Contacts of the helix formed by residues 424 - 438 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363E GLU* 3.7 11.9 + - - -
422E GLY 3.5 0.6 + - - -
423E PRO* 1.3 71.8 - - - +
425E ALA* 1.3 59.2 + - - +
426E GLY 3.3 2.9 - - - -
427E GLU* 3.3 11.4 + - - +
428E MET* 2.8 34.2 + - - +
455E LEU* 3.9 12.9 - - - +
427F GLU* 6.1 2.7 - - - -
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Residues in contact with ALA 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E GLU* 3.3 14.9 + - + -
365E ALA* 3.3 19.2 - - + +
420E ILE* 3.5 42.9 - - + +
422E GLY 3.5 15.4 + - - +
423E PRO 3.2 3.0 - - - -
424E GLY* 1.3 76.8 - - - +
426E GLY* 1.3 64.0 + - - +
428E MET* 3.1 1.8 + - - +
429E VAL 3.0 21.8 + - - -
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Residues in contact with GLY 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E VAL* 3.5 31.2 - - - +
363E GLU* 2.9 14.9 + - - -
365E ALA* 4.0 0.6 - - - +
425E ALA* 1.3 77.9 - - - +
427E GLU* 1.3 57.2 + - - +
429E VAL* 3.2 12.1 - - - +
430E ASN* 3.1 17.0 + - - -
393F ARG* 4.5 5.8 - - - -
454F THR* 3.8 12.6 - - - +
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Residues in contact with GLU 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424E GLY* 3.3 11.9 + - - +
426E GLY* 1.3 74.6 - - - +
428E MET* 1.3 65.0 + - - +
430E ASN* 3.2 21.2 + - - +
431E GLU* 4.3 1.6 + - - +
393F ARG* 3.0 26.6 + - - +
424F GLY* 6.3 1.1 - - - -
427F GLU* 5.1 15.7 - - + -
428F MET* 5.0 3.9 - - - +
454F THR* 3.4 8.5 - - - -
455F LEU* 2.8 43.1 + - + +
456F SER* 2.9 31.6 + - - -
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Residues in contact with MET 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388E PHE* 3.9 13.7 - - + -
404E VAL* 4.1 8.7 - - - -
420E ILE* 4.0 26.2 - - + +
423E PRO 4.0 7.2 - - - +
424E GLY 2.8 15.1 + - - +
425E ALA 3.1 4.0 + - - +
427E GLU* 1.3 78.3 - - - +
429E VAL* 1.3 61.5 + - - +
430E ASN 3.1 1.5 + - - -
431E GLU* 3.1 18.5 + - - +
432E ALA* 3.5 6.9 + - - +
455E LEU* 3.4 42.2 - - + +
456E SER* 4.0 9.4 - - - +
459E PHE* 3.7 34.6 - - + -
427F GLU* 5.1 2.9 - - - +
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Residues in contact with VAL 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355E PRO* 3.9 19.5 - - + -
357E VAL* 4.1 8.1 - - + -
365E ALA* 3.6 18.6 - - + -
366E TRP* 3.7 38.1 - - - +
367E VAL* 3.9 11.2 - - + -
418E ALA 5.1 0.2 - - - +
420E ILE* 3.9 11.2 - - + +
425E ALA 3.0 7.4 + - - +
426E GLY 3.2 19.5 - - - +
428E MET* 1.3 76.6 - - - +
430E ASN* 1.3 63.2 + - - +
431E GLU 3.3 0.2 - - - -
432E ALA* 3.2 6.1 + - + +
433E ALA* 2.8 26.2 + - - +
451F ALA* 4.5 0.4 - - + -
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Residues in contact with ASN 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355E PRO* 4.5 1.2 - - - +
426E GLY 3.1 24.6 + - - -
427E GLU* 3.2 13.0 + - - +
428E MET 3.1 0.8 - - - -
429E VAL* 1.3 77.2 - - - +
431E GLU* 1.3 66.9 + - - +
432E ALA 3.1 0.2 - - - -
433E ALA* 3.8 5.8 - - - +
434E LEU* 3.1 21.1 + - - +
431F GLU* 3.8 19.8 - - - +
448F VAL* 4.9 1.2 - - - +
449F CYS 4.4 1.4 - - - +
450F HIS* 3.2 13.8 + - + -
451F ALA* 2.8 29.1 + - - +
454F THR* 3.6 8.3 + - - +
456F SER* 2.8 31.1 + - - +
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Residues in contact with GLU 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E GLU 4.3 1.6 + - - +
428E MET* 3.1 13.7 + - - +
430E ASN* 1.3 77.8 - - - +
432E ALA* 1.3 63.2 + - - +
434E LEU* 3.3 4.4 + - - +
435E ALA* 3.0 18.2 + - - +
445E ILE* 4.0 3.5 - - - +
450E HIS* 2.7 37.1 + - - -
456E SER* 4.1 7.6 - - - -
