Contacts of the helix formed by residues 424 - 439 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A GLU* 3.4 13.6 + - - -
423A PRO* 1.3 71.7 - - - +
425A ALA* 1.3 64.4 + - - +
426A GLY 3.3 2.9 - - - -
427A GLU* 3.1 11.7 + - - +
428A MET* 2.9 26.0 + - - +
455A LEU* 3.7 15.3 - - - +
427B GLU* 6.1 1.8 - - - -
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Residues in contact with ALA 425 (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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363A GLU* 3.2 23.1 + - + -
365A ALA* 3.3 17.1 - - + +
420A ILE* 3.6 42.5 - - + +
422A GLY 3.7 8.3 - - - +
423A PRO 3.1 4.2 + - - -
424A GLY* 1.3 75.2 - - - +
426A GLY* 1.3 63.9 + - - +
428A MET* 3.0 13.1 + - - +
429A VAL 3.1 11.8 + - - -
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Residues in contact with GLY 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL* 3.8 28.2 - - - +
363A GLU* 2.8 23.0 + - - +
365A ALA* 4.0 0.4 - - - +
425A ALA* 1.3 73.1 - - - +
427A GLU* 1.3 58.3 + - - +
429A VAL* 3.3 11.6 - - - +
430A ASN* 3.2 16.8 + - - -
393B ARG* 4.6 4.7 - - - -
454B THR* 3.7 12.9 - - - +
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Residues in contact with GLU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLU* 4.5 0.4 + - - -
424A GLY* 3.1 11.8 + - - +
426A GLY* 1.3 74.5 - - - +
428A MET* 1.3 64.7 + - - +
430A ASN* 3.3 19.8 + - - +
431A GLU* 4.3 1.9 + - - +
393B ARG* 2.8 30.5 + - - +
424B GLY* 6.0 2.2 - - - -
427B GLU* 5.2 14.6 - - + -
428B MET* 5.1 2.1 - - - +
431B GLU* 5.3 0.3 - - - +
454B THR* 3.1 10.7 - - - -
455B LEU* 2.8 39.4 + - + +
456B SER* 2.9 30.8 + - - -
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Residues in contact with MET 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PHE* 3.9 16.2 - - + -
404A VAL* 4.1 8.3 - - - -
420A ILE* 4.1 26.4 - - + +
423A PRO 4.2 6.5 - - - +
424A GLY 2.9 14.3 + - - +
425A ALA 3.0 5.1 + - - +
427A GLU* 1.3 78.4 - - - +
429A VAL* 1.3 61.1 + - - +
431A GLU* 3.1 23.3 + - - +
432A ALA* 3.4 5.0 + - - +
455A LEU* 3.4 43.5 - - + +
456A SER* 4.0 9.0 - - - +
459A PHE* 3.8 31.0 - - + -
427B GLU* 5.1 2.4 - - - +
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PRO* 3.6 31.2 - - + -
357A VAL* 4.1 14.4 - - + -
365A ALA* 3.7 13.0 - - + +
366A TRP* 3.7 30.5 - - - +
367A VAL* 4.0 7.4 - - + -
418A ALA 5.3 0.4 - - - +
420A ILE* 4.0 10.7 - - + +
425A ALA 3.1 4.4 + - - +
426A GLY 3.3 20.2 - - - +
428A MET* 1.3 73.1 - - - +
430A ASN* 1.3 68.7 + - - +
431A GLU 3.2 0.2 - - - -
432A ALA* 3.2 4.5 + - + +
433A ALA* 2.7 27.9 + - - +
451B ALA* 4.4 1.6 - - + -
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Residues in contact with ASN 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PRO* 4.5 1.0 - - - +
426A GLY 3.2 25.3 + - - -
427A GLU* 3.3 14.6 + - - +
428A MET 3.1 0.8 - - - -
429A VAL* 1.3 80.1 - - - +
431A GLU* 1.3 63.0 + - - +
433A ALA* 3.4 6.6 + - - +
434A LEU* 3.1 20.6 + - - +
431B GLU* 3.6 18.4 - - - +
448B VAL* 4.8 2.8 - - - +
449B CYS 4.3 0.9 - - - +
450B HIS* 3.1 14.3 + - + -
451B ALA* 2.9 27.7 + - - +
454B THR* 3.5 9.3 + - - +
456B SER* 2.9 29.1 + - - +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLU 4.3 1.2 + - - +
428A MET* 3.1 15.6 + - - +
430A ASN* 1.3 77.2 - - - +
432A ALA* 1.3 65.8 + - - +
434A LEU* 3.1 5.0 + - - +
435A ALA* 2.9 17.8 + - - +
445A ILE* 4.7 0.7 - - - +
450A HIS* 2.9 35.7 + - - -
456A SER* 3.8 11.3 - - - -
459A PHE* 3.4 23.5 - - + -
427B GLU 5.3 0.3 - - - +
430B ASN* 3.7 20.0 - - - +
431B GLU* 3.8 31.9 + - + +
434B LEU* 3.6 20.9 - - + +
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Residues in contact with ALA 432 (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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367A VAL* 3.9 11.0 - - + -
415A VAL* 6.0 0.3 - - - +
418A ALA* 3.8 19.7 - - + -
