Contacts of the helix formed by residues 424 - 439 (chain G) in PDB entry 1ZMD
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 GLY 424 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363G GLU* 3.7 11.7 + - - -
422G GLY 3.6 0.8 + - - -
423G PRO* 1.3 71.8 - - - +
425G ALA* 1.3 59.8 + - - +
426G GLY 3.4 2.7 - - - -
427G GLU* 3.3 12.7 + - - +
428G MET* 2.9 33.2 + - - +
455G LEU* 4.0 13.1 - - - +
427H GLU* 6.1 2.0 - - - -
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Residues in contact with ALA 425 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363G GLU* 3.3 25.4 + - + +
365G ALA* 3.4 20.4 - - + +
420G ILE* 3.6 33.3 - - + +
422G GLY 3.6 13.0 + - - +
423G PRO 3.2 3.0 - - - -
424G GLY* 1.3 77.0 - - - +
426G GLY* 1.3 63.7 + - - +
428G MET* 3.2 1.9 + - - +
429G VAL 3.0 21.7 + - - -
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Residues in contact with GLY 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G VAL* 3.8 31.1 - - - +
363G GLU* 2.9 16.6 + - - -
365G ALA* 4.0 0.2 - - - +
425G ALA* 1.3 76.6 - - - +
427G GLU* 1.3 57.9 + - - +
429G VAL* 3.3 9.9 - - - +
430G ASN* 3.0 19.2 + - - -
393H ARG* 4.8 2.9 - - - -
454H THR* 3.7 14.4 - - - +
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Residues in contact with GLU 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363G GLU* 4.6 0.6 + - - +
424G GLY* 3.3 12.6 + - - +
425G ALA 3.3 0.2 - - - -
426G GLY* 1.3 73.8 - - - +
428G MET* 1.3 65.9 + - - +
430G ASN* 3.1 21.9 + - - +
431G GLU* 4.2 1.7 + - - +
393H ARG* 3.0 28.0 + - - +
424H GLY* 6.2 2.5 - - - -
427H GLU* 5.1 15.0 - - + -
428H MET* 5.1 2.7 - - - +
454H THR* 3.3 7.4 - - - -
455H LEU* 2.7 38.3 + - + +
456H SER* 2.9 31.0 + - - -
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Residues in contact with MET 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388G PHE* 3.9 14.4 - - + -
404G VAL* 4.2 8.3 - - - -
420G ILE* 4.0 24.9 - - + -
423G PRO 4.0 8.7 - - - +
424G GLY 2.9 14.8 + - - +
425G ALA 3.7 4.0 - - - +
427G GLU* 1.3 77.9 - - - +
429G VAL* 1.3 61.7 + - - +
430G ASN 3.0 0.4 - - - -
431G GLU* 3.0 21.8 + - - +
432G ALA* 3.5 7.4 + - - +
455G LEU* 3.5 42.0 - - + +
456G SER* 4.1 9.9 - - - +
459G PHE* 3.8 32.3 - - + -
427H GLU* 5.0 4.4 - - + +
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Residues in contact with VAL 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355G PRO* 4.0 14.1 - - + -
357G VAL* 3.9 19.3 - - + -
365G ALA* 3.6 6.1 - - + -
366G TRP* 3.7 41.1 - - - +
367G VAL* 3.9 11.4 - - + -
418G ALA 5.0 0.4 - - - +
420G ILE* 3.8 12.1 - - + +
425G ALA 3.0 12.5 + - - +
426G GLY 3.3 20.4 - - - +
428G MET* 1.3 75.1 - - - +
430G ASN* 1.3 62.9 + - - +
431G GLU 3.3 0.2 - - - -
432G ALA* 3.1 7.5 + - + +
433G ALA* 2.7 26.9 + - - +
451H ALA* 4.4 0.7 - - + -
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Residues in contact with ASN 430 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355G PRO* 4.4 1.6 - - - +
426G GLY 3.0 27.0 + - - -
427G GLU* 3.1 12.6 + - - +
428G MET 3.0 0.8 - - - -
429G VAL* 1.3 78.1 - - - +
431G GLU* 1.3 65.8 + - - +
432G ALA 3.1 1.3 - - - -
433G ALA* 3.2 6.6 + - - +
434G LEU* 3.0 22.3 + - - +
431H GLU* 3.6 22.9 - - - +
448H VAL* 4.7 2.3 - - - +
449H CYS 4.3 1.4 - - - +
450H HIS* 3.2 14.6 - - + -
451H ALA* 2.8 27.4 + - - +
454H THR* 3.7 7.7 + - - +
456H SER* 3.0 24.8 + - - +
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Residues in contact with GLU 431 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427G GLU 4.2 1.6 + - - +
428G MET* 3.0 15.6 + - - +
430G ASN* 1.3 77.5 - - - +
432G ALA* 1.3 58.8 + - - +
434G LEU* 3.3 1.7 + - - +
435G ALA* 3.0 23.0 + - - +
445G ILE* 4.4 1.6 - - - +
450G HIS* 2.6 37.0 + - - -
456G SER* 4.0 8.0 - - - -
459G PHE* 3.6 23.7 - - + +
427H GLU 5.5 0.2 - - - +
430H ASN* 3.8 25.0 - - - +
