Contacts of the helix formed by residues 565 - 571 (chain A) in PDB entry 4P3N
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 PHE 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A MET* 4.4 3.6 - - + -
506A LEU 4.9 2.2 - - - +
507A GLY* 5.4 7.9 - - - -
511A VAL* 3.6 34.3 - - + -
512A TRP* 3.8 33.7 - + - -
515A ALA* 3.6 30.3 - - + -
540A TYR 3.1 12.1 + - - +
542A PRO* 3.8 24.9 - - + -
563A LEU* 4.5 4.5 - - + -
564A ASP* 1.3 76.5 - - - +
566A GLN* 1.3 65.1 + - - +
568A PRO* 3.4 13.9 - - - +
569A ILE* 3.5 24.0 - - + +
586A PRO 5.6 1.1 - - - -
587A VAL* 4.0 26.2 - - + -
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Residues in contact with GLN 566 (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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506A LEU* 3.5 45.4 - - + +
507A GLY* 4.3 7.1 + - - -
539A PHE* 4.8 6.1 - - + -
540A TYR* 3.7 21.1 + - + -
564A ASP* 2.8 7.9 + - - +
565A PHE* 1.3 80.4 - - - +
567A LEU* 1.3 61.3 + - - +
569A ILE* 3.1 23.7 + - - +
570A ARG* 2.9 51.8 + - + +
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Residues in contact with LEU 567 (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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386A SER* 4.3 24.9 - - - +
388A HIS* 6.3 0.7 - - + -
413A CYS* 3.8 20.0 - - + -
414A PRO* 5.6 1.3 - - + -
417A CYS* 3.6 20.9 - - - -
464A HIS* 5.6 0.2 - - + -
564A ASP* 3.0 26.5 + - - +
566A GLN* 1.3 77.3 - - - +
568A PRO* 1.4 67.6 - - + +
570A ARG* 3.4 3.9 + - + +
571A PHE* 3.1 44.8 + - + +
573A LEU* 4.6 0.5 - - - +
588A ILE* 3.5 12.8 - - + -
590A HIS* 3.7 20.6 - - + -
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Residues in contact with PRO 568 (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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564A ASP 3.5 15.3 - - - +
565A PHE* 3.4 19.7 - - - +
567A LEU* 1.4 95.4 - - + +
569A ILE* 1.3 56.9 + - - +
572A ASN* 3.0 8.3 + - - -
573A LEU* 2.8 45.1 + - + -
585A ARG* 3.7 17.0 + - + -
586A PRO* 3.3 28.3 - - + +
588A ILE* 3.8 15.5 - - + -
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Residues in contact with ILE 569 (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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507A GLY* 5.6 8.5 - - - -
565A PHE* 3.5 19.5 - - + +
566A GLN* 3.1 27.2 + - - +
568A PRO* 1.3 74.6 - - - +
570A ARG* 1.3 67.6 + - + +
572A ASN* 3.1 13.3 + - - +
585A ARG* 4.0 35.4 + - - +
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Residues in contact with ARG 570 (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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384A MET 4.0 9.6 + - - -
385A THR* 3.0 45.4 + - - +
386A SER 4.6 9.6 - - - +
387A GLY* 5.0 3.2 - - - -
390A GLN* 4.1 16.8 + - - +
566A GLN* 2.9 44.8 + - + +
567A LEU* 4.0 8.3 - - + +
569A ILE* 1.3 78.0 - - + +
571A PHE* 1.3 63.9 + - + +
572A ASN* 3.7 1.0 + - - +
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Residues in contact with PHE 571 (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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382A LEU* 3.5 26.7 - - + -
385A THR* 3.8 25.6 - - + -
386A SER* 4.2 13.7 - - - -
414A PRO* 3.7 28.5 - - + -
417A CYS* 3.8 19.1 - - + -
418A LEU* 3.7 31.6 - - + -
421A ASP* 4.1 11.9 - - + +
567A LEU* 3.1 27.5 + - + +
570A ARG* 1.3 76.6 - - + +
572A ASN* 1.3 72.9 + - - +
573A LEU* 3.4 21.1 - - + +
338B LEU* 5.6 0.7 - - + -
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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