Contacts of the helix formed by residues 424 - 438 (chain H) in PDB entry 1ZMC
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G GLU* 6.3 1.6 - - - -
363H GLU* 3.5 12.3 + - - -
422H GLY 3.3 1.0 + - - -
423H PRO* 1.3 72.4 - - - +
425H ALA* 1.3 64.8 + - - +
426H GLY 3.3 2.7 - - - -
427H GLU* 3.4 9.9 + - - +
428H MET* 2.9 29.5 + - - +
455H LEU* 3.9 12.0 - - - +
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Residues in contact with ALA 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H GLU* 3.1 18.6 + - + -
365H ALA* 3.3 18.5 - - + +
420H ILE* 3.7 41.5 - - + +
422H GLY 3.4 14.3 + - - +
423H PRO 3.3 3.2 - - - -
424H GLY* 1.3 76.6 - - - +
426H GLY* 1.3 64.3 + - - +
428H MET* 3.2 1.7 + - - +
429H VAL 3.0 21.0 + - - -
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Residues in contact with GLY 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393G ARG* 4.4 6.7 - - - -
454G THR* 3.7 12.0 - - - +
357H VAL* 3.7 29.2 - - - +
363H GLU* 2.8 21.1 + - - -
365H ALA* 4.0 0.4 - - - +
425H ALA* 1.3 71.8 - - - +
427H GLU* 1.3 58.0 + - - +
429H VAL* 3.3 12.5 - - - +
430H ASN* 3.1 16.5 + - - -
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Residues in contact with GLU 427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393G ARG* 3.1 27.5 + - - +
424G GLY* 6.1 2.0 - - - -
427G GLU* 5.3 15.3 - - + -
428G MET* 4.9 3.9 - - + +
431G GLU* 5.1 0.7 - - - +
454G THR* 3.3 8.2 - - - -
455G LEU* 2.8 38.9 + - + +
456G SER* 2.9 33.5 + - - -
363H GLU* 4.6 0.2 + - - -
424H GLY* 3.4 10.1 + - - +
425H ALA 3.3 0.4 - - - -
426H GLY* 1.3 72.9 - - - +
428H MET* 1.3 66.5 + - - +
429H VAL 3.2 1.4 + - - -
430H ASN* 3.2 20.2 + - - +
431H GLU* 4.1 1.9 + - - +
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Residues in contact with MET 428 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427G GLU* 5.0 3.1 - - - +
388H PHE* 4.0 11.7 - - + -
404H VAL* 4.2 7.9 - - - -
420H ILE* 3.8 27.9 - - + +
423H PRO 4.0 2.7 - - - +
424H GLY* 2.9 20.5 + - - +
425H ALA 3.7 3.8 - - - +
427H GLU* 1.3 78.8 - - - +
429H VAL* 1.3 62.4 + - - +
431H GLU* 3.1 22.9 + - - +
432H ALA* 3.5 4.3 + - - +
455H LEU* 3.5 41.3 - - + +
456H SER* 4.0 7.6 - - - +
459H PHE* 3.7 34.5 - - + -
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Residues in contact with VAL 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451G ALA* 4.5 0.4 - - + -
355H PRO* 4.0 18.6 - - + -
357H VAL* 4.1 9.2 - - + -
365H ALA* 3.7 13.2 - - + -
366H TRP* 3.7 38.8 - - - +
367H VAL* 3.9 11.2 - - + -
418H ALA* 5.1 0.7 - - + +
420H ILE* 3.9 9.6 - - + +
425H ALA 3.0 12.7 + - - +
426H GLY 3.3 17.5 - - - +
428H MET* 1.3 77.3 - - - +
430H ASN* 1.3 66.3 + - - +
432H ALA* 3.0 6.4 + - + +
433H ALA* 2.8 26.7 + - - +
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Residues in contact with ASN 430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431G GLU* 3.4 22.2 - - - +
448G VAL* 4.8 2.1 - - - +
449G CYS 4.5 0.9 - - - +
450G HIS* 3.4 12.5 - - + -
451G ALA* 3.0 30.4 + - - +
454G THR* 3.5 8.5 + - - +
456G SER* 2.8 26.8 + - - +
355H PRO* 4.5 1.6 - - - +
426H GLY 3.1 25.0 + - - -
427H GLU* 3.2 13.4 + - - +
428H MET 3.2 0.8 - - - -
429H VAL* 1.3 80.2 - - - +
431H GLU* 1.3 61.5 + - - +
433H ALA* 3.7 7.3 - - - +
434H LEU* 3.1 23.2 + - - +
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Residues in contact with GLU 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427G GLU 5.2 0.7 - - - +
430G ASN* 3.7 22.4 - - - +
431G GLU* 3.8 29.8 + - + +
434G LEU* 3.6 19.4 - - + +
427H GLU 4.1 1.4 + - - +
