Contacts of the helix formed by residues 422 - 433 (chain D) in PDB entry 3ZXR
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 GLN 422 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327D TYR* 3.7 15.0 - - + -
420D PRO 3.5 1.2 - - - -
421D THR* 1.3 91.4 - - + +
423D LEU* 1.3 64.2 + - - +
424D SER* 2.9 24.4 + - - +
425D ASP* 3.1 38.0 + - - +
426D VAL* 3.6 7.6 + - - +
507D CL 3.9 13.0 - - + +
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Residues in contact with LEU 423 (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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318D ALA* 4.9 0.7 - - - -
321D ASN 4.0 6.5 - - - +
322D PRO* 3.4 36.8 - - + +
323D THR* 3.7 17.3 - - - +
324D VAL* 3.7 10.9 - - + +
327D TYR* 3.5 17.7 - - + -
422D GLN* 1.3 73.2 - - - +
424D SER* 1.3 63.6 + - - +
426D VAL* 3.1 24.6 + - + +
427D ILE* 3.0 37.7 + - + +
455D LYS* 4.3 8.1 - - + -
459D GLU* 4.0 9.4 - - + +
460D ILE* 4.0 18.6 - - + -
507D CL 3.8 9.2 - - + +
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Residues in contact with SER 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D GLN* 2.9 29.3 + - - -
423D LEU* 1.3 77.7 - - - +
425D ASP* 1.3 60.2 + - - +
427D ILE* 3.5 1.1 + - - +
428D ASP* 2.9 42.7 + - - +
460D ILE* 3.9 26.4 - - - +
464D ASN* 5.8 1.1 - - - -
507D CL 3.4 14.1 - - - +
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Residues in contact with ASP 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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420D PRO* 4.7 10.3 - - + -
421D THR* 4.0 12.8 + - - -
422D GLN* 3.1 38.9 + - - +
424D SER* 1.3 87.7 + - - +
426D VAL* 1.3 57.0 + - - +
428D ASP* 3.5 10.2 + - - +
429D ARG* 3.0 29.0 + - - +
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Residues in contact with VAL 426 (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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314D PRO 3.5 17.5 - - - +
315D SER* 4.3 0.3 - - - -
317D LEU* 4.2 5.8 - - + -
318D ALA* 3.6 30.0 - - + +
327D TYR* 3.3 30.5 - - + +
420D PRO* 3.5 35.7 - - + -
422D GLN 4.1 1.6 - - - +
423D LEU* 3.1 26.9 + - + +
425D ASP* 1.3 72.6 - - - +
427D ILE* 1.3 56.1 + - - +
429D ARG* 3.6 0.9 - - - +
430D LEU* 2.7 35.5 + - - +
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Residues in contact with ILE 427 (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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318D ALA* 3.9 20.2 - - + +
423D LEU* 3.0 37.9 + - + +
424D SER 3.9 3.6 - - - +
426D VAL* 1.3 73.9 - - - +
428D ASP* 1.3 64.3 + - - +
430D LEU* 3.3 5.0 + - + +
431D GLU* 2.9 24.1 + - - +
451D TRP* 4.2 13.2 - - + +
452D ILE* 3.7 26.3 - - + +
455D LYS* 4.0 23.1 - - + -
456D ARG* 3.7 29.2 - - + +
460D ILE* 4.1 10.8 - - + -
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Residues in contact with ASP 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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424D SER* 2.9 31.2 + - - +
425D ASP* 3.6 9.1 - - - +
427D ILE* 1.3 76.0 - - - +
429D ARG* 1.3 58.8 + - - +
431D GLU* 3.3 5.7 + - - +
432D ALA* 3.1 26.7 + - - +
456D ARG* 2.9 29.3 + - - +
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Residues in contact with ARG 429 (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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311D HIS* 5.3 3.4 + - - -
314D PRO* 3.6 57.6 - - + +
315D SER* 3.8 6.8 - - - +
425D ASP 3.0 18.1 + - - +
426D VAL 3.7 0.4 - - - +
427D ILE 3.2 0.2 - - - -
428D ASP* 1.3 75.2 - - - +
430D LEU* 1.3 58.8 + - - +
432D ALA* 3.2 8.4 + - - +
433D ASP* 2.8 49.2 + - - +
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Residues in contact with LEU 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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315D SER* 3.8 21.0 - - - +
318D ALA* 3.8 20.9 - - + -
319D PHE* 3.8 19.5 - - + -
426D VAL 2.7 21.2 + - - +
427D ILE* 3.6 5.2 - - + +
429D ARG* 1.3 74.2 - - - +
431D GLU* 1.3 53.8 + - - +
432D ALA 3.5 0.2 + - - -
433D ASP 3.5 2.0 + - - -
434D HIS* 2.7 47.2 + - + +
437D LEU* 3.6 31.4 - - + -
448D ILE* 4.1 12.1 - - + -
451D TRP* 3.9 16.4 - - + -
452D ILE* 4.0 15.5 - - + -
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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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427D ILE 2.9 17.2 + - - +
428D ASP* 3.5 6.9 - - - +
430D LEU* 1.3 78.6 - - - +
432D ALA* 1.3 60.6 - - - +
434D HIS* 3.5 17.8 + - - -
452D ILE* 3.6 24.4 - - + +
456D ARG* 2.9 39.0 + - - +
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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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428D ASP 3.1 15.9 + - - +
429D ARG* 3.7 12.1 - - - +
431D GLU* 1.3 79.5 - - - +
433D ASP* 1.3 61.1 + - + +
434D HIS* 4.7 1.9 + - - -
435D GLU* 5.8 0.2 - - - +
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Residues in contact with ASP 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D HIS* 5.8 1.2 + - - -
312D HIS* 4.6 15.8 + - - -
315D SER* 3.6 19.1 + - - -
429D ARG* 2.8 37.2 + - - +
430D LEU 3.6 2.1 - - - +
431D GLU 3.5 0.4 - - - -
432D ALA* 1.3 82.2 - - + +
434D HIS* 1.3 64.7 + - - +
435D GLU* 4.1 14.4 + - - +
436D TYR* 4.1 4.0 + - - -
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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