Contacts of the helix formed by residues 394 - 402 (chain A) in PDB entry 2HHQ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A MET 2.7 17.9 + - - +
371A PHE* 3.8 15.3 - - + -
392A PHE* 3.8 22.6 - - + -
393A ASP* 1.3 68.9 - - - +
395A LEU* 1.3 59.8 + - - +
397A ALA* 4.1 0.2 - - - -
398A ALA* 2.9 29.1 + - - +
410A VAL* 4.5 7.0 - - + -
413A ALA* 3.9 20.2 - - + -
454A ILE* 4.1 24.0 - - + -
457A LEU* 4.2 20.9 - - + -
461A PHE* 3.7 44.9 - - + -
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Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A PHE* 3.5 28.3 - - + -
372A ASP* 3.7 38.4 - - + +
393A ASP* 3.0 11.2 + - - +
394A LEU* 1.3 78.3 - - - +
396A LEU* 1.3 64.5 + - + +
398A ALA* 3.6 3.5 - - - +
399A TYR* 2.9 28.4 + - - +
407A VAL* 3.4 27.1 - - + +
609A ALA* 3.8 19.1 - - + -
2D FRU 3.6 29.6 - - - +
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Residues in contact with LEU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ASP* 3.2 32.8 + - + +
395A LEU* 1.3 79.2 - - + +
397A ALA* 1.3 66.2 + - - +
399A TYR* 3.4 7.6 + - + +
400A LEU* 3.0 29.1 + - - +
474A LEU* 3.8 12.6 - - + -
478A GLU* 3.8 34.3 - - + +
479A GLN* 4.1 6.5 - - + -
482A SER* 4.1 13.5 - - - +
608A GLN* 3.7 38.8 - - + +
609A ALA* 4.5 9.2 - - + -
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Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A PHE* 3.7 29.2 - - + -
393A ASP 2.9 16.3 + - - +
394A LEU 3.6 4.7 - - - +
395A LEU 3.3 0.2 - - - -
396A LEU* 1.3 77.0 - - - +
398A ALA* 1.3 61.9 + - - +
400A LEU* 3.3 3.6 + - - +
401A LEU* 3.1 26.9 + - - +
461A PHE* 4.0 11.7 - - + -
465A LEU* 3.9 17.9 - - + +
474A LEU* 3.8 9.8 - - + +
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A LEU 2.9 18.4 + - - +
395A LEU 3.6 3.8 - - - +
397A ALA* 1.3 78.6 - - - +
399A TYR* 1.3 61.7 + - - +
401A LEU* 3.2 4.5 + - - +
402A ASP 3.0 24.2 + - - +
407A VAL* 3.9 35.8 - - + +
413A ALA* 4.1 3.4 - - + -
416A MET* 4.1 8.4 - - - +
461A PHE* 3.8 21.5 - - + -
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Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A LEU* 2.9 18.2 + - + +
396A LEU* 3.5 10.8 - - + +
398A ALA* 1.3 78.1 - - - +
400A LEU* 1.3 68.5 + - + +
402A ASP 4.6 0.7 - - - -
403A PRO* 3.0 51.2 - - + +
407A VAL* 5.4 2.2 - - - +
478A GLU* 4.8 3.4 - - - -
608A GLN 3.2 24.4 + - - -
609A ALA* 3.5 37.7 - - + -
610A LEU 3.5 2.5 - - - -
611A THR* 2.6 36.6 + - - -
614A GLY* 3.4 20.2 - - - -
615A ARG 3.9 3.1 + - - -
769A ARG* 3.9 19.7 - - - -
805A LYS* 4.8 2.9 - - - -
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Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A LEU 3.0 21.0 + - - +
397A ALA 3.8 3.8 - - - +
399A TYR* 1.3 80.6 - - + +
401A LEU* 1.3 65.1 + - - +
402A ASP 3.5 0.3 + - - -
403A PRO* 4.3 3.6 - - - +
465A LEU* 4.0 11.0 - - + -
470A GLN* 3.0 29.0 + - + +
473A LEU* 3.7 23.8 - - + -
474A LEU* 3.7 45.5 - - + +
478A GLU* 3.9 16.6 - - + -
769A ARG* 3.6 32.2 - - + +
770A ARG* 4.1 7.4 + - - +
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ALA 3.1 13.8 + - - +
398A ALA 3.2 6.9 + - - +
400A LEU* 1.3 78.8 - - - +
402A ASP* 1.3 61.8 + - - +
416A MET* 4.1 13.0 - - + -
417A LYS* 5.1 0.9 - - - -
461A PHE* 3.5 40.8 - - + +
464A GLU* 3.4 42.0 - - + +
465A LEU* 3.5 24.2 - - + +
468A ASN* 3.5 24.8 + - - +
470A GLN* 4.2 1.3 - - - -
770A ARG* 4.3 4.7 - - - +
772A TYR* 3.3 22.2 + - - -
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Residues in contact with ASP 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ALA 3.0 12.1 + - - +
399A TYR* 3.5 3.5 - - - -
400A LEU 3.3 0.4 - - - -
401A LEU* 1.3 81.3 - - - +
403A PRO* 1.3 69.6 - - - +
404A ALA* 3.0 23.1 + - - +
405A GLN* 2.9 52.3 + - + +
406A GLY 4.6 0.7 + - - -
407A VAL* 5.5 0.5 - - - +
416A MET* 4.5 8.3 - - + -
772A TYR* 3.9 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