Contacts of the helix formed by residues 379 - 385 (chain D) in PDB entry 4PKY
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 ARG 379 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D THR* 5.4 2.4 - - + -
362D ARG* 3.1 36.1 + - - +
363D PHE* 3.7 3.8 - - + +
364D ILE* 3.4 37.8 - - - +
377D ASP* 2.9 25.9 + - - +
378D HIS* 1.3 95.1 - - + +
380D CYS* 1.3 61.6 + - - +
381D VAL 3.1 0.4 - - - -
382D ALA* 3.1 17.7 + - + +
383D THR* 2.9 19.8 + - - +
618F THR* 3.2 29.8 + - - +
622F ASP* 2.6 25.7 + - - -
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Residues in contact with CYS 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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363D PHE* 3.8 25.3 - - + +
376D VAL* 3.6 24.9 - - + -
377D ASP 3.1 22.8 + - - +
378D HIS 3.0 1.9 - - - -
379D ARG* 1.3 79.7 - - - +
381D VAL* 1.3 58.6 + - - +
383D THR* 3.7 0.4 - - - -
384D VAL* 2.9 43.0 + - + +
385D GLY 3.2 1.6 + - - -
386D TYR 3.5 14.0 - - - +
387D GLN 4.2 0.7 - - - -
388D PRO* 3.9 23.6 - - - -
391D LEU* 4.4 6.1 - - + -
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Residues in contact with VAL 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D HIS* 3.4 17.7 - - + +
379D ARG 3.1 0.4 - - - -
380D CYS* 1.3 79.0 - - - +
382D ALA* 1.3 56.5 + - - +
385D GLY* 3.1 33.6 + - - +
386D TYR 3.4 16.6 - - - +
387D GLN* 3.4 41.5 - - - +
388D PRO* 4.2 5.8 - - + -
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Residues in contact with ALA 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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361D THR* 3.8 23.0 + - + +
378D HIS 5.5 0.2 - - - +
379D ARG* 3.1 12.7 + - + +
381D VAL* 1.3 80.2 - - + +
383D THR* 1.3 60.5 + - - +
463D ASN* 5.8 0.9 + - - -
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Residues in contact with THR 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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361D THR* 3.6 26.1 + - - +
362D ARG 4.1 4.9 + - - -
363D PHE* 3.6 36.6 - - + -
379D ARG 2.9 15.2 + - - -
380D CYS 4.0 0.9 - - - -
382D ALA* 1.3 80.2 - - - +
384D VAL* 1.3 59.6 + - + +
437D LEU* 3.5 18.0 - - - +
439D MET* 3.9 10.8 - - + -
461D ASN 4.6 0.2 - - - +
463D ASN* 3.8 32.5 + - + +
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Residues in contact with VAL 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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363D PHE* 4.2 10.8 - - + -
380D CYS* 2.9 30.4 + - + +
383D THR* 1.3 84.4 - - + +
385D GLY* 1.3 58.3 + - - +
386D TYR* 3.3 13.6 + - + +
391D LEU* 4.6 6.1 - - + -
429D PHE* 3.4 43.3 - - + -
431D SER* 3.3 7.5 - - - -
432D LYS 3.0 24.3 + - - -
433D ASN* 5.8 0.2 - - - -
437D LEU* 4.2 10.5 - - + -
439D MET* 4.2 20.0 - - - -
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Residues in contact with GLY 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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380D CYS 3.2 2.0 + - - -
381D VAL* 3.1 28.5 + - - +
383D THR 3.8 0.2 - - - -
384D VAL* 1.3 76.0 - - - +
386D TYR* 1.3 60.5 + - - +
387D GLN* 3.9 2.1 + - - +
390D GLU* 4.7 1.4 - - - +
432D LYS* 3.6 22.2 - - - +
433D ASN* 5.0 7.6 - - - -
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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