Contacts of the helix formed by residues 424 - 439 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427C GLU* 6.2 2.0 - - - -
363D GLU* 3.6 13.2 + - - +
422D GLY 3.5 0.8 + - - -
423D PRO* 1.3 72.6 - - - +
425D ALA* 1.3 64.3 + - - +
426D GLY 3.3 2.5 - - - -
427D GLU* 3.3 12.2 + - - +
428D MET* 3.0 27.5 + - - +
455D LEU* 4.0 12.7 - - - +
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Residues in contact with ALA 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D GLU* 3.3 24.2 + - + +
365D ALA* 3.4 16.6 - - + +
420D ILE* 3.7 35.0 - - + +
422D GLY 3.5 15.9 + - - +
423D PRO 3.3 3.6 + - - -
424D GLY* 1.3 76.4 - - - +
426D GLY* 1.3 62.7 + - - +
428D MET* 3.2 2.2 + - - +
429D VAL* 3.0 21.7 + - - +
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Residues in contact with GLY 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ARG* 4.8 4.9 - - - -
454C THR* 3.7 13.5 - - - +
357D VAL* 3.8 28.2 - - - +
363D GLU* 2.8 22.6 + - - +
365D ALA* 4.1 0.2 - - - +
425D ALA* 1.3 73.0 - - - +
427D GLU* 1.3 56.8 + - - +
429D VAL* 3.2 12.1 - - - +
430D ASN* 3.0 17.8 + - - -
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Residues in contact with GLU 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ARG* 2.9 25.8 + - - +
424C GLY* 6.1 3.1 - - - +
427C GLU* 5.1 16.4 - - + -
428C MET* 5.1 3.2 - - - +
454C THR* 3.4 7.2 - - - -
455C LEU* 2.8 42.2 + - + +
456C SER* 2.9 31.6 + - - -
363D GLU* 4.5 0.8 + - - -
424D GLY* 3.3 12.6 + - - +
425D ALA 3.3 0.4 - - - -
426D GLY* 1.3 74.2 - - - +
428D MET* 1.3 65.6 + - - +
430D ASN* 3.1 21.3 + - - +
431D GLU* 4.2 1.9 + - - +
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Residues in contact with MET 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C GLU* 5.3 2.4 - - - +
388D PHE* 3.7 18.4 - - + -
404D VAL* 4.0 18.6 - - - -
420D ILE* 4.0 18.6 - - + -
423D PRO 4.1 7.9 - - - +
424D GLY 3.0 14.7 + - - +
425D ALA 3.7 3.6 - - - +
427D GLU* 1.3 79.0 - - - +
429D VAL* 1.3 60.4 + - - +
431D GLU* 3.1 20.4 + - - +
432D ALA* 3.4 8.0 + - - +
455D LEU* 3.4 39.3 - - + +
456D SER* 4.1 8.7 - - - +
459D PHE* 3.8 32.4 - - + -
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Residues in contact with VAL 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C ALA* 4.4 0.4 - - + -
355D PRO* 3.8 20.6 - - + +
357D VAL* 4.0 14.1 - - + -
365D ALA* 3.7 6.1 - - + -
366D TRP* 3.6 42.2 - - - +
367D VAL* 4.1 8.0 - - + +
418D ALA 5.1 0.4 - - - +
420D ILE* 3.9 11.8 - - + +
425D ALA 3.0 13.2 + - - +
426D GLY 3.2 20.9 - - - +
428D MET* 1.3 76.4 - - - +
430D ASN* 1.3 65.2 + - - +
432D ALA* 3.3 4.6 + - + +
433D ALA* 2.8 26.0 + - - +
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Residues in contact with ASN 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C GLU* 3.7 18.6 - - - +
448C VAL* 4.8 2.3 - - - +
450C HIS* 3.2 12.9 - - + -
451C ALA* 2.8 30.2 + - - +
454C THR* 3.7 7.5 + - - +
456C SER* 3.0 29.8 + - - +
355D PRO* 4.4 2.1 - - - +
426D GLY 3.0 26.4 + - - -
427D GLU* 3.1 15.3 + - - +
428D MET 3.1 0.6 - - - -
429D VAL* 1.3 78.4 - - - +
431D GLU* 1.3 64.3 + - - +
433D ALA* 3.3 7.2 + - - +
434D LEU* 3.1 21.3 + - - +
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Residues in contact with GLU 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C GLU 5.3 0.3 - - - +
430C ASN* 3.6 23.6 - - - +
431C GLU* 4.1 27.8 + - + +
434C LEU* 3.5 22.5 - - + +
427D GLU 4.2 1.4 + - - +
428D MET* 3.1 15.3 + - - +
430D ASN* 1.3 77.0 - - - +
432D ALA* 1.3 63.9 + - - +
434D LEU* 3.2 5.2 + - - +
435D ALA* 3.0 18.1 + - - +
445D ILE* 4.5 1.4 - - - +
450D HIS* 2.6 39.0 + - - -
456D SER* 4.0 8.1 - - - -
459D PHE* 3.4 23.6 - - + +
