Contacts of the helix formed by residues 412 - 421 (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 ASN 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A THR* 4.9 1.6 + - - +
409A LYS* 2.3 40.5 + - - -
411A MET* 1.3 72.9 - - - +
413A CYS* 1.3 65.8 + - - +
414A PRO* 3.6 2.2 - - - -
415A GLY* 3.4 5.2 + - - -
416A HIS* 3.4 33.1 + - + +
436A ASP* 3.6 19.2 + - - +
438A GLY* 4.2 7.1 + - - -
440A LEU* 3.6 24.7 - - - +
460A GLN* 5.0 0.6 - - - +
462A ASP* 3.3 35.4 + - - +
464A HIS* 4.2 1.1 - - - -
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Residues in contact with CYS 413 (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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388A HIS* 5.5 2.7 - - + -
411A MET* 4.0 29.2 - - - -
412A ASN* 1.3 76.5 - - - +
414A PRO* 1.4 71.3 - - + +
416A HIS* 3.0 7.3 + - - +
417A CYS* 2.9 24.8 + - - -
462A ASP* 5.0 1.6 - - - -
464A HIS* 3.0 37.6 - - + +
567A LEU* 3.8 20.4 - - + -
590A HIS* 3.5 15.3 - - - -
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Residues in contact with PRO 414 (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* 3.7 20.6 - - + -
383A TRP* 3.8 17.5 - - + -
386A SER* 3.6 23.8 - - - -
388A HIS* 3.9 9.4 - - + -
411A MET 4.0 10.1 - - - +
412A ASN 3.6 2.0 - - - -
413A CYS* 1.4 94.6 - - + +
415A GLY* 1.3 56.9 + - - +
417A CYS* 3.1 6.5 + - + +
418A LEU* 2.9 32.0 + - - +
567A LEU* 5.5 2.2 - - + -
571A PHE* 3.7 24.8 - - + -
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Residues in contact with GLY 415 (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 THR* 4.8 4.3 - - - -
378A PHE* 4.3 15.2 - - - -
382A LEU* 4.7 2.6 - - - +
412A ASN 3.4 6.0 + - - -
413A CYS 3.3 0.8 - - - -
414A PRO* 1.3 78.7 - - - +
416A HIS* 1.3 59.2 + - - +
418A LEU* 3.1 10.3 + - - +
419A MET* 2.9 34.1 + - - +
344B PHE* 3.8 18.5 - - - -
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Residues in contact with HIS 416 (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 VAL* 3.7 10.8 - - + +
374A THR* 3.9 17.3 - - + -
412A ASN* 3.4 16.4 + - + +
413A CYS 3.0 9.3 + - - +
415A GLY* 1.3 72.9 - - - +
417A CYS* 1.3 61.3 + - - +
419A MET* 3.1 10.3 + - - +
420A PHE* 2.9 28.1 + - - +
434A LEU* 3.8 28.6 + - + +
435A ALA 4.3 0.2 - - - -
436A ASP* 3.0 42.6 + - + +
462A ASP* 4.6 1.8 - - - -
464A HIS* 3.0 30.9 + + + +
466A PHE* 3.9 17.8 - - + -
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Residues in contact with CYS 417 (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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413A CYS 2.9 17.5 + - - -
414A PRO* 3.1 9.4 + - - +
416A HIS* 1.3 76.8 - - - +
418A LEU* 1.3 57.1 + - - +
420A PHE* 3.2 3.2 + - - +
421A ASP* 2.9 29.3 + - - +
464A HIS* 6.6 0.2 - - - -
466A PHE* 4.5 3.4 - - - -
567A LEU* 3.6 22.0 - - - -
571A PHE* 3.8 25.1 - - + -
573A LEU* 3.5 18.8 - - + +
588A ILE* 3.6 31.4 - - - -
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Residues in contact with LEU 418 (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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378A PHE* 4.7 4.7 - - + -
382A LEU* 3.6 20.2 - - + -
414A PRO 2.9 15.8 + - - +
415A GLY* 3.3 9.6 - - - +
417A CYS* 1.3 76.5 - - - +
419A MET* 1.3 57.4 + - - +
421A ASP* 3.2 10.6 + - + +
422A HIS* 2.9 27.5 + - - +
571A PHE* 3.7 21.5 - - + -
334B PHE* 4.2 5.8 - - + -
336B HIS* 3.6 36.8 - - + +
338B LEU* 4.1 13.5 - - + -
344B PHE* 4.1 26.5 - - + -
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Residues in contact with MET 419 (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 VAL* 3.7 23.6 - - + -
374A THR* 3.6 26.2 - - + -
415A GLY 2.9 18.1 + - - +
416A HIS* 3.1 14.7 + - - +
418A LEU* 1.3 72.5 - - - +
420A PHE* 1.3 62.0 + - - +
422A HIS* 3.5 9.7 - - - +
425A ARG* 2.9 21.9 + - - -
434A LEU* 4.4 12.1 - - + -
334B PHE* 4.1 9.2 - - + -
344B PHE* 3.8 18.6 - - + -
345B PHE 3.3 35.2 - - - +
346B LEU* 3.7 26.6 - - + +
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Residues in contact with PHE 420 (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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416A HIS 2.9 12.2 + - - +
417A CYS* 3.2 8.7 + - - +
419A MET* 1.3 76.1 - - - +
421A ASP* 1.3 61.1 + - - +
422A HIS 3.2 1.2 + - - -
423A ARG 3.5 6.4 - - - +
425A ARG* 2.8 50.9 + - + +
430A LEU* 4.0 16.4 - - + -
432A LEU* 4.2 9.2 - - + -
434A LEU* 5.1 0.8 - - - +
466A PHE* 3.5 52.3 - + + -
573A LEU* 3.9 27.8 - - + -
574A THR 3.6 25.6 - - - -
575A TYR* 4.6 5.8 - - + -
586A PRO* 4.1 15.3 - - + -
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Residues in contact with ASP 421 (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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417A CYS 2.9 16.9 + - - +
418A LEU* 3.2 13.4 + - + +
420A PHE* 1.3 76.5 - - - +
422A HIS* 1.3 64.6 + - - +
423A ARG* 3.3 5.4 + - - +
571A PHE* 4.1 13.0 - - + +
572A ASN 3.9 12.1 - - - +
573A LEU* 3.7 18.0 - - + +
574A THR* 5.4 1.6 + - - -
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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