Contacts of the helix formed by residues 411 - 429 (chain G) in PDB entry 1QZW
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 VAL 411 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400G MET* 5.4 8.5 - - + -
401G ARG* 5.1 21.3 - - + -
404G ALA* 4.0 17.7 - - + +
409G LEU 3.0 6.6 + - - -
410G GLU* 1.3 92.5 - - + +
412G GLU* 1.3 68.1 + - + +
413G GLU* 2.5 15.9 + - - +
414G VAL* 2.9 21.2 + - + +
415G ARG* 5.2 14.6 - - + +
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Residues in contact with GLU 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410G GLU* 3.0 28.7 - - - +
411G VAL* 1.3 82.1 - - + +
413G GLU* 1.3 72.7 + - - +
414G VAL 2.5 3.1 + - - -
415G ARG* 3.0 6.4 + - - +
416G GLU* 2.7 46.2 + - - +
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Residues in contact with GLU 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376G ARG* 3.9 20.6 - - - +
377G TRP* 3.9 7.5 - - + -
409G LEU* 3.2 26.8 - - + +
410G GLU* 2.4 57.4 + - - +
411G VAL 2.5 4.8 + - - +
412G GLU* 1.3 76.1 - - - +
414G VAL* 1.3 55.9 + - + +
416G GLU* 2.7 33.6 + - - +
417G LEU* 2.9 12.0 - - + +
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Residues in contact with VAL 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395G ILE* 5.7 0.2 - - + -
400G MET* 4.5 16.8 - - + -
403G ILE* 6.1 6.5 - - + -
404G ALA* 4.4 23.1 - - + -
407G SER* 5.5 2.0 - - - +
409G LEU* 4.8 8.5 - - + +
411G VAL* 2.9 17.1 + - + +
412G GLU 2.5 4.4 + - - -
413G GLU* 1.3 72.0 - - + +
415G ARG* 1.3 70.9 + - - +
416G GLU 2.7 1.1 - - - -
417G LEU* 2.4 51.6 + - + +
418G LEU* 2.9 17.2 + - + -
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Residues in contact with ARG 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397G LYS* 6.0 4.8 - - - +
400G MET* 4.6 13.6 - - + +
411G VAL* 4.5 11.0 + - + +
412G GLU* 3.0 12.8 + - - +
414G VAL* 1.3 77.5 - - - +
416G GLU* 1.3 52.0 + - + +
417G LEU 2.5 1.2 + - - -
418G LEU* 3.1 23.2 + - + +
419G GLU* 2.4 39.4 - - - +
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Residues in contact with GLU 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377G TRP* 3.4 9.0 - - - -
412G GLU* 2.7 46.9 + - - +
413G GLU* 2.7 17.8 - - - +
414G VAL 2.7 0.2 - - - -
415G ARG* 1.3 75.1 - - + +
417G LEU* 1.3 60.1 + - - +
419G GLU* 3.5 9.4 - - - -
420G TRP* 4.2 12.3 + - + -
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Residues in contact with LEU 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376G ARG 5.8 0.4 - - - +
377G TRP* 3.0 37.5 - - + +
409G LEU* 6.3 1.8 - - + -
413G GLU* 2.9 20.0 - - + +
414G VAL* 2.4 42.6 + - + +
415G ARG 2.5 8.9 + - - -
416G GLU* 1.3 73.4 - - - +
418G LEU* 1.3 76.7 + - + +
419G GLU* 2.5 9.7 + - - -
420G TRP* 2.4 33.5 + - - -
421G TYR* 2.5 47.7 - - + +
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Residues in contact with LEU 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395G ILE* 3.9 36.1 - - + +
400G MET* 4.0 10.5 - - + -
414G VAL* 3.0 20.6 - - + +
415G ARG* 3.2 31.0 - - + +
417G LEU* 1.3 94.1 - - + +
419G GLU* 1.3 60.4 + - + +
421G TYR* 3.0 28.7 - - + +
422G ASN* 2.9 26.6 + - - +
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Residues in contact with GLU 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G ARG 2.4 33.0 - - - +
416G GLU* 3.6 7.1 - - - -
417G LEU* 2.5 16.5 + - - -
418G LEU* 1.3 66.5 - - + +
420G TRP* 1.3 78.1 + - + +
421G TYR 2.4 17.7 + - - -
422G ASN* 3.9 9.2 - - + +
423G ASN* 2.6 36.0 + - + +
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Residues in contact with TRP 420 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377G TRP* 3.7 26.4 - + - +