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Residues in contact with ALA 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D VAL* 3.7 9.2 - - + -
415D VAL* 6.1 0.2 - - - +
418D ALA* 3.7 29.6 - - + -
420D ILE* 5.2 1.1 - - + -
428D MET 3.4 3.1 + - - +
429D VAL* 3.3 18.1 + - + +
430D ASN 3.2 0.4 - - - -
431D GLU* 1.3 80.9 - - - +
433D ALA* 1.3 61.6 + - - +
435D ALA* 3.2 4.3 + - - +
436D LEU* 3.0 26.3 + - - +
459D PHE* 3.7 23.3 - - + -
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Residues in contact with ALA 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448C VAL* 3.9 18.3 - - + +
449C CYS 4.0 13.0 - - - +
353D CYS* 4.2 14.8 - - - +
355D PRO* 4.6 4.3 - - + -
367D VAL* 4.1 14.8 - - + +
429D VAL 2.8 17.0 + - - +
430D ASN* 3.6 9.6 - - - +
431D GLU 3.2 0.2 - - - -
432D ALA* 1.3 76.8 - - - +
434D LEU* 1.3 62.6 + - - +
436D LEU* 3.4 3.7 + - - +
437D GLU* 2.9 23.6 + - - +
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Residues in contact with LEU 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C GLU* 3.6 40.4 - - + +
434C LEU* 4.1 11.0 - - + -
435C ALA* 3.9 22.2 - - + +
438C TYR* 5.7 1.6 - - + -
440C ALA* 5.2 4.3 - - + -
444C ASP* 5.2 1.6 - - + +
445C ILE* 4.8 14.6 - - + +
448C VAL* 3.9 28.8 - - + +
430D ASN 3.1 13.3 + - - +
431D GLU* 3.2 8.3 + - - +
433D ALA* 1.3 74.8 - - - +
435D ALA* 1.3 64.8 + - - +
437D GLU* 3.1 4.7 + - + +
438D TYR* 3.1 43.0 + - + +
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Residues in contact with ALA 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C LEU* 3.8 14.3 - - + +
438C TYR* 5.3 0.9 - - - -
415D VAL* 5.6 4.0 - - + -
431D GLU 3.0 12.5 + - - +
432D ALA* 3.3 13.0 - - - +
434D LEU* 1.3 75.6 - - - +
436D LEU* 1.3 63.3 + - + +
438D TYR* 3.1 5.1 + - - -
439D GLY 3.0 4.0 + - - -
440D ALA* 2.9 46.1 + - + +
445D ILE* 4.0 20.0 - - + -
459D PHE* 4.8 1.3 - - + -
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Residues in contact with LEU 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D ASN* 4.6 7.4 - - - +
353D CYS* 4.1 19.2 - - - -
367D VAL* 3.8 22.7 - - + +
368D GLY* 3.6 35.0 - - - +
414D ARG* 5.1 5.2 + - - +
415D VAL* 3.0 45.3 - - + +
416D LEU* 4.3 7.4 - - - +
417D GLY* 5.0 1.3 - - - -
418D ALA* 5.3 1.1 - - + +
432D ALA 3.0 14.7 + - - +
433D ALA* 3.8 4.9 - - - +
435D ALA* 1.3 75.8 - - - +
437D GLU* 1.3 63.1 + - - +
439D GLY* 3.1 12.7 + - - +
440D ALA 4.9 1.3 - - - +
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Residues in contact with GLU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C ASP* 5.3 3.8 - - + +
447C ARG* 5.9 3.4 - - - -
448C VAL* 4.0 27.7 - - + -
350D ASP* 6.1 0.7 - - - +
353D CYS* 4.5 15.5 - - + +
433D ALA 2.9 17.2 + - - +
434D LEU* 3.1 6.4 + - + +
436D LEU* 1.3 77.7 - - - +
438D TYR* 1.3 72.1 + - + +
439D GLY 3.5 0.3 + - - -
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Residues in contact with TYR 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438C TYR* 3.6 60.3 + + + -
439C GLY 4.4 1.7 + - - -
440C ALA* 3.5 20.0 + - + -
444C ASP* 2.6 40.0 + - + -
434D LEU* 3.1 26.5 + - + +
435D ALA 3.1 6.7 + - - +
437D GLU* 1.3 84.9 - - + +
439D GLY* 1.3 62.3 + - - +
440D ALA 3.5 0.8 + - - +
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Residues in contact with GLY 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414D ARG* 3.1 40.0 + - - -
415D VAL 6.1 0.2 - - - -
435D ALA 3.0 2.6 + - - -
436D LEU* 3.1 12.7 + - - -
437D GLU 3.3 1.2 + - - -
438D TYR* 1.3 79.5 - - - +
440D ALA* 1.3 69.9 + - - +
441D SER* 5.3 0.3 - - - -
444D ASP* 4.8 1.2 - - - +
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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