Contacts of the helix formed by residues 379 - 386 (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 ILE 379 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375D LEU* 4.3 10.8 - - + -
376D ARG* 3.1 50.7 + - + +
378D ASP* 1.3 82.8 + - - +
380D LYS* 1.3 66.0 + - - +
381D ASP 3.3 2.9 - - - -
382D TYR* 3.2 19.3 + - + +
383D TYR* 3.1 17.8 + - - +
414D ILE* 4.2 14.8 - - + +
417D GLU* 3.7 33.0 - - + +
418D PHE* 3.5 32.8 - - + -
421D LYS* 5.9 2.0 - - - -
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Residues in contact with LYS 380 (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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372D VAL* 3.6 15.9 - - + +
373D GLU* 2.9 54.0 + - - +
375D LEU* 3.2 35.3 - - + +
376D ARG 3.5 3.9 + - - +
377D GLU* 3.0 39.1 + - - +
379D ILE* 1.3 76.6 - - - +
381D ASP* 1.3 61.2 + - - +
383D TYR* 3.3 4.3 + - - +
384D THR* 3.1 29.1 + - - -
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Residues in contact with ASP 381 (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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377D GLU 4.8 3.9 + - - +
378D ASP 5.3 1.1 - - - +
379D ILE 3.3 1.0 - - - +
380D LYS* 1.3 79.9 - - - +
382D TYR* 1.3 69.7 + - + +
384D THR* 3.2 12.4 + - - +
385D ASP* 3.0 28.0 + - - +
459D LYS* 6.4 0.4 - - - +
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Residues in contact with TYR 382 (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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378D ASP 3.4 25.4 - - - -
379D ILE* 3.2 17.0 + - + +
381D ASP* 1.3 79.4 - - + +
383D TYR* 1.3 60.6 + - - +
385D ASP* 3.2 21.7 + - - +
386D LEU* 3.5 4.2 + - - +
404D TRP* 3.3 64.1 + + + -
406D MET* 4.1 16.6 - - - +
414D ILE* 3.9 25.6 - - + -
418D PHE* 4.3 8.5 - - + -
459D LYS* 5.7 2.2 - - - -
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Residues in contact with TYR 383 (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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368D MET* 3.5 18.7 - - + +
372D VAL* 3.6 35.9 - - + -
375D LEU* 3.7 20.6 - - + -
379D ILE 3.1 6.8 + - - +
380D LYS 3.7 7.2 - - - +
381D ASP 3.2 0.4 - - - -
382D TYR* 1.3 73.8 - - - +
384D THR* 1.3 68.6 + - - +
386D LEU* 3.0 34.5 + - + +
387D SER 4.0 1.4 + - - -
418D PHE* 3.7 32.4 - + + -
423D LEU* 2.6 44.6 + - + +
437D LEU* 3.8 8.6 - - + +
445D LEU* 3.7 28.1 - - + +
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Residues in contact with THR 384 (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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372D VAL* 5.8 2.3 - - - +
380D LYS 3.1 14.8 + - - -
381D ASP* 3.2 16.9 + - - +
383D TYR* 1.3 76.7 - - - +
385D ASP* 1.3 64.0 + - - +
387D SER* 2.7 29.4 + - - -
445D LEU* 5.2 0.7 - - - -
448D LYS* 4.4 10.0 + - - -
449D ASN* 3.8 30.0 + - - +
452D GLN* 3.9 24.4 + - - +
456D LEU* 3.6 12.5 - - + +
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Residues in contact with ASP 385 (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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381D ASP* 3.0 18.4 + - - +
382D TYR* 3.2 12.9 + - - +
384D THR* 1.3 75.8 - - - +
386D LEU* 1.3 60.1 + - - +
387D SER 3.0 5.1 + - - -
388D ILE* 3.2 27.7 + - - +
403D LEU* 3.9 13.3 - - + +
404D TRP* 2.6 31.1 + - + +
456D LEU* 3.3 26.6 - - - +
459D LYS* 2.9 32.6 + - - +
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Residues in contact with LEU 386 (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 3.8 9.2 - - - +
383D TYR* 3.0 33.2 + - + +
385D ASP* 1.3 73.5 - - - +
387D SER* 1.3 63.6 + - - +
388D ILE 3.0 2.7 - - - -
389D LEU* 3.0 40.9 + - + +
400D LEU* 3.7 32.8 - - + -
403D LEU* 5.5 0.4 - - + -
404D TRP* 3.9 11.0 - - + -
415D LEU* 4.4 2.7 - - + -
418D PHE* 4.2 8.3 - - + -
424D LEU* 3.9 35.7 - - + -
437D LEU* 3.8 12.5 - - + +
445D LEU* 4.3 4.3 - - + -
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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