416G GLU* 4.2 11.2 + - + -
417G LEU* 2.4 20.7 + - - +
419G GLU* 1.3 102.2 - - + +
421G TYR* 1.3 70.1 + - + +
423G ASN* 5.0 10.1 - - + -
424G MET* 3.6 18.8 - - - +
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Residues in contact with TYR 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G LEU* 4.4 19.0 - - + +
332G VAL* 6.0 9.2 - - + -
377G TRP* 3.0 40.8 + + - -
381G LEU* 6.5 0.9 - - + -
392G PRO* 6.2 0.7 - - + -
417G LEU* 2.5 65.0 - - + +
418G LEU* 3.0 23.8 - - + +
419G GLU 2.4 1.4 + - - -
420G TRP* 1.3 94.0 - - + +
422G ASN* 1.3 56.2 + - - +
423G ASN 3.1 4.0 - - - -
424G MET* 3.7 5.4 - - - +
425G ASN* 2.7 31.1 + - - +
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Residues in contact with ASN 422 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G LEU* 4.4 2.9 - - - +
392G PRO* 3.4 32.7 + - - +
393G ASN* 4.4 3.8 - - - +
395G ILE* 5.4 2.8 - - - +
418G LEU* 2.9 26.9 + - - +
419G GLU* 2.9 6.6 + - - +
421G TYR* 1.3 75.9 - - - +
423G ASN* 1.3 55.3 + - - +
425G ASN* 2.5 26.5 + - - +
426G ARG* 3.0 22.6 - - - -
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Residues in contact with ASN 423 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419G GLU* 2.6 28.8 + - + +
420G TRP* 5.0 9.2 - - + -
422G ASN* 1.3 73.1 - - - +
424G MET* 1.3 71.2 + - - +
425G ASN* 2.7 1.8 - - - -
426G ARG* 2.7 38.7 + - - +
427G LEU* 2.7 48.6 + - + +
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Residues in contact with MET 424 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G GLN* 4.1 19.1 - - - +
355G LEU* 4.1 4.3 - - + +
356G GLY* 3.3 35.9 - - - +
419G GLU 3.8 2.4 + - - -
420G TRP* 3.6 22.2 - - - +
421G TYR* 3.7 8.3 - - - +
423G ASN* 1.3 82.2 - - - +
425G ASN* 1.3 54.6 + - + +
427G LEU* 3.0 6.9 + - - +
428G LEU* 2.4 62.2 + - + +
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Residues in contact with ASN 425 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G LEU* 5.0 9.1 - - + +
421G TYR 2.7 11.4 + - - +
422G ASN* 2.5 50.4 - - - +
423G ASN 2.7 4.0 - - - -
424G MET* 1.3 73.4 - - + +
426G ARG* 1.3 63.8 + - - +
428G LEU* 2.4 28.4 + - + -
429G LYS* 2.3 48.6 + - + +
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Residues in contact with ARG 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422G ASN* 3.0 18.8 - - - -
423G ASN* 2.7 43.5 + - - +
425G ASN* 1.3 78.3 - - - +
427G LEU* 1.3 63.7 + - + +
429G LYS* 2.7 34.2 - - + +
430G MET* 3.6 10.0 + - - +
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Residues in contact with LEU 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360G PRO 6.0 1.8 - - - +
362G PRO* 5.3 17.0 - - + -
423G ASN* 2.7 39.7 + - + +
424G MET* 3.4 5.6 - - - +
425G ASN 2.7 4.1 + - - -
426G ARG* 1.3 81.4 - - + +
428G LEU* 1.3 55.0 + - - +
430G MET* 2.3 44.0 + - - +
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Residues in contact with LEU 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G GLN* 4.8 16.2 - - + -
315G LYS* 3.5 26.9 - - - +
357G ILE* 4.7 16.6 - - + -
359G LEU* 5.3 14.5 - - + +
424G MET* 2.4 62.5 + - + +
425G ASN* 2.4 14.6 + - + +
427G LEU* 1.3 66.6 - - - +
429G LYS* 1.3 76.7 + - + +
430G MET* 2.5 17.5 + - - +
431G VAL* 4.8 4.5 - - - +
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Residues in contact with LYS 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315G LYS 4.9 4.3 - - - +
425G ASN* 2.3 31.1 + - + +
426G ARG* 2.7 51.6 - - + +
428G LEU* 1.3 78.3 - - + +
430G MET* 1.3 57.5 + - - +
431G VAL* 2.6 26.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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