Contacts of the helix formed by residues 395 - 406 (chain D) in PDB entry 4ZZ7
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 THR 395 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487B ARG 3.9 10.4 + - - -
488B GLU* 5.0 7.6 + - - -
289D VAL* 3.6 8.1 - - - -
393D VAL* 3.5 7.4 - - - +
394D ALA* 1.3 78.5 - - + +
396D MET* 1.3 72.6 + - - +
397D GLN* 3.5 12.4 + - + +
398D ASP* 3.1 45.6 + - - +
399D ALA 3.3 8.5 + - - -
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Residues in contact with MET 396 (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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487B ARG* 3.3 40.5 + - + +
254D ILE* 4.5 10.1 - - + -
256D MET* 3.8 32.1 - - + -
289D VAL* 3.7 10.4 - - - +
395D THR* 1.3 75.5 + - - +
397D GLN* 1.3 62.7 + - - +
399D ALA* 3.2 8.3 + - - +
400D MET* 3.0 45.8 + - + +
414D ILE* 3.7 21.1 - - + -
421D ALA* 3.4 26.9 - - - +
425D PHE* 3.8 10.5 - - + +
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Residues in contact with GLN 397 (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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487B ARG* 5.0 3.4 + - - +
395D THR* 3.3 12.7 + - + +
396D MET* 1.3 76.8 - - - +
398D ASP* 1.3 62.5 + - - +
400D MET* 3.3 16.6 + - + +
401D ASP* 2.8 59.5 + - - +
404D ASP* 5.6 1.4 + - - -
424D TYR* 3.2 35.2 + - - -
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Residues in contact with ASP 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393D VAL* 4.0 17.1 - - + +
394D ALA* 3.9 12.3 + - - +
395D THR* 3.1 35.2 + - - +
397D GLN* 1.3 78.8 - - - +
399D ALA* 1.3 58.2 + - - +
401D ASP* 3.8 10.6 - - - +
402D LEU* 3.0 28.9 + - - +
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Residues in contact with ALA 399 (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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254D ILE* 3.5 27.4 - - + -
287D VAL* 3.4 31.9 - - + +
393D VAL* 4.0 8.4 - - + +
395D THR 3.3 3.0 + - - +
396D MET* 3.2 12.3 + - - +
397D GLN 3.2 0.2 - - - -
398D ASP* 1.3 77.5 - - - +
400D MET* 1.3 58.8 + - - +
402D LEU* 3.5 6.6 - - - +
403D ILE* 3.0 30.8 + - - +
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Residues in contact with MET 400 (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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487B ARG* 5.1 2.2 - - + +
254D ILE* 3.7 17.3 - - + -
396D MET* 3.0 39.6 + - + +
397D GLN* 3.3 25.3 + - - +
399D ALA* 1.3 73.0 - - - +
401D ASP* 1.3 61.6 + - - +
403D ILE* 3.2 2.9 + - - +
404D ASP* 2.8 37.6 + - - +
424D TYR* 3.4 31.0 - - + +
425D PHE* 3.7 33.2 - - + +
428D ASN* 5.4 4.7 - - - -
429D ILE* 3.9 17.0 - - + -
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Residues in contact with ASP 401 (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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397D GLN* 2.8 53.1 + - - +
398D ASP* 3.8 10.9 - - - +
400D MET* 1.3 70.5 - - - +
402D LEU* 1.3 59.1 + - - +
404D ASP* 3.4 10.1 + - - +
405D ALA* 2.9 32.7 + - - +
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Residues in contact with LEU 402 (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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252D HIS* 4.6 1.1 - - + +
287D VAL* 4.1 24.0 - - + -
374D PRO* 3.5 33.7 - - + -
379D TYR* 3.3 33.7 + - + +
391D VAL* 3.7 31.0 - - + -
393D VAL* 4.7 5.2 - - + -
398D ASP 3.0 19.5 + - - +
399D ALA 3.5 4.5 - - - +
401D ASP* 1.3 77.4 - - - +
403D ILE* 1.3 62.4 + - - +
405D ALA* 3.5 6.8 + - + +
406D HIS* 3.4 12.1 + - - +
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Residues in contact with ILE 403 (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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250D LYS 6.0 0.4 - - - +
252D HIS* 3.6 39.9 - - + +
254D ILE* 4.0 23.1 - - + -
287D VAL* 5.3 0.9 - - + -
399D ALA 3.0 20.2 + - - +
400D MET 3.2 5.4 + - - +
402D LEU* 1.3 71.3 - - - +
404D ASP* 1.3 59.6 + - - +
405D ALA 3.0 1.6 - - - -
406D HIS* 2.7 31.1 + - + +
408D TYR 4.4 2.1 - - - +
412D THR* 3.6 21.8 - - - +
425D PHE* 4.4 0.7 - - + -
429D ILE* 3.9 19.1 - - + -
431D VAL* 3.7 30.3 - - + -
453D LYS* 3.4 5.6 + - - +
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Residues in contact with ASP 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D GLN* 5.6 1.4 + - - -
400D MET* 2.8 27.9 + - - +
401D ASP* 3.9 9.6 - - - +
403D ILE* 1.3 72.7 - - - +
405D ALA* 1.3 59.3 + - - +
406D HIS 3.8 0.7 - - - +
428D ASN 4.3 6.6 - - - +
429D ILE* 3.6 10.9 - - - +
430D GLN* 2.8 47.3 + - + +
453D LYS* 2.9 26.3 + - - +
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Residues in contact with ALA 405 (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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401D ASP 2.9 18.7 + - - +
402D LEU* 3.8 8.7 - - + +
403D ILE 3.0 0.2 - - - -
404D ASP* 1.3 78.0 - - - +
406D HIS* 1.3 61.7 + - - +
407D GLU* 3.8 0.9 + - - -
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Residues in contact with HIS 406 (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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250D LYS* 3.4 27.4 + - + +
252D HIS* 4.1 13.5 - + + -
379D TYR* 3.2 53.6 + + - -
380D GLN* 3.3 23.1 + - + -
402D LEU 3.4 8.0 + - - +
403D ILE* 2.7 16.9 + - + +
404D ASP 3.8 0.3 - - - +
405D ALA* 1.3 79.2 - - - +
407D GLU* 1.3 79.1 + - + +
408D TYR* 3.4 26.2 + + - +
453D LYS* 2.9 22.2 + - - +
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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