Contacts of the helix formed by residues 397 - 405 (chain D) in PDB entry 1Z6T
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 397 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS* 4.4 2.3 + - - -
395D VAL 3.8 0.4 + - - -
396D PRO* 1.3 72.8 - - - +
398D LYS* 1.3 57.8 + - - +
400D LEU* 2.9 23.3 + - - +
401D CYS* 3.0 22.1 + - - -
408D THR* 4.3 7.6 - - + +
411D VAL* 3.8 15.5 - - + -
412D GLU* 3.2 40.4 + - + +
433D PHE* 3.4 24.0 + - - +
435D TYR* 3.5 14.3 - - + -
478D GLU* 3.4 8.1 + - - -
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Residues in contact with LYS 398 (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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396D PRO 3.1 0.2 + - - -
397D THR* 1.3 71.9 - - - +
399D VAL* 1.3 61.4 + - - +
401D CYS* 3.4 19.2 + - + +
402D ILE* 3.1 31.4 + - + +
408D THR* 5.9 1.8 - - - +
467D TYR* 4.1 26.6 - - - -
468D HIS* 5.1 5.6 - - - -
478D GLU* 2.6 34.7 + - + +
479D ASP* 3.3 29.6 - - + +
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Residues in contact with VAL 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D LEU* 6.1 0.7 - - + -
395D VAL* 3.5 26.0 - - + -
396D PRO* 3.1 10.8 + - + +
398D LYS* 1.3 77.8 - - - +
400D LEU* 1.3 61.2 + - + +
402D ILE* 3.4 5.6 + - - +
403D LEU* 3.1 23.2 + - - +
460D ILE* 4.0 24.9 - - + +
479D ASP* 3.7 21.8 - - + -
482D TYR* 3.7 38.8 - - + +
483D TRP* 4.2 12.9 - - + -
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Residues in contact with LEU 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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386D LEU* 3.7 27.8 - - + -
389D LEU* 4.9 10.5 - - + -
395D VAL* 4.5 13.5 - - + -
396D PRO 4.5 7.2 - - - +
397D THR 2.9 8.3 + - - +
399D VAL* 1.3 79.1 - - + +
401D CYS* 1.3 65.2 + - - +
402D ILE 3.1 1.1 - - - -
403D LEU* 3.6 16.0 - - + +
404D TRP* 2.9 44.2 + - + +
411D VAL* 3.9 13.0 - - + -
415D LEU* 3.6 30.1 - - + -
435D TYR* 4.2 17.3 - - + -
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Residues in contact with CYS 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 THR* 3.0 20.8 + - - -
398D LYS* 3.4 28.0 - - + +
400D LEU* 1.3 75.5 - - - +
402D ILE* 1.3 53.2 + - - +
405D ASP* 2.6 30.5 + - - -
406D MET 3.0 30.1 + - - +
407D GLU* 5.7 0.2 - - - -
408D THR* 3.8 28.7 - - - -
411D VAL* 3.6 18.6 - - - +
467D TYR* 4.2 4.2 + - + -
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Residues in contact with ILE 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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398D LYS* 3.1 19.3 + - + +
399D VAL 3.5 7.9 - - - +
400D LEU 3.1 0.2 - - - -
401D CYS* 1.3 77.3 - - - +
403D LEU* 1.3 56.7 + - - +
404D TRP 3.3 0.5 + - - -
405D ASP* 3.3 3.6 + - - -
460D ILE* 4.9 1.1 - - + +
463D GLN* 2.8 40.3 + - + +
464D PHE* 3.7 29.8 - - + +
467D TYR* 3.7 29.7 - - + -
468D HIS* 3.6 24.2 - - + +
479D ASP* 3.5 24.7 - - - +
483D TRP* 4.0 19.7 - - + -
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Residues in contact with LEU 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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385D ASP* 3.9 19.1 - - + +
388D ILE* 4.5 14.6 - - + -
399D VAL 3.1 12.7 + - - +
400D LEU* 3.6 22.4 - - + +
402D ILE* 1.3 76.6 - - - +
404D TRP* 1.3 89.2 + - + +
456D LEU 4.7 0.7 - - - +
459D LYS* 3.8 26.1 - - + -
460D ILE* 3.6 49.1 - - + +
463D GLN* 3.4 22.5 + - - +
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Residues in contact with TRP 404 (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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382D TYR* 3.3 57.6 + + + -
385D ASP* 2.6 32.0 + - + -
386D LEU* 3.9 19.3 - - + -
400D LEU* 2.9 32.6 + - + +
403D LEU* 1.3 93.0 - - + +
405D ASP* 1.3 73.4 + - - +
406D MET* 3.2 39.4 + - + +
411D VAL* 4.3 4.7 - - + -
414D ILE* 4.4 11.0 - - + -
415D LEU* 3.5 36.3 - - + -
418D PHE* 4.8 0.9 - + - -
459D LYS* 4.2 4.3 - - - +
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Residues in contact with ASP 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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315C LYS* 3.0 24.2 + - - -
401D CYS 2.6 15.9 + - - -
402D ILE 3.3 4.9 + - - -
404D TRP* 1.3 76.8 - - - +
406D MET* 1.3 57.5 + - - +
463D GLN* 3.6 15.0 + - - +
466D ARG* 5.7 3.2 - - - +
467D TYR* 2.6 42.2 + - - -
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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