Contacts of the helix formed by residues 479 - 486 (chain A) in PDB entry 3WSZ
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 GLN 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A ALA 4.8 0.3 - - - +
413A ASP* 3.3 24.8 + - - +
414A PHE 3.4 19.6 + - - -
415A HIS* 3.8 11.3 + - - +
425A ILE* 3.1 31.7 + - - +
427A THR* 4.1 10.2 + - - +
440A SER* 5.9 0.2 + - - -
477A LEU 3.6 7.2 + - - +
478A ALA* 1.3 74.4 - - - +
480A ARG* 1.3 68.4 + - - +
481A LEU 3.1 1.6 + - - -
482A SER* 3.0 7.4 + - - -
483A GLN* 3.0 29.1 + - - +
493A PRO* 4.7 5.2 - - + -
494A ILE* 3.3 37.2 - - + +
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Residues in contact with ARG 480 (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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406A PHE 5.0 5.3 + - - -
407A ALA* 4.5 19.4 - - - +
411A PHE* 3.5 30.4 - - + +
412A ALA 5.8 1.3 - - - +
413A ASP* 4.4 2.9 - - - +
479A GLN* 1.3 76.8 - - - +
481A LEU* 1.3 62.3 + - - +
483A GLN* 3.7 9.6 + - - +
484A LEU* 3.5 39.2 + - - +
493A PRO* 4.7 15.2 - - + +
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Residues in contact with LEU 481 (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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390A LEU* 3.6 32.1 - - + +
391A TYR* 3.8 28.0 - - - +
392A TYR* 3.9 11.7 - - + +
403A VAL* 4.1 24.2 - - + -
411A PHE* 3.4 32.5 - - + +
413A ASP* 2.9 24.0 + - - +
480A ARG* 1.3 71.1 - - - +
482A SER* 1.3 64.5 - - - +
483A GLN 3.0 3.0 + - - -
484A LEU* 3.1 13.2 + - + +
485A LEU* 3.4 23.3 + - + +
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Residues in contact with SER 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 4.1 2.9 - - - -
413A ASP* 3.3 12.7 + - - -
427A THR* 4.9 2.1 + - - -
438A MET* 3.4 26.3 - - - +
477A LEU 4.7 0.5 + - - -
478A ALA* 3.7 8.3 - - - -
479A GLN 3.0 26.5 + - - -
481A LEU* 1.3 78.8 - - - +
483A GLN* 1.3 59.3 + - - +
485A LEU* 3.5 15.8 + - - +
486A ASN* 3.2 27.3 + - - -
514A LEU* 3.8 10.2 - - - +
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Residues in contact with GLN 483 (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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478A ALA* 3.1 29.4 + - + +
479A GLN 3.0 30.3 + - - +
480A ARG* 3.8 7.5 + - - +
482A SER* 1.3 76.0 - - - +
484A LEU* 1.3 56.7 + - + +
486A ASN 3.2 3.0 + - - +
487A LEU 2.8 8.1 + - - -
488A GLN* 2.4 66.5 + - + +
491A ARG* 3.5 28.6 - - - +
492A MET 2.7 28.7 + - - +
493A PRO* 4.0 1.9 - - - +
507A THR* 4.5 4.9 - - - -
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Residues in contact with LEU 484 (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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402A LEU* 4.2 15.2 - - - +
403A VAL* 4.0 32.8 - - + -
406A PHE* 4.1 29.9 - - + -
407A ALA* 5.4 0.4 - - + -
411A PHE* 4.7 5.2 - - + -
480A ARG* 3.5 39.2 + - - +
481A LEU 3.1 7.2 + - - +
483A GLN* 1.3 77.5 - - - +
485A LEU* 1.3 58.7 + - - +
487A LEU* 2.9 19.2 + - - +
488A GLN 4.4 4.0 - - - +
489A LEU* 4.1 33.6 - - + +
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Residues in contact with LEU 485 (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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390A LEU* 4.7 7.9 - - + -
401A THR* 3.8 36.3 - - + +
402A LEU* 5.0 10.9 - - + +
403A VAL* 3.9 11.7 - - + -
438A MET* 3.6 29.2 - - + -
481A LEU* 3.4 31.0 - - + +
482A SER* 3.6 8.7 - - - +
483A GLN 3.2 0.4 - - - -
484A LEU* 1.3 74.5 - - - +
486A ASN* 1.3 62.0 + - - +
487A LEU* 3.1 7.1 + - - +
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Residues in contact with ASN 486 (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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438A MET* 5.1 12.3 - - - +
482A SER 3.2 14.9 + - - +
483A GLN* 3.2 3.8 + - - +
485A LEU* 1.3 81.2 - - - +
487A LEU* 1.3 70.5 + - - +
488A GLN* 3.1 22.8 + - + +
514A LEU* 4.6 14.5 + - - +
515A ALA 4.3 17.6 + - - -
516A SER* 5.0 9.6 - - - +
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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