428H MET* 3.1 17.4 + - - +
430H ASN* 1.3 79.4 - - - +
432H ALA* 1.3 62.6 + - - +
434H LEU* 3.5 2.1 + - - +
435H ALA* 3.1 18.5 + - - +
445H ILE* 4.1 3.6 - - - +
450H HIS* 2.9 35.2 + - - -
456H SER* 4.1 6.9 - - - -
459H PHE* 3.3 25.3 - - + -
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Residues in contact with ALA 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367H VAL* 3.7 19.5 - - + -
415H VAL* 6.4 0.4 - - + -
418H ALA* 3.7 22.4 - - + -
420H ILE* 5.5 0.4 - - + -
428H MET 3.5 1.4 + - - -
429H VAL* 3.0 17.4 + - + +
431H GLU* 1.3 78.0 - - - +
433H ALA* 1.3 58.3 - - - +
435H ALA* 3.2 5.8 + - - +
436H LEU* 2.9 32.3 + - + +
459H PHE* 3.8 20.5 - - + -
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Residues in contact with ALA 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448G VAL* 4.0 6.8 - - + +
449G CYS 3.8 23.1 - - - +
353H CYS* 4.4 13.4 - - - +
355H PRO* 4.6 5.2 - - + -
367H VAL* 4.1 12.3 - - + +
429H VAL 2.8 15.0 + - - +
430H ASN* 3.7 9.6 - - - +
431H GLU 3.3 0.2 - - - -
432H ALA* 1.3 76.8 - - - +
434H LEU* 1.3 55.6 + - - +
436H LEU* 3.4 7.9 + - - +
437H GLU* 3.0 31.2 + - - +
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Residues in contact with LEU 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431G GLU* 3.4 41.7 - - + +
434G LEU* 4.2 10.8 - - + -
435G ALA* 3.8 23.3 - - + +
445G ILE* 4.8 13.2 - - + -
448G VAL* 3.5 31.8 - - + +
450G HIS* 6.3 0.2 - - + -
459G PHE* 5.6 0.2 - - + -
430H ASN 3.1 16.8 + - - +
431H GLU* 3.6 5.4 - - - +
433H ALA* 1.3 73.1 - - - +
435H ALA* 1.3 66.4 + - - +
437H GLU* 3.3 9.5 + - - +
438H TYR* 3.4 33.9 + - + +
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Residues in contact with ALA 435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434G LEU* 3.9 14.1 - - + +
415H VAL* 5.4 3.1 - - + -
431H GLU 3.1 11.3 + - - +
432H ALA* 3.2 12.1 + - - +
434H LEU* 1.3 78.8 - - - +
436H LEU* 1.3 65.7 + - + +
438H TYR* 3.1 9.4 + - - +
440H ALA* 3.0 36.5 + - + +
445H ILE* 3.9 28.0 - - + -
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Residues in contact with LEU 436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352H ASN* 4.1 13.9 - - - +
353H CYS* 4.4 16.2 - - + -
367H VAL* 4.0 21.5 - - + +
368H GLY* 3.7 34.8 - - - +
414H ARG* 5.0 3.3 + - - -
415H VAL* 3.1 46.0 - - + +
416H LEU 4.7 4.0 - - - +
417H GLY* 5.4 0.4 - - - -
418H ALA* 6.3 0.7 - - + -
432H ALA 2.9 16.4 + - - +
433H ALA* 3.5 7.4 - - - +
435H ALA* 1.3 77.6 - - + +
437H GLU* 1.3 61.5 + - - +
439H GLY* 3.0 15.5 + - - +
440H ALA 5.0 0.9 - - - +
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Residues in contact with GLU 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444G ASP 5.8 0.7 - - - +
447G ARG* 4.6 5.3 - - + +
448G VAL* 4.0 33.9 - - + +
449G CYS* 4.2 6.8 + - - +
350H ASP* 5.0 6.2 + - - +
353H CYS* 3.8 31.3 - - - +
433H ALA 3.0 16.7 + - - +
434H LEU 3.7 7.0 - - - +
435H ALA 3.3 0.8 - - - -
436H LEU* 1.3 75.6 - - - +
438H TYR* 1.3 62.0 + - + +
439H GLY 3.4 0.2 - - - -
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Residues in contact with TYR 438 (chain H).
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* 5.8 1.8 - - + -
435G ALA* 5.4 0.4 - - - -
438G TYR* 3.5 56.1 + + + -
440G ALA* 3.0 26.7 - - + +
444G ASP* 2.8 41.1 + - + +
448G VAL* 5.6 0.9 - - + -
434H LEU* 3.4 44.1 + - + +
435H ALA* 3.1 10.0 + - - +
437H GLU* 1.3 82.3 - - + +
439H GLY* 1.3 63.4 + - - +
440H ALA* 4.3 1.1 - - + +
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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