459E PHE* 3.5 27.3 - - + -
427F GLU 5.2 0.5 - - - +
430F ASN* 3.6 26.2 - - - +
431F GLU* 4.0 24.7 + - + +
434F LEU* 3.6 20.0 - - + +
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Residues in contact with ALA 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367E VAL* 3.7 18.6 - - + -
418E ALA* 3.7 11.0 - - + -
420E ILE* 5.3 0.7 - - + -
428E MET 3.5 1.6 + - - -
429E VAL* 3.2 17.7 + - + +
430E ASN 3.1 0.2 - - - -
431E GLU* 1.3 81.6 - - - +
433E ALA* 1.3 61.2 + - - +
435E ALA* 3.2 6.0 + - - +
436E LEU* 3.1 27.2 + - + +
459E PHE* 3.6 32.5 - - + -
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Residues in contact with ALA 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353E CYS* 4.2 13.4 - - - +
355E PRO* 4.6 4.7 - - + -
367E VAL* 4.1 16.6 - - + +
429E VAL 2.8 17.9 + - - +
430E ASN* 3.8 9.0 - - - +
431E GLU 3.3 0.6 - - - -
432E ALA* 1.3 73.2 - - - +
434E LEU* 1.3 62.6 + - - +
436E LEU* 3.4 4.1 + - - +
437E GLU* 3.1 26.5 + - - +
448F VAL* 3.8 8.3 - - + -
449F CYS 3.7 22.7 - - - +
450F HIS* 5.6 0.2 - - - -
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Residues in contact with LEU 434 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430E ASN 3.1 13.4 + - - +
431E GLU 3.5 7.9 - - - +
433E ALA* 1.3 77.6 - - - +
435E ALA* 1.3 64.3 + - - +
437E GLU* 3.2 11.4 + - - +
438E TYR* 3.3 42.5 + - + +
431F GLU* 3.6 38.1 - - + +
434F LEU* 3.8 13.5 - - + -
435F ALA* 3.7 24.0 - - + +
444F ASP 5.3 0.2 - - - +
445F ILE* 4.9 13.7 - - + -
448F VAL* 3.6 31.1 - - + +
459F PHE* 6.0 0.2 - - + -
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Residues in contact with ALA 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415E VAL* 5.2 2.2 - - + -
431E GLU 3.0 12.9 + - - +
432E ALA* 3.2 11.6 + - - +
434E LEU* 1.3 76.6 - - - +
436E LEU* 1.3 66.0 + - + +
438E TYR* 3.0 5.8 + - - -
439E GLY 3.0 3.3 + - - -
440E ALA* 2.9 45.1 + - + +
445E ILE* 4.0 24.2 - - + -
434F LEU* 3.9 13.2 - - + +
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Residues in contact with LEU 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E ASN* 4.0 11.2 - - - +
353E CYS* 3.9 19.1 - - + -
367E VAL* 3.9 20.4 - - + -
368E GLY* 3.6 35.2 - - - +
414E ARG* 4.6 6.6 + - - -
415E VAL* 3.6 48.7 - - + +
416E LEU 4.5 4.0 - - - +
417E GLY* 4.9 1.3 - - - +
418E ALA* 5.6 0.2 - - + -
432E ALA* 3.1 17.0 + - + +
433E ALA* 3.8 7.9 - - - +
435E ALA* 1.3 78.4 - - + +
437E GLU* 1.3 58.7 + - - +
439E GLY* 2.9 19.6 + - - +
440E ALA 4.9 0.2 - - - +
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Residues in contact with GLU 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A PRO* 3.7 21.7 - - - +
349E ILE* 6.1 0.7 - - - +
350E ASP* 5.9 1.0 - - - +
353E CYS* 3.9 27.7 - - + +
433E ALA 3.1 19.0 + - - +
434E LEU 3.2 9.2 + - - +
436E LEU* 1.3 76.0 - - - +
438E TYR* 1.3 64.7 + - + +
439E GLY 3.7 0.2 + - - -
447F ARG 4.2 6.6 - - - +
448F VAL* 3.5 40.6 - - + -
449F CYS* 4.3 5.7 + - - +
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Residues in contact with TYR 438 (chain E).
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* 3.9 14.4 - - - -
309A GLN* 2.8 44.5 + - - -
313A PRO* 4.6 8.0 - - + +
434E LEU* 3.3 46.2 + - + +
435E ALA* 3.0 8.9 + - - +
437E GLU* 1.3 83.0 - - + +
439E GLY* 1.3 61.4 + - - +
440E ALA* 3.3 2.0 + - + +
434F LEU* 5.8 1.6 - - + -
435F ALA* 5.2 0.4 - - - -
438F TYR* 3.5 43.1 - + + -
440F ALA* 3.1 17.5 - - + +
444F ASP* 2.7 45.1 + - + +
448F VAL* 5.7 0.4 - - + -
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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