Contacts of the helix formed by residues 424 - 439 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427E GLU* 6.2 1.6 - - - -
363F GLU* 3.5 12.7 + - - -
422F GLY 3.5 0.8 + - - -
423F PRO* 1.3 72.2 - - - +
425F ALA* 1.3 64.5 + - - +
426F GLY 3.3 3.3 + - - -
427F GLU* 3.3 11.3 + - - +
428F MET* 3.0 27.6 + - - +
455F LEU* 4.1 12.5 - - - +
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Residues in contact with ALA 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363F GLU* 3.1 28.0 + - + +
364F VAL* 3.8 3.6 - - - +
365F ALA* 3.4 21.6 - - - +
420F ILE* 3.8 25.0 - - + +
422F GLY 3.4 15.7 - - - +
423F PRO 3.2 3.6 + - - -
424F GLY* 1.3 76.2 - - - +
426F GLY* 1.3 56.3 + - - +
428F MET* 3.2 2.8 + - - +
429F VAL* 3.0 27.7 + - - +
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Residues in contact with GLY 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E ARG* 4.8 4.0 - - - -
454E THR* 3.7 12.2 - - - +
357F VAL* 3.7 30.1 - - - +
363F GLU* 2.9 20.8 + - - +
365F ALA* 4.0 0.4 - - - +
425F ALA* 1.3 72.9 - - - +
427F GLU* 1.3 58.8 + - - +
429F VAL* 3.4 10.0 - - - +
430F ASN* 3.0 18.9 + - - -
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Residues in contact with GLU 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E ARG* 2.9 30.0 + - - +
424E GLY* 6.1 2.2 - - - -
427E GLU* 5.3 13.9 - - + -
428E MET* 5.0 1.4 - - - +
431E GLU* 5.1 1.0 - - - +
454E THR* 3.3 9.4 - - - -
455E LEU* 2.7 37.3 + - + +
456E SER* 2.9 30.8 + - - -
424F GLY* 3.3 11.9 + - - +
426F GLY* 1.3 75.8 - - - +
428F MET* 1.3 63.5 + - - +
430F ASN* 3.2 19.9 + - - +
431F GLU* 4.3 1.4 + - - +
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Residues in contact with MET 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E GLU* 4.9 2.2 - - - +
388F PHE* 4.1 14.6 - - + -
404F VAL* 4.2 5.2 - - - -
420F ILE* 3.7 26.9 - - + -
423F PRO 4.3 7.0 - - - +
424F GLY 3.0 15.0 + - - +
425F ALA 3.6 4.0 - - - +
427F GLU* 1.3 74.2 - - - +
429F VAL* 1.3 63.0 + - - +
430F ASN 2.8 7.4 + - - -
431F GLU* 2.9 25.5 + - - +
432F ALA* 3.4 4.2 + - - +
455F LEU* 3.5 42.2 - - + +
456F SER* 4.0 7.6 - - - +
459F PHE* 3.8 32.2 - - + -
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Residues in contact with VAL 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451E ALA* 4.5 0.9 - - + -
355F PRO* 3.9 17.7 - - + -
357F VAL* 4.1 6.7 - - + -
365F ALA* 3.6 21.8 - - + -
366F TRP* 3.6 41.1 - - - +
367F VAL* 3.7 13.5 - - + -
418F ALA 4.8 0.7 - - - +
420F ILE* 3.7 10.5 - - + +
425F ALA 3.0 6.1 + - - -
426F GLY 3.4 17.3 - - - +
428F MET* 1.3 76.2 - - - +
430F ASN* 1.3 65.6 + - - +
432F ALA* 3.2 5.5 + - + +
433F ALA* 2.7 26.7 + - - +
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Residues in contact with ASN 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431E GLU* 3.7 17.8 - - - +
448E VAL* 4.8 2.4 - - - +
449E CYS 4.3 0.2 - - - +
450E HIS* 3.3 14.7 + - + -
451E ALA* 2.9 26.7 + - - +
454E THR* 3.7 9.9 + - - +
456E SER* 2.9 29.2 + - - +
355F PRO* 4.3 3.3 - - - +
426F GLY 3.0 26.0 + - - -
427F GLU* 3.2 14.0 + - - +
428F MET 2.8 1.0 + - - -
429F VAL* 1.3 80.3 - - - +
431F GLU* 1.3 64.1 + - - +
433F ALA* 3.2 6.4 + - - +
434F LEU* 3.2 21.1 + - - +
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Residues in contact with GLU 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E GLU 5.3 0.7 - - - +
430E ASN* 3.9 14.3 - - - +
431E GLU* 3.9 33.0 + - + +
434E LEU* 3.6 19.8 - - + +
427F GLU 4.3 1.8 + - - +
428F MET* 2.9 16.2 + - - +
430F ASN* 1.3 76.6 - - - +
432F ALA* 1.3 62.7 + - - +
434F LEU* 3.2 5.4 + - - +
435F ALA* 3.1 18.1 + - - -
445F ILE* 4.6 1.4 - - - +
450F HIS* 2.9 32.8 + - - -
456F SER* 3.8 17.3 - - - -
459F PHE* 3.3 25.5 - - + -
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Residues in contact with ALA 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F VAL* 3.8 8.1 - - + -
