Contacts of the helix formed by residues 443 - 457 (chain A) in PDB entry 5C16
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 ASP 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A ILE* 3.9 17.1 - - + +
438A SER* 4.7 0.8 + - - -
442A TRP* 1.3 94.9 + - - +
444A ARG* 1.3 71.4 + - + +
445A THR 3.4 0.2 - - - -
446A ALA* 3.7 2.8 + - - +
447A GLN* 3.4 25.5 + - - +
474A TRP* 4.3 0.3 - - - -
479A HIS* 3.1 19.3 + - - -
480A ARG 5.1 0.5 + - - -
484A ARG* 2.8 47.3 + - - +
500A ILE* 3.6 19.6 - - + +
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Residues in contact with ARG 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ALA* 3.8 17.9 - - + -
343A ARG* 3.7 29.1 - - - +
344A GLN* 5.2 0.4 + - - +
347A VAL* 4.9 8.5 - - - +
374A ILE* 3.0 55.7 + - + -
375A HIS 3.5 17.4 + - - +
376A ASN* 3.9 14.2 - - - +
377A ILE* 5.5 4.8 - - + +
438A SER* 4.1 10.4 + - - -
439A SER* 4.0 21.2 + - - +
443A ASP* 1.3 82.6 - - + +
445A THR* 1.3 66.5 + - - +
447A GLN* 3.4 13.7 + - - +
448A LEU* 3.1 31.4 + - + +
500A ILE* 5.7 4.5 - - + -
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Residues in contact with THR 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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304A ARG* 3.8 41.1 - - + +
305A CYS 4.2 2.2 - - - +
342A ALA* 5.4 0.2 - - - -
436A VAL* 3.8 17.5 - - + +
437A HIS* 3.4 4.5 - - - -
438A SER* 2.7 39.2 + - - -
441A GLY* 3.4 19.5 - - - +
443A ASP 3.4 0.4 - - - -
444A ARG* 1.3 80.0 - - - +
446A ALA* 1.3 57.3 + - - +
448A LEU* 3.3 1.6 + - - +
449A THR* 3.0 32.9 + - + +
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 3.9 18.6 - - - +
442A TRP 4.0 16.3 - - - +
443A ASP 3.7 4.5 + - - +
444A ARG 3.2 0.6 - - - -
445A THR* 1.3 78.1 - - - +
447A GLN* 1.3 56.3 + - - +
449A THR* 3.8 1.4 + - - -
450A SER* 2.7 36.8 + - - -
473A GLU* 3.7 21.0 - - - +
474A TRP* 3.8 21.6 + - + -
479A HIS* 5.3 1.3 - - + +
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Residues in contact with GLN 447 (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 ILE* 4.9 1.0 - - - +
416A LEU* 3.4 34.8 - - + +
443A ASP 3.4 9.1 + - - +
444A ARG* 3.5 24.6 - - - +
446A ALA* 1.3 78.4 - - - +
448A LEU* 1.3 56.0 + - - +
450A SER* 3.8 1.0 + - - -
451A LEU* 3.2 37.0 + - + +
474A TRP* 3.7 21.9 - - + -
500A ILE* 3.0 33.9 + - - +
503A GLN* 2.9 28.7 + - - +
504A PHE* 4.1 10.6 - - + +
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Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ALA* 3.5 31.9 - - + -
372A LEU* 3.6 18.6 - - + -
374A ILE* 3.6 20.0 - - + -
416A LEU* 3.8 17.7 - - + +
419A GLY 3.9 7.0 - - - -
420A ALA* 3.8 29.2 - - + +
423A ILE* 3.9 12.6 - - + +
436A VAL* 4.2 12.8 - - + -
444A ARG 3.1 16.9 + - - +
445A THR 3.9 2.5 - - - +
446A ALA 3.3 0.2 - - - -
447A GLN* 1.3 74.5 - - - +
449A THR* 1.3 66.4 + - - +
450A SER 3.3 0.2 - - - -
451A LEU* 4.1 2.3 - - - +
452A ALA* 3.0 25.6 + - - +
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Residues in contact with THR 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A SER* 4.3 2.9 - - - +
302A ILE* 4.0 19.5 - - + +
304A ARG* 3.9 22.4 + - + -
423A ILE* 5.5 0.4 - - - -
436A VAL* 3.9 29.8 - - + -
445A THR* 3.0 22.2 + - + +
446A ALA 3.8 3.6 + - - -
448A LEU* 1.3 75.1 - - - +
450A SER* 1.3 61.8 + - - +
452A ALA* 3.4 4.6 + - - +
453A MET* 2.8 37.2 + - - +
473A GLU* 2.9 25.9 + - - +
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Residues in contact with SER 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ALA 2.7 21.0 + - - -
447A GLN 3.8 0.2 + - - -
449A THR* 1.3 80.3 + - - +
451A LEU* 1.3 64.2 + - - +
453A MET* 4.3 6.3 - - - -
454A LEU* 3.0 24.8 + - - +
469A LEU* 3.5 25.4 - - - +
