Contacts of the helix formed by residues 394 - 402 (chain D) in PDB entry 2HHW
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 LEU 394 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370D MET 2.8 17.1 + - - +
371D PHE* 3.7 17.4 - - + -
392D PHE* 3.8 22.6 - - + -
393D ASP* 1.3 68.7 - - - +
395D LEU* 1.3 60.4 + - - +
397D ALA* 4.1 0.4 - - - -
398D ALA* 2.9 28.9 + - - +
410D VAL* 4.4 9.2 - - + -
413D ALA* 3.8 17.3 - - + -
454D ILE* 4.1 23.3 - - + -
457D LEU* 4.3 19.7 - - + -
461D PHE* 3.9 43.7 - - + -
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Residues in contact with LEU 395 (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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371D PHE* 3.5 29.4 - - + -
372D ASP* 3.7 38.1 - - + +
393D ASP* 3.0 11.8 + - - +
394D LEU* 1.3 78.9 - - - +
396D LEU* 1.3 63.5 + - + +
398D ALA* 3.9 1.9 - - - +
399D TYR* 3.0 29.6 + - + +
407D VAL* 3.5 26.5 - - + +
408D ASP* 4.7 2.2 - - - -
609D ALA* 3.8 18.4 - - + -
2H FRU 3.7 27.8 - - - +
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Residues in contact with LEU 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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393D ASP* 3.2 31.4 + - + +
395D LEU* 1.3 79.0 - - + +
397D ALA* 1.3 64.9 + - - +
399D TYR* 3.5 7.0 - - + +
400D LEU* 3.0 30.3 + - - +
474D LEU* 3.7 15.5 - - + -
478D GLU* 3.9 33.0 - - + +
479D GLN* 4.2 5.6 - - + -
482D SER* 4.2 9.2 - - - +
608D GLN* 3.6 47.1 - - + +
609D ALA* 4.5 8.5 - - + -
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Residues in contact with ALA 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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392D PHE* 3.8 27.4 - - + -
393D ASP 3.0 16.6 + - - +
394D LEU 3.7 4.3 - - - +
396D LEU* 1.3 75.5 - - - +
398D ALA* 1.3 65.1 + - - +
400D LEU* 3.4 4.6 + - - +
401D LEU* 3.1 26.7 + - - +
461D PHE* 4.0 13.0 - - + -
465D LEU* 4.0 16.9 - - + +
474D LEU* 3.8 8.7 - - + +
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Residues in contact with ALA 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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394D LEU 2.9 17.9 + - - +
395D LEU 3.9 3.6 - - - +
397D ALA* 1.3 76.0 - - - +
399D TYR* 1.3 62.8 + - - +
401D LEU* 3.3 2.6 + - - +
402D ASP 3.1 24.7 + - - +
407D VAL* 4.0 34.5 - - + -
413D ALA* 4.1 4.3 - - + -
416D MET* 4.0 11.5 - - - +
461D PHE* 3.9 21.4 - - + -
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Residues in contact with TYR 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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395D LEU* 3.0 19.4 + - + +
396D LEU* 3.5 10.3 - - + +
397D ALA 3.2 0.2 - - - -
398D ALA* 1.3 76.7 - - - +
400D LEU* 1.3 72.1 + - + +
402D ASP 4.7 2.9 - - - -
403D PRO* 3.1 51.9 - - + +
407D VAL* 5.4 2.4 - - - +
478D GLU* 4.9 3.4 - - - -
608D GLN 3.2 23.1 + - - -
609D ALA* 3.5 23.3 - - + -
610D LEU 3.4 17.0 - - - -
611D THR* 2.6 36.9 + - - -
614D GLY* 3.4 18.8 - - - -
615D ARG 3.8 4.2 + - - -
769D ARG* 4.1 18.8 - - - -
805D LYS* 5.0 1.6 - - - -
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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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396D LEU 3.0 21.2 + - - +
397D ALA 3.8 3.8 - - - +
399D TYR* 1.3 86.3 - - + +
401D LEU* 1.3 63.6 + - - +
402D ASP 3.3 0.2 + - - -
403D PRO* 4.2 6.2 - - - +
465D LEU* 4.1 10.3 - - + -
470D GLN* 3.1 28.8 + - - +
473D LEU* 3.8 22.4 - - + -
474D LEU* 3.7 44.2 - - + +
478D GLU* 4.0 13.9 - - + -
769D ARG* 3.7 32.5 - - + +
770D ARG* 4.2 6.2 + - - +
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Residues in contact with LEU 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 ALA 3.1 12.0 + - - +
398D ALA 3.3 4.7 + - - +
400D LEU* 1.3 77.5 - - - +
402D ASP* 1.3 62.6 + - - +
403D PRO* 4.3 0.2 - - - -
416D MET* 3.7 18.6 - - + -
417D LYS* 4.8 0.9 - - - -
461D PHE* 3.5 36.3 - - + +
464D GLU* 3.4 40.0 - - + +
465D LEU* 3.5 25.1 - - + +
468D ASN* 3.6 23.7 + - - +
470D GLN* 3.7 2.7 - - - +
770D ARG* 4.3 4.7 - - - +
772D TYR* 3.4 21.3 + - - -
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Residues in contact with ASP 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 ALA 3.1 13.0 + - - +
399D TYR* 3.4 3.6 - - - -
400D LEU 3.3 0.4 - - - -
401D LEU* 1.3 83.3 - - + +
403D PRO* 1.3 69.6 - - - +
404D ALA* 3.1 24.1 + - - +
405D GLN* 3.2 45.6 + - + +
406D GLY 4.5 0.5 + - - -
407D VAL* 5.4 1.0 + - - +
416D MET* 5.2 4.9 - - + -
772D TYR* 4.0 25.2 + - + +
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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