Contacts of the helix formed by residues 439 - 446 (chain A) in PDB entry 4PLA
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 SER 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A ALA 3.3 11.2 - - - -
373A LYS* 3.3 27.9 + - - -
374A VAL 3.8 5.8 - - - -
375A PRO* 3.9 4.5 - - - +
376A PHE* 4.4 2.2 - - - -
437A ASN 4.0 0.4 + - - -
438A LYS* 1.3 77.9 - - - +
440A PRO* 1.3 74.9 - - - +
441A LEU* 3.2 1.7 - - - +
442A HIS* 3.1 34.4 + - - +
443A LEU* 3.1 21.1 + - - +
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Residues in contact with PRO 440 (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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294A PHE* 4.4 6.7 - - + -
295A GLU* 5.8 3.4 - - + -
298A VAL* 4.1 28.7 - - + -
366A TRP* 4.2 5.0 - - + -
371A GLN 4.5 1.1 - - - +
372A ALA* 3.4 23.8 - - + +
374A VAL 3.2 18.8 - - - +
376A PHE* 4.1 26.7 - - + -
438A LYS 4.3 2.0 - - - +
439A SER* 1.3 88.2 - - - +
441A LEU* 1.3 61.2 + - - +
443A LEU* 3.1 21.7 - - + +
444A VAL* 3.2 13.7 + - - +
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Residues in contact with LEU 441 (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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367A ALA* 3.9 28.0 - - + +
368A TRP* 6.6 0.7 - - + -
372A ALA* 3.0 20.8 + - - +
373A LYS* 4.0 30.7 - - + -
439A SER* 3.2 0.9 - - - +
440A PRO* 1.3 74.4 - - - +
442A HIS* 1.3 81.1 + - + +
444A VAL* 3.2 25.0 + - + +
445A GLN* 3.3 36.4 + - + +
1201A ATP 5.5 3.6 - - - +
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Residues in contact with HIS 442 (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 LYS* 4.2 20.7 - - + +
439A SER* 3.1 30.1 + - - +
440A PRO 3.4 0.2 - - - -
441A LEU* 1.3 92.5 - - + +
443A LEU* 1.3 61.9 + - - +
445A GLN* 3.6 20.6 + - - +
446A MET* 3.5 21.1 + - - +
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Residues in contact with LEU 443 (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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298A VAL* 3.9 25.8 - - + -
302A TYR* 3.7 51.2 + - + +
376A PHE* 4.1 6.3 - - + -
429A ASN 4.2 4.3 - - - +
430A LEU* 4.0 24.2 - - + -
433A ALA* 3.6 28.3 - - + -
438A LYS* 4.9 0.4 - - - +
439A SER 3.1 13.7 + - - +
440A PRO 3.1 9.4 - - - +
442A HIS* 1.3 77.8 - - - +
444A VAL* 1.3 63.9 + - + +
446A MET* 3.3 22.8 + - - +
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Residues in contact with VAL 444 (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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302A TYR* 4.1 14.5 + - + -
364A PHE* 3.7 26.0 - - + -
366A TRP* 3.9 20.6 - - + -
367A ALA* 3.9 19.7 - - + -
440A PRO 3.9 8.5 - - - +
441A LEU* 3.2 17.4 + - + +
443A LEU* 1.3 82.6 - - + +
445A GLN* 1.3 61.5 + - + +
446A MET 3.2 8.6 - - - +
448A PRO* 4.9 2.3 - - - +
1201A ATP 3.2 47.5 + - + +
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Residues in contact with GLN 445 (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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441A LEU* 3.3 40.3 + - - +
442A HIS* 4.0 24.1 + - - +
443A LEU 3.2 0.8 - - - -
444A VAL* 1.3 75.8 - - + +
446A MET* 1.3 65.1 + - - +
447A PRO* 3.2 8.3 - - - +
1201A ATP 2.9 56.5 + - + +
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Residues in contact with MET 446 (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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302A TYR* 4.3 1.7 + - - -
429A ASN* 3.0 47.9 + - - +
432A GLN* 4.3 5.2 - - + -
433A ALA* 3.6 24.9 - - + +
438A LYS* 2.5 56.1 - - + +
442A HIS 3.5 8.8 + - - +
443A LEU* 3.3 14.9 - - - +
444A VAL 3.2 6.4 - - - +
445A GLN* 1.3 76.7 - - - +
447A PRO* 1.3 73.1 - - + +
448A PRO* 3.0 10.6 - - - +
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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