Contacts of the helix formed by residues 428 - 433 (chain A) in PDB entry 6DWN
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 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A ARG* 4.7 7.9 - - - +
374A GLU* 2.7 10.6 + - - -
422A VAL 5.4 1.3 - - - +
423A ASN* 6.4 1.6 - - + -
426A GLU* 4.4 8.5 - - + +
427A PHE* 1.3 73.4 - - - +
429A PRO* 1.3 68.5 - - - +
430A GLU* 3.0 31.6 + - + +
431A ARG* 3.1 57.8 + - + +
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Residues in contact with PRO 429 (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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338A ARG* 4.5 0.7 - - - +
339A VAL* 4.3 10.3 - - + -
367A TYR* 4.2 22.0 - - + +
370A ALA* 3.3 35.7 - - + +
371A PHE* 3.9 15.3 - - + +
374A GLU* 3.7 14.1 - - + -
427A PHE* 3.6 36.6 - - + +
428A LEU* 1.3 87.1 - - - +
430A GLU* 1.3 65.9 + - - +
431A ARG 3.0 5.4 + - - -
432A PHE* 3.3 8.7 + - + -
433A LEU* 5.0 0.4 - - - -
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Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG* 2.9 30.4 + - - -
342A LYS* 3.4 17.1 + - - +
367A TYR* 2.9 27.9 + - + -
428A LEU* 3.0 29.0 + - + +
429A PRO* 1.3 81.1 - - - +
431A ARG* 1.3 63.1 + - - +
432A PHE 3.2 0.4 - - - -
433A LEU* 3.1 35.2 + - + +
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Residues in contact with ARG 431 (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 GLU* 2.6 48.1 + - - -
377A ARG* 3.2 14.4 - - - +
421A TRP* 4.2 11.5 - - - +
422A VAL* 2.3 41.8 + - - +
423A ASN* 3.2 10.5 + - - +
424A PRO* 4.2 2.4 - - - +
426A GLU* 3.0 16.2 + - - +
428A LEU* 3.1 33.1 + - + +
429A PRO 3.0 2.2 + - - -
430A GLU* 1.3 77.7 - - - +
432A PHE* 1.3 77.7 + - + +
433A LEU 3.3 4.2 + - - +
440A ASP* 5.1 1.9 - - - +
443A LEU* 3.0 28.0 - - + +
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Residues in contact with PHE 432 (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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370A ALA* 3.7 26.5 - - + -
373A LEU* 3.6 21.1 - - + -
374A GLU* 3.4 28.5 - - + -
377A ARG* 4.2 2.7 - - - -
421A TRP* 3.5 28.9 - + - -
429A PRO 3.3 9.0 + - - +
430A GLU 3.2 1.0 - - - -
431A ARG* 1.3 82.0 - - + +
433A LEU* 1.3 56.5 + - - +
439A ILE* 3.4 11.0 - - + +
440A ASP* 2.6 36.5 + - - +
443A LEU* 3.5 21.3 - - + -
444A SER* 3.8 22.2 - - - -
447A VAL* 3.4 26.9 - - + -
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Residues in contact with LEU 433 (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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342A LYS* 5.6 1.3 - - - +
366A PRO* 4.0 24.0 - - + +
367A TYR* 3.6 32.8 - - + +
370A ALA* 4.0 13.0 - - + -
429A PRO 4.3 0.4 - - - +
430A GLU* 3.1 33.0 + - + +
431A ARG 3.3 3.1 - - - +
432A PHE* 1.3 81.1 - - - +
434A THR* 1.3 69.2 + - - +
437A GLY* 4.0 16.8 - - - +
438A ALA 3.2 18.6 - - - +
439A ILE* 4.2 2.2 - - + -
440A ASP* 5.0 1.3 - - - -
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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