Contacts of the helix formed by residues 400 - 415 (chain A) in PDB entry 3C98
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 400 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A THR* 5.7 0.4 - - - +
398A ASN 3.9 2.4 + - - -
399A VAL* 1.3 77.0 - - - +
401A THR* 1.3 65.5 + - - +
402A TYR* 3.6 7.0 + - - +
403A ASP* 3.0 39.8 + - - +
404A LYS* 2.9 22.6 + - - +
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Residues in contact with THR 401 (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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399A VAL 3.8 1.6 + - - -
400A SER* 1.3 71.6 - - - +
402A TYR* 1.3 67.2 + - + +
404A LYS* 3.4 5.7 + - - +
405A ILE* 3.1 26.1 + - + +
431A GLN 5.6 0.2 + - - -
432A ILE* 3.7 29.1 - - + +
433A PRO* 4.1 9.8 - - + +
436A ASP* 3.8 37.6 + - + +
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Residues in contact with TYR 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A SER* 3.2 6.7 + - - +
401A THR* 1.3 87.4 - - + +
403A ASP* 1.3 64.4 + - - +
405A ILE* 3.3 7.5 + - + +
406A ARG* 3.0 30.7 + - - +
436A ASP* 3.5 22.2 - - - -
439A ILE* 4.1 9.2 - - + +
576A GLN* 3.9 23.3 - - + -
579A LEU* 3.6 35.2 - - + +
580A ASP* 2.6 32.1 + - - -
583A LYS* 3.9 22.6 + - - +
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Residues in contact with ASP 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A HIS* 3.4 20.5 + - - -
361A THR* 4.8 5.0 - - - +
362A VAL* 5.4 3.1 - - - +
365A LEU* 3.6 27.4 - - + +
369A GLU* 5.4 0.5 - - - +
399A VAL* 3.8 15.3 - - + +
400A SER* 3.0 34.0 + - - +
402A TYR* 1.3 76.5 - - - +
404A LYS* 1.3 64.6 + - - +
406A ARG* 3.1 27.4 + - - +
407A ILE* 3.1 17.7 + - - +
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Residues in contact with LYS 404 (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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393A ILE* 3.9 3.8 - - + +
394A LEU* 2.9 48.8 + - + +
395A LEU 4.6 1.0 - - - -
396A ASP 3.1 28.7 + - - -
397A ALA* 4.5 4.8 - - - +
399A VAL* 3.4 26.0 + - + +
400A SER 2.9 13.2 + - - +
401A THR* 3.6 8.3 - - - +
403A ASP* 1.3 76.4 - - - +
405A ILE* 1.3 62.5 + - + +
407A ILE* 3.4 7.1 + - - +
408A ILE* 3.2 28.6 + - - +
430A ALA* 3.1 33.3 + - + +
431A GLN* 5.5 0.8 - - - +
432A ILE* 4.4 7.9 - - + -
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Residues in contact with ILE 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A THR* 3.1 19.3 + - + +
402A TYR* 3.6 11.7 - - + +
403A ASP 3.2 0.4 - - - -
404A LYS* 1.3 74.7 - - - +
406A ARG* 1.3 63.6 + - - +
408A ILE* 3.4 7.7 + - - +
409A LEU* 3.1 36.4 + - + +
432A ILE* 3.9 18.4 - - + -
436A ASP* 3.4 43.1 - - + +
437A SER* 4.8 0.4 - - - -
439A ILE* 4.2 21.1 - - + -
440A ILE* 4.1 20.9 - - + -
579A LEU* 4.2 8.3 - - + -
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 2.9 40.8 + - + +
245A HIS* 3.4 37.9 + - + +
255A ASP* 3.0 37.6 + - - -
369A GLU* 4.5 7.6 - - - +
402A TYR* 3.0 20.6 + - - +
403A ASP* 3.1 21.1 + - - +
405A ILE* 1.3 76.5 - - - +
407A ILE* 1.3 62.4 + - - +
409A LEU* 3.7 7.8 + - - +
410A LEU* 3.3 29.5 + - - +
575A PRO* 3.4 23.3 - - - +
576A GLN* 5.1 1.8 - - - +
579A LEU* 4.0 17.5 - - + -
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Residues in contact with ILE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 4.5 15.5 - - + +
368A VAL* 4.3 18.4 - - + -
369A GLU* 3.7 32.8 - - + +
372A LEU* 3.8 7.5 - - + +
390A ILE* 3.8 38.4 - - + -
393A ILE* 4.3 20.2 - - + -
394A LEU* 4.6 6.5 - - + -
403A ASP 3.1 13.9 + - - +
404A LYS* 3.6 10.3 - - - +
406A ARG* 1.3 75.4 - - - +
408A ILE* 1.3 63.0 - - - +
410A LEU* 3.5 2.7 + - - -
411A TYR* 3.2 20.8 + - - +
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Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ILE* 5.5 1.6 - - + -
394A LEU* 4.0 25.1 - - + -
