GLY* 1.3 60.8 + - - +
362A ALA* 3.4 5.6 + - - +
363A GLU* 3.2 24.9 + - - +
394A ARG* 2.8 39.3 + - - +
395A ILE* 5.2 1.3 - - - +
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Residues in contact with GLY 360 (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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356A LEU 3.4 5.8 + - - -
357A ILE 3.1 8.1 + - - -
359A SER* 1.3 78.3 - - - +
361A VAL* 1.3 63.7 + - - +
363A GLU* 3.3 12.1 + - - -
364A GLY 3.3 0.7 + - - -
365A ALA* 3.3 30.1 + - - +
386A PHE* 4.6 4.9 - - - -
393A MET* 4.2 10.5 - - - -
395A ILE* 4.6 14.1 - - - +
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Residues in contact with VAL 361 (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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357A ILE* 3.2 18.3 + - + +
358A GLN* 3.9 17.3 - - + +
359A SER 3.3 0.4 - - - -
360A GLY* 1.3 79.2 - - - +
362A ALA* 1.3 60.4 + - + +
363A GLU 3.3 0.7 + - - -
364A GLY* 4.2 3.8 + - - -
365A ALA 4.1 12.3 - - - +
367A LEU* 4.4 24.9 - - + -
371A GLY* 6.1 0.2 - - - -
386A PHE* 3.9 18.4 - - + -
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Residues in contact with ALA 362 (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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358A GLN 3.6 11.1 + - - +
359A SER* 3.4 5.3 + - - +
360A GLY 3.3 0.2 - - - -
361A VAL* 1.3 79.0 - - + +
363A GLU* 1.3 59.8 + - - +
364A GLY 3.7 0.4 - - - -
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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