Contacts of the helix formed by residues 372 - 378 (chain A) in PDB entry 4RA4
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 LYS 372 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LEU 3.9 0.6 + - - -
371A LYS* 1.4 68.6 - - - +
373A ASP* 1.3 58.7 + - - +
375A VAL* 3.8 7.9 - - - +
376A ILE* 3.0 36.4 + - - +
408A GLN* 2.7 24.8 + - - -
409A THR 2.6 27.2 + - - +
410A VAL 3.7 13.5 - - - +
411A ASP 2.9 19.6 + - - +
412A ARG 3.8 11.0 - - - +
413A LEU* 4.1 14.8 - - + -
648A ILE* 4.3 12.8 - - + -
650A GLN* 2.7 32.8 + - - +
653A PHE* 3.7 29.7 - - + -
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Residues in contact with ASP 373 (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 LYS* 3.8 26.7 + - - +
372A LYS* 1.3 69.5 - - - +
374A VAL* 1.4 65.8 + - - +
376A ILE* 3.5 5.6 + - - +
377A GLN* 3.1 44.8 + - - +
411A ASP* 3.8 20.4 - - - +
640A PRO* 6.0 0.5 - - - +
644A VAL* 3.7 29.3 - - + +
645A ILE* 5.9 0.7 - - - +
648A ILE* 4.1 15.0 - - + +
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Residues in contact with VAL 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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349A SER 4.1 15.9 - - - +
350A PHE 4.8 6.7 - - - +
351A GLY* 6.2 0.4 - - - -
371A LYS* 3.2 33.0 + - + +
373A ASP* 1.4 82.1 - - - +
375A VAL* 1.3 60.4 + - + +
377A GLN* 3.9 4.2 - - - -
378A ASP* 3.0 49.6 + - - +
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Residues in contact with VAL 375 (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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350A PHE 5.4 2.9 - - - +
370A LEU* 3.8 33.9 - - + -
371A LYS 2.9 22.6 + - - +
372A LYS* 3.8 7.4 - - - +
373A ASP 3.3 0.2 - - - -
374A VAL* 1.3 78.7 - - + +
376A ILE* 1.4 59.8 + - - +
378A ASP* 3.7 1.6 + - - -
379A ASP 3.2 3.3 + - - -
380A ASP* 2.9 63.2 + - + +
381A VAL* 3.8 12.3 + - + +
384A THR* 3.7 10.3 - - - +
413A LEU* 4.3 5.6 - - + -
653A PHE* 4.5 7.2 - - + -
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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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372A LYS 3.0 25.3 + - - +
373A ASP* 3.5 4.5 + - - +
375A VAL* 1.4 72.1 - - - +
377A GLN* 1.4 72.8 + - - +
379A ASP* 3.0 23.9 + - - +
381A VAL* 3.7 22.4 - - + +
648A ILE* 4.3 23.1 - - + -
649A ASP* 4.7 5.6 - - + +
652A ASP* 4.6 11.2 - - - +
653A PHE* 4.1 18.6 - - + -
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Residues in contact with GLN 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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373A ASP* 3.1 29.7 + - - +
374A VAL* 4.0 4.5 - - - +
376A ILE* 1.4 89.0 - - - +
378A ASP* 1.4 62.0 + - - +
379A ASP* 3.3 6.1 + - - +
644A VAL* 5.9 2.2 - - - +
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Residues in contact with ASP 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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349A SER* 4.4 16.1 + - - +
374A VAL* 3.0 38.5 + - + +
375A VAL* 4.1 2.0 - - - +
377A GLN* 1.4 77.1 - - - +
379A ASP* 1.4 63.3 + - - +
380A ASP* 3.0 31.7 - - + +
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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