Contacts of the helix formed by residues 373 - 378 (chain A) in PDB entry 3H0G
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 PRO 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A THR* 5.7 0.9 - - + -
371A GLY 3.7 8.0 - - - +
372A VAL* 1.3 90.4 - - + +
374A ARG* 1.3 66.6 + - - +
375A SER* 4.3 9.0 - - - +
376A ILE* 3.0 39.3 + - + +
377A ALA 3.1 9.2 + - - -
469A MET 3.1 9.9 - - - +
470A PRO* 4.7 0.7 - - + -
471A TYR 3.4 23.3 - - - +
472A SER* 4.2 13.7 - - - -
473A THR 3.9 13.4 - - - +
474A PHE* 4.6 7.4 - - + -
475A ARG* 4.8 0.6 - - - +
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Residues in contact with ARG 374 (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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372A VAL 3.5 0.6 + - - -
373A PRO* 1.3 70.5 - - - +
375A SER* 1.3 66.2 + - - +
376A ILE 2.9 0.3 + - - -
377A ALA* 3.0 8.7 + - - -
378A LYS* 2.7 41.4 + - + +
405A HIS* 4.6 20.4 - - + +
468A VAL* 3.6 10.5 - - + +
469A MET 3.2 29.3 + - - -
470A PRO* 3.5 28.2 - - - +
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Residues in contact with SER 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PRO* 3.1 8.9 - - - +
374A ARG* 1.3 81.8 - - - +
376A ILE* 1.3 68.1 + - - +
378A LYS* 3.9 13.9 + - - +
379A THR* 3.9 14.0 + - - -
472A SER* 5.7 7.6 - - - -
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Residues in contact with ILE 376 (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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355A ALA* 4.1 22.4 - - + -
356A ARG 5.1 5.4 - - - +
357A THR* 5.3 4.3 - - - -
372A VAL* 4.4 4.9 - - + -
373A PRO* 3.0 30.0 + - + +
375A SER* 1.3 81.1 - - - +
377A ALA* 1.3 57.8 + - - +
378A LYS 2.9 1.8 - - - -
379A THR* 2.5 41.3 + - - +
380A LEU* 3.6 29.2 - - + +
474A PHE* 4.1 20.2 - - + -
495A MET* 4.3 9.9 - - + -
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Residues in contact with ALA 377 (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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372A VAL* 4.2 7.7 - - + +
373A PRO 3.1 9.8 + - - +
374A ARG* 3.0 9.6 + - - +
376A ILE* 1.3 78.9 - - - +
378A LYS* 1.3 56.5 + - - +
379A THR 3.1 2.6 + - - -
380A LEU 4.2 2.1 + - - -
405A HIS* 3.8 28.5 - - + +
441A HIS* 2.9 26.4 - - - +
442A ILE* 3.4 34.0 + - + +
468A VAL* 4.7 3.4 - - + -
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Residues in contact with LYS 378 (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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374A ARG* 2.7 29.2 + - + +
375A SER* 4.0 10.1 - - - +
376A ILE 2.8 0.8 + - - -
377A ALA* 1.3 73.5 - - - +
379A THR* 1.3 66.3 + - - +
402A PRO 4.2 3.6 - - - +
403A ASP* 3.6 47.1 + - - +
405A HIS* 3.9 25.8 - - + +
409A LYS* 4.2 5.9 - - - +
441A HIS* 2.9 25.8 + - + +
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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