418F ALA* 3.7 29.6 - - + -
420F ILE* 5.5 1.1 - - + -
428F MET 3.4 1.5 + - - +
429F VAL* 3.2 16.5 + - - +
430F ASN 3.2 0.2 - - - -
431F GLU* 1.3 77.8 - - - +
433F ALA* 1.3 65.7 + - - +
434F LEU 3.2 0.2 + - - -
435F ALA* 3.2 4.7 + - - +
436F LEU* 3.0 26.4 + - + +
459F PHE* 3.7 23.7 - - + -
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Residues in contact with ALA 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448E VAL* 3.9 8.9 - - + +
449E CYS 3.9 20.6 - - - +
353F CYS* 4.3 17.2 - - - +
355F PRO* 4.6 4.9 - - + -
367F VAL* 4.2 15.0 - - + +
429F VAL 2.7 18.8 + - - +
430F ASN* 3.6 10.3 - - - +
431F GLU 3.2 0.4 - - - -
432F ALA* 1.3 74.5 - - - +
434F LEU* 1.3 61.4 + - - +
436F LEU* 3.5 3.9 + - - +
437F GLU* 3.1 21.5 + - - +
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Residues in contact with LEU 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431E GLU* 3.8 35.7 - - + +
434E LEU* 4.3 11.0 - - + -
435E ALA* 4.0 23.3 - - + +
438E TYR* 6.0 2.2 - - + -
440E ALA* 5.5 1.3 - - + -
444E ASP* 5.0 2.5 - - + +
445E ILE* 4.2 18.6 - - + -
448E VAL* 3.6 30.7 - - + +
430F ASN 3.2 11.4 + - - +
431F GLU* 3.6 8.1 - - - +
432F ALA 3.2 0.4 - - - -
433F ALA* 1.3 73.0 - - - +
435F ALA* 1.3 68.8 + - - +
437F GLU* 2.9 15.3 + - + +
438F TYR* 3.0 33.5 + - + +
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Residues in contact with ALA 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434E LEU* 3.6 23.5 - - + +
438E TYR* 5.4 0.7 - - - -
415F VAL* 5.6 3.1 - - + -
431F GLU 3.1 7.9 + - - +
432F ALA* 3.4 12.3 - - - +
434F LEU* 1.3 77.0 - - - +
436F LEU* 1.3 62.2 + - - +
438F TYR* 3.1 6.1 + - - -
439F GLY 3.0 4.0 + - - -
440F ALA* 3.0 43.9 + - + +
445F ILE* 3.8 18.4 - - + -
459F PHE* 5.0 0.4 - - + -
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Residues in contact with LEU 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A THR* 4.8 1.9 - - - +
352F ASN* 4.4 9.4 - - - +
353F CYS* 4.2 19.1 - - - -
367F VAL* 3.8 20.0 - - + +
368F GLY* 3.6 35.7 - - - +
414F ARG* 5.6 0.2 + - - -
415F VAL* 3.1 47.3 - - + +
416F LEU* 4.1 7.4 - - - +
417F GLY* 4.7 0.7 - - - +
418F ALA* 5.9 1.1 - - + +
432F ALA* 3.0 16.9 + - + +
433F ALA 3.8 4.5 - - - +
435F ALA* 1.3 76.6 - - - +
437F GLU* 1.3 63.5 + - - +
439F GLY* 3.2 12.4 + - - +
440F ALA 4.9 1.6 - - - +
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Residues in contact with GLU 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A THR* 2.6 27.4 + - - +
307A ARG* 3.1 30.4 + - - +
348A HIS* 4.4 18.2 + - - -
444E ASP* 5.4 1.1 - - + +
447E ARG* 5.3 3.7 - - - +
448E VAL* 4.0 29.4 - - + +
350F ASP* 5.8 1.9 - - - +
353F CYS* 4.5 17.9 - - + +
433F ALA 3.1 13.3 + - - +
434F LEU 2.9 10.2 + - - +
436F LEU* 1.3 78.7 - - - +
438F TYR* 1.3 53.6 + - + +
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Residues in contact with TYR 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ASN* 2.9 36.1 - - - +
306A THR* 3.0 14.7 + - - -
307A ARG* 3.5 50.0 - - + +
309A GLN* 3.9 12.2 + - - -
438E TYR* 3.4 56.9 + + + -
439E GLY 4.5 1.0 + - - -
440E ALA* 3.5 17.9 + - + -
444E ASP* 2.7 32.1 + - + -
434F LEU* 3.0 23.8 + - + +
435F ALA* 3.1 7.2 + - - +
437F GLU* 1.3 76.2 - - + +
439F GLY* 1.3 57.1 + - - +
440F ALA 4.4 1.3 - - - +
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Residues in contact with GLY 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ASN* 3.7 10.1 - - - +
306A THR* 3.7 10.2 - - - +
414F ARG* 3.0 45.7 + - - -
415F VAL 6.1 0.4 - - - -
435F ALA 3.0 4.0 + - - -
436F LEU* 3.2 12.2 + - - -
437F GLU 3.3 0.8 - - - -
438F TYR* 1.3 79.7 - - - +
440F ALA* 1.3 63.0 + - - +
441F SER* 3.8 0.5 + - - -
444F ASP* 4.9 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
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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