473A GLU* 4.0 15.9 - - - -
474A TRP* 3.0 21.6 + - - -
504A PHE* 3.2 14.2 - - - -
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Residues in contact with LEU 451 (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 LEU* 4.5 22.4 - - + +
417A LEU* 4.7 5.8 - - + -
420A ALA* 3.5 18.4 - - + -
447A GLN* 3.2 25.2 + - + +
448A LEU 4.1 0.2 - - - +
450A SER* 1.3 76.2 + - - +
452A ALA* 1.3 61.8 + - - +
454A LEU* 3.3 6.5 + - + +
455A MET* 3.1 27.3 + - + +
504A PHE* 3.8 24.2 - - + -
507A CYS* 3.8 38.4 - - + -
508A VAL* 4.1 11.9 - - + +
511A MET* 4.4 18.6 - - - +
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Residues in contact with ALA 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 4.3 6.5 - - + -
420A ALA* 3.7 19.6 - - - +
423A ILE* 3.6 29.2 - - + -
424A ALA* 4.1 4.5 - - + +
448A LEU 3.0 19.3 + - - +
449A THR 3.9 2.5 - - - +
451A LEU* 1.3 76.5 - - - +
453A MET* 1.3 57.2 + - - +
455A MET* 3.2 7.8 + - - +
456A LEU* 2.9 35.3 + - + +
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Residues in contact with MET 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A SER* 3.2 34.1 - - - +
293A TRP* 3.9 20.0 - - + -
302A ILE* 4.3 7.2 - - + -
449A THR* 2.8 29.9 + - - +
450A SER 3.9 3.6 - - - +
452A ALA* 1.3 72.9 - - - +
454A LEU* 1.3 54.3 + - - +
456A LEU* 4.3 5.8 - - - +
457A ASP* 2.8 31.9 + - - +
460A TYR* 3.4 41.4 - - + +
469A LEU* 3.7 14.4 - - + -
472A LYS* 3.8 4.0 - - - +
473A GLU* 3.5 34.1 - - - +
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Residues in contact with LEU 454 (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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450A SER 3.0 15.0 + - - +
451A LEU* 3.4 8.7 - - + +
453A MET* 1.3 75.9 - - - +
455A MET* 1.3 59.7 + - - +
457A ASP 4.1 1.6 - - - +
460A TYR* 3.3 43.5 - - + +
461A ARG* 3.0 37.0 + - + +
466A PHE* 4.3 9.9 - - + -
469A LEU* 3.9 13.0 - - + +
504A PHE* 5.8 0.4 - - + -
508A VAL* 4.1 26.5 - - + -
511A MET* 4.1 19.1 - - - +
519A PHE* 3.9 20.2 - - + -
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Residues in contact with MET 455 (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 LEU* 3.9 9.4 - - + +
420A ALA* 3.6 31.9 - - + +
421A VAL* 3.8 28.0 - - + +
424A ALA* 4.0 12.1 - - + -
451A LEU* 3.1 18.2 + - + +
452A ALA* 3.2 6.7 + - - +
454A LEU* 1.3 75.7 - - - +
456A LEU* 1.3 56.6 + - - +
461A ARG* 2.6 22.6 + - - +
511A MET* 3.6 22.4 - - + -
584A VAL* 3.3 4.9 - - + -
585A LEU* 3.1 34.5 + - - +
586A TYR* 5.2 0.2 - - - -
587A PRO* 3.5 30.7 - - + -
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Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A TRP* 4.0 33.1 - - + -
302A ILE* 3.9 26.9 - - + -
424A ALA* 3.7 33.4 - - + +
427A ILE* 4.1 18.6 - - + -
428A GLU* 3.8 21.3 - - + +
452A ALA 2.9 21.8 + - - +
453A MET* 3.8 4.5 - - - +
455A MET* 1.3 80.3 - - - +
457A ASP* 1.3 59.0 + - - +
458A SER 4.1 1.3 + - - -
461A ARG* 4.2 2.2 + - - -
582A ASN 5.4 2.1 - - - +
583A HIS 5.2 0.7 - - - +
584A VAL* 4.0 22.8 + - + +
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Residues in contact with ASP 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ARG* 3.0 29.9 + - - -
239A GLN* 5.1 0.7 - - - +
293A TRP* 3.0 38.0 + - + +
453A MET 2.8 16.5 + - - +
454A LEU 4.1 4.7 - - - +
455A MET 3.6 0.6 - - - -
456A LEU* 1.3 74.0 - - - +
458A SER* 1.3 62.2 + - - +
459A TYR* 3.2 16.2 + - - +
460A TYR* 3.0 31.7 + - + +
461A ARG* 4.2 3.2 + - - -
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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
------------------------------------------------------------
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