404A LYS 3.2 19.1 + - - +
405A ILE* 3.4 5.3 + - - +
407A ILE* 1.3 74.9 - - + +
409A LEU* 1.3 66.6 + - - +
411A TYR* 3.3 6.4 + - - +
412A ILE* 3.0 48.0 + - + +
423A LEU* 4.9 3.1 - - + -
426A LEU* 4.0 39.3 - - + +
427A ILE* 4.8 4.3 - - + +
430A ALA* 4.7 6.7 - - + -
432A ILE* 5.2 3.4 - - + -
440A ILE* 3.9 29.2 - - + -
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 4.2 17.9 - - + -
405A ILE* 3.1 35.4 + - + +
406A ARG* 3.9 6.1 - - - +
408A ILE* 1.3 76.0 - - - +
410A LEU* 1.3 58.8 + - - +
412A ILE* 3.3 4.9 + - + +
413A PHE* 2.8 58.5 + - + -
439A ILE* 5.0 5.6 - - + -
440A ILE* 4.1 36.8 - - + +
443A MET* 4.0 26.5 - - + -
450A ILE* 4.8 2.9 - - + -
579A LEU* 4.6 10.1 - - + -
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Residues in contact with LEU 410 (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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240A SER* 4.1 23.6 - - - +
243A VAL* 3.6 25.1 - - + +
244A LEU* 3.5 32.8 - - + -
369A GLU* 3.8 30.3 - - + +
372A LEU* 4.1 18.1 - - + +
373A ALA* 4.8 8.3 - - + -
406A ARG 3.3 18.7 + - - +
407A ILE* 3.9 4.7 - - - +
408A ILE 3.2 0.8 - - - -
409A LEU* 1.3 77.6 - - - +
411A TYR* 1.3 60.3 + - - +
413A PHE* 3.3 7.7 + - + +
414A LEU* 3.0 27.2 + - - +
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Residues in contact with TYR 411 (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 LEU* 3.9 11.1 - - + +
386A PRO* 3.8 27.6 - - + -
387A MET* 3.2 37.6 - - + +
390A ILE* 3.3 35.4 - - + -
407A ILE 3.2 12.5 + - - +
408A ILE* 3.8 5.4 - - - +
410A LEU* 1.3 76.3 - - - +
412A ILE* 1.3 65.2 + - + +
414A LEU* 3.3 3.1 + - + +
415A LYS* 3.0 55.0 + - + +
418A ILE* 3.8 21.4 - - + +
422A ASN* 4.7 7.3 + - + -
426A LEU* 4.2 21.5 - - + -
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Residues in contact with ILE 412 (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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408A ILE* 3.0 39.3 + - + +
409A LEU* 3.6 6.3 - - - +
410A LEU 3.2 0.2 - - - -
411A TYR* 1.3 82.8 - - + +
413A PHE* 1.3 58.4 + - + +
415A LYS 3.8 0.2 - - - -
416A ASN 2.9 4.5 + - - -
417A GLY* 2.7 38.5 + - - -
418A ILE* 3.6 38.1 - - + +
423A LEU* 4.6 3.4 - - + -
440A ILE* 4.0 19.5 - - + -
449A PRO 4.2 3.5 - - - +
450A ILE* 3.8 41.7 - - + +
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Residues in contact with PHE 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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239A PRO* 3.5 39.0 - - + -
240A SER* 3.6 25.4 - - - +
243A VAL* 4.7 2.9 - - + -
409A LEU* 2.8 50.2 + - + +
410A LEU* 3.7 12.6 - - + +
411A TYR 3.3 0.2 - - - -
412A ILE* 1.3 79.2 - - + +
414A LEU* 1.3 61.3 + - - +
416A ASN* 3.3 10.0 + - - +
443A MET* 4.4 7.6 - - + -
448A VAL* 3.7 27.8 - - + -
449A PRO 4.8 2.0 - - - -
450A ILE* 4.1 13.9 - - + -
461A LYS* 2.7 32.0 + - - +
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Residues in contact with LEU 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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371A ASP 5.3 0.4 - - - +
372A LEU* 3.3 34.3 + - + +
373A ALA 5.7 0.2 - - - -
375A GLY* 4.0 20.4 - - - +
383A ILE* 6.3 2.0 - - + -
386A PRO* 4.2 26.2 - - + -
410A LEU 3.0 13.7 + - - +
411A TYR* 3.5 11.4 - - - +
413A PHE* 1.3 74.0 - - - +
415A LYS* 1.3 74.5 + - + +
416A ASN 3.0 4.9 + - - -
461A LYS* 3.3 29.9 - - + +
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Residues in contact with LYS 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PRO* 4.7 19.4 - - - +
411A TYR* 3.0 53.9 + - + +
412A ILE 4.4 0.7 - - - +
414A LEU* 1.3 81.7 - - + +
416A ASN* 1.3 69.4 + - - +
417A GLY 3.9 11.2 - - - +
418A ILE* 4.0 9.6 - - + -
458A ARG* 3.0 22.0 + - - +
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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