420A ILE* 5.2 1.3 - - + -
428A MET 3.4 2.7 + - - +
429A VAL* 3.2 17.9 + - + +
431A GLU* 1.3 79.2 - - - +
433A ALA* 1.3 56.4 + - - +
435A ALA* 2.8 20.9 + - - +
436A LEU* 3.0 15.7 + - + +
459A PHE* 3.7 33.5 - - + -
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A CYS* 4.3 15.7 - - + +
355A PRO* 4.8 3.4 - - + -
367A VAL* 4.0 15.5 - - + +
429A VAL 2.7 17.8 + - - +
430A ASN* 3.5 10.1 - - - +
431A GLU 3.1 0.2 - - - -
432A ALA* 1.3 76.5 - - - +
434A LEU* 1.3 61.3 + - - +
436A LEU* 3.4 4.8 + - - +
437A GLU* 3.2 23.4 + - - +
448B VAL* 4.1 10.3 - - + +
449B CYS 4.0 20.4 - - - +
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ASN 3.1 11.9 + - - +
431A GLU 3.1 9.0 + - - +
433A ALA* 1.3 76.5 - - - +
435A ALA* 1.3 65.4 + - - +
437A GLU* 3.4 1.6 + - - +
438A TYR* 3.3 36.1 + - + +
431B GLU* 3.5 41.3 - - + +
434B LEU* 4.3 10.5 - - + -
435B ALA* 4.0 23.6 - - + +
438B TYR* 5.8 2.0 - - + -
440B ALA* 5.5 0.9 - - + -
444B ASP* 5.1 1.6 - - + -
445B ILE* 4.4 18.4 - - + +
448B VAL* 3.6 32.3 - - + +
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Residues in contact with ALA 435 (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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415A VAL* 5.4 4.0 - - + -
431A GLU 2.9 12.1 + - - +
432A ALA* 2.8 14.3 + - - +
434A LEU* 1.3 77.8 - - - +
436A LEU* 1.3 61.3 + - + +
438A TYR* 3.2 4.9 + - - -
439A GLY 3.0 4.3 + - - -
440A ALA* 2.8 37.0 + - + +
445A ILE* 3.6 31.0 - - + -
459A PHE* 5.0 0.4 - - + -
434B LEU* 3.9 14.1 - - + +
438B TYR* 5.5 0.2 - - - -
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Residues in contact with LEU 436 (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 ASN* 4.5 8.3 - - - +
353A CYS* 4.0 18.9 - - - -
367A VAL* 3.6 37.2 - - + +
368A GLY* 3.7 22.4 - - - +
415A VAL* 3.1 45.5 - - + +
416A LEU* 4.1 9.2 - - - +
417A GLY* 5.1 0.9 - - - -
418A ALA* 6.4 0.2 - - + -
432A ALA 3.0 11.5 + - - +
433A ALA 3.8 6.7 - - - +
435A ALA* 1.3 76.0 - - - +
437A GLU* 1.3 61.6 + - - +
439A GLY* 3.1 13.5 + - - +
440A ALA 4.8 1.6 - - - +
306F THR* 4.9 2.1 - - - +
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Residues in contact with GLU 437 (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 ASP* 6.0 1.6 - - - +
353A CYS* 4.6 16.8 - - + +
433A ALA 3.2 16.4 + - - +
434A LEU 3.7 4.7 - - - +
435A ALA 3.3 0.2 - - - -
436A LEU* 1.3 75.7 - - - +
438A TYR* 1.3 55.3 + - + +
439A GLY 3.1 1.0 + - - -
444B ASP 5.4 0.7 - - - +
447B ARG 5.6 2.7 - - - +
448B VAL* 4.0 28.6 - - + +
306F THR* 2.6 29.5 + - - +
307F ARG* 3.1 35.8 + - - +
347F VAL 5.3 0.9 - - - +
348F HIS* 4.2 22.0 + - - -
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Residues in contact with TYR 438 (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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434A LEU* 3.3 22.5 + - + +
435A ALA 3.2 8.3 + - - +
437A GLU* 1.3 77.7 - - + +
439A GLY* 1.3 59.4 + - - +
440A ALA* 4.5 1.1 - - - +
438B TYR* 3.6 48.6 + + + -
439B GLY 4.5 1.0 + - - -
440B ALA* 3.5 24.6 + - + -
444B ASP* 2.5 35.0 + - + -
305F ASN* 3.1 26.2 - - - +
306F THR* 2.9 30.6 + - - -
307F ARG* 3.6 44.7 + - + +
309F GLN* 3.7 12.5 + - - -
341F GLY 5.7 0.7 + - - -
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Residues in contact with GLY 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ARG* 3.2 33.9 + - - +
415A VAL 6.1 0.7 - - - -
435A ALA 3.0 2.6 + - - -
436A LEU* 3.1 15.2 + - - -
437A GLU 3.1 1.0 - - - -
438A TYR* 1.3 80.6 - - - +
440A ALA* 1.3 66.6 + - - +
441A SER* 3.8 0.3 + - - -
444A ASP* 5.1 0.5 - - - +
305F ASN* 3.8 8.1 - - - +
306F THR* 3.9 11.9 - - - -
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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
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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