431H GLU* 4.2 25.4 + - + +
434H LEU* 3.4 25.1 - - + +
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Residues in contact with ALA 432 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367G VAL* 3.8 16.8 - - + -
418G ALA* 3.8 12.1 - - + -
420G ILE* 5.1 1.1 - - + -
428G MET 3.5 1.8 + - - +
429G VAL* 3.1 20.1 + - + +
430G ASN 3.1 0.4 - - - -
431G GLU* 1.3 77.9 - - - +
433G ALA* 1.3 58.3 + - - +
435G ALA* 3.2 3.6 + - - +
436G LEU* 2.9 32.7 + - - +
459G PHE* 3.8 32.9 - - + -
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Residues in contact with ALA 433 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353G CYS* 4.4 15.9 - - + +
355G PRO* 4.7 4.0 - - + -
367G VAL* 4.1 15.0 - - + +
429G VAL 2.7 18.1 + - - +
430G ASN* 3.2 9.1 + - - +
432G ALA* 1.3 72.8 - - - +
434G LEU* 1.3 64.2 + - - +
436G LEU* 3.4 3.9 + - - +
437G GLU* 3.0 23.2 + - - +
448H VAL* 3.8 19.0 - - + +
449H CYS 4.0 13.5 - - - +
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Residues in contact with LEU 434 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430G ASN 3.0 13.1 + - - +
431G GLU* 3.5 8.5 - - - +
433G ALA* 1.3 77.8 - - - +
435G ALA* 1.3 63.3 + - - +
437G GLU* 3.1 4.0 + - - +
438G TYR* 3.1 41.7 + - + +
431H GLU* 3.5 40.6 - - + +
434H LEU* 4.1 11.4 - - + -
435H ALA* 3.9 21.8 - - + +
438H TYR* 5.8 2.0 - - + -
440H ALA* 5.3 3.6 - - + -
444H ASP 5.2 1.1 - - - +
445H ILE* 4.7 14.8 - - + +
448H VAL* 3.8 28.4 - - + +
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Residues in contact with ALA 435 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G VAL* 5.5 3.1 - - + -
431G GLU 3.0 14.0 + - - +
432G ALA* 3.2 10.7 + - - +
434G LEU* 1.3 77.3 - - - +
436G LEU* 1.3 63.3 + - - +
438G TYR* 3.1 10.1 + - - -
440G ALA* 3.0 33.6 + - + +
445G ILE* 3.5 32.8 - - + -
459G PHE* 4.9 0.9 - - + -
434H LEU* 3.8 14.7 - - + +
438H TYR* 5.2 1.1 - - - -
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Residues in contact with LEU 436 (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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352G ASN* 4.3 9.2 - - - +
353G CYS* 4.0 18.4 - - - -
367G VAL* 3.9 20.9 - - + +
368G GLY* 3.5 36.1 - - - +
414G ARG* 4.6 7.6 + - - +
415G VAL* 3.2 45.8 - - + +
416G LEU 4.3 6.7 - - - +
417G GLY* 4.7 0.9 - - - +
418G ALA* 5.5 1.1 - - + +
432G ALA* 2.9 20.4 + - + +
433G ALA* 3.8 4.5 - - - +
435G ALA* 1.3 72.0 - - - +
437G GLU* 1.3 63.6 + - - +
439G GLY* 2.9 14.9 + - - +
440G ALA 4.9 1.6 - - - +
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Residues in contact with GLU 437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350G ASP* 6.1 0.7 - - - +
353G CYS* 4.5 14.2 - - + +
433G ALA 3.0 14.7 + - - +
434G LEU 3.4 9.2 - - - +
436G LEU* 1.3 78.4 - - - +
438G TYR* 1.3 72.5 + - + +
439G GLY 3.5 0.3 + - - -
444H ASP* 5.2 3.6 - - + +
447H ARG* 5.4 4.6 - - - +
448H VAL* 3.9 26.4 - - + +
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Residues in contact with TYR 438 (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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434G LEU* 3.1 23.6 + - + +
435G ALA 3.1 9.1 + - - +
437G GLU* 1.3 84.5 - - + +
439G GLY* 1.3 63.0 + - - +
440G ALA* 4.4 0.2 - - - -
438H TYR* 3.6 60.5 + + + -
439H GLY 4.5 1.4 + - - -
440H ALA* 3.5 23.0 + - + -
444H ASP* 2.6 39.5 + - + -
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Residues in contact with GLY 439 (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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414G ARG* 3.6 38.3 + - - -
415G VAL 6.0 0.2 - - - -
436G LEU* 2.9 16.8 + - - -
437G GLU 3.2 1.4 + - - -
438G TYR* 1.3 80.3 - - - +
440G ALA* 1.3 67.1 + - - +
441G SER* 3.8 0.7 + - - -
444G ASP* 4.7 0.9 - - - +
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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