Contacts of the helix formed by residues 402 - 418 (chain A) in PDB entry 3WOO
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 THR 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A GLN* 5.5 1.8 - - - +
398A LEU 3.6 2.0 + - - +
399A PHE* 3.0 18.7 + - - +
401A ASN* 1.3 79.3 - - - +
403A ALA* 1.3 59.5 + - - +
404A MET 3.4 0.7 - - - -
405A LEU* 3.9 16.1 + - - +
406A GLY* 2.8 27.2 + - - -
453A ASP* 3.5 14.3 + - - -
456A LEU* 4.2 18.6 - - + -
457A GLN* 4.0 16.3 - - - +
460A TRP* 3.9 26.9 - - + +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A TYR* 5.7 0.7 - - - +
401A ASN 4.6 0.9 - - - -
402A THR* 1.3 71.0 - - - +
404A MET* 1.3 65.1 + - + +
406A GLY* 4.1 0.4 - - - -
407A SER* 3.0 32.2 + - - -
444A LEU* 4.0 20.3 - - + +
447A ARG 5.6 0.7 - - - +
448A TYR* 3.4 32.1 - - + -
453A ASP* 3.0 14.8 + - - +
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Residues in contact with MET 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A THR* 4.8 0.2 + - - -
403A ALA* 1.3 87.4 - - + +
405A LEU* 1.3 63.1 + - + +
407A SER* 3.4 6.4 + - - +
408A ALA* 2.9 30.3 + - - +
444A LEU* 4.1 13.0 - - + -
448A TYR* 3.6 37.9 - - + +
453A ASP* 3.8 14.8 + - - +
457A GLN* 4.3 11.7 - - - +
495A LEU* 6.5 0.2 - - + -
498A THR* 4.1 19.5 - - + -
500A LEU* 3.4 48.8 - - + +
501A GLY* 3.4 6.5 - - - -
506A ARG* 4.2 1.6 - - - +
524A ALA* 4.2 7.1 - - + +
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Residues in contact with LEU 405 (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 PHE* 3.3 57.4 - - + +
400A ASN* 3.6 7.4 - - - +
402A THR* 3.6 13.7 + - - +
403A ALA 3.5 0.2 - - - -
404A MET* 1.3 79.3 - - + +
406A GLY* 1.3 52.4 + - - +
408A ALA* 3.9 2.6 - - - +
409A THR* 2.8 41.8 + - - +
457A GLN* 4.5 8.3 - - + +
495A LEU* 4.0 31.2 - - + -
524A ALA* 4.5 8.5 - - + +
527A TYR* 3.8 32.1 - - + -
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Residues in contact with GLY 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASN 3.0 18.9 + - - -
401A ASN* 4.7 2.9 - - - -
402A THR 2.8 17.5 + - - -
403A ALA 4.1 0.2 - - - -
405A LEU* 1.3 74.2 - - - +
407A SER* 1.3 64.2 + - - +
409A THR* 3.3 3.3 + - - -
410A GLN* 3.1 27.1 + - - +
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Residues in contact with SER 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ALA 3.0 20.9 + - - -
404A MET* 3.7 8.5 - - - -
406A GLY* 1.3 75.8 - - - +
408A ALA* 1.3 64.1 + - - +
410A GLN* 3.9 3.8 - - - +
411A LEU* 3.0 36.2 + - - +
441A LEU* 4.1 9.8 - - - +
444A LEU* 3.7 9.9 - - - +
500A LEU* 4.5 9.4 - - - -
506A ARG* 3.6 27.6 - - - -
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Residues in contact with ALA 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A MET 2.9 18.1 + - - +
405A LEU* 3.9 4.7 - - + +
406A GLY 3.3 0.2 - - - -
407A SER* 1.3 77.4 - - - +
409A THR* 1.3 58.1 + - - +
411A LEU* 3.8 3.0 - - - +
412A TYR* 2.9 32.7 + - - +
500A LEU* 3.8 15.2 - - + +
517A PHE* 4.6 2.7 - - - -
524A ALA* 3.3 33.7 - - + +
525A ILE* 4.1 4.9 - - - +
527A TYR* 5.9 0.2 - - + -
528A ALA* 3.7 8.6 - - + +
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Residues in contact with THR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASN* 4.2 11.5 + - - +
405A LEU 2.8 24.1 + - - +
406A GLY* 3.3 8.8 + - - -
408A ALA* 1.3 76.2 - - - +
410A GLN* 1.3 59.7 + - - +
413A ARG* 3.0 30.7 + - - +
527A TYR* 4.4 8.7 - - + -
528A ALA* 3.8 25.6 - - + -
531A VAL* 4.3 7.4 - - + -
532A MET* 3.4 11.4 - - + +
535A LEU* 4.2 22.9 - - + -
806A GOL 5.1 5.2 + - - -
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Residues in contact with GLN 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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406A GLY 3.1 20.1 + - - +
407A SER* 3.9 3.6 - - - +
409A THR* 1.3 78.4 + - - +
411A LEU* 1.3 58.1 + - + +
413A ARG 3.4 0.7 + - - -
414A LEU* 2.9 25.0 + - + +
428A GLY 5.6 0.6 + - - -
429A TYR* 3.6 31.0 + - + +
437A ILE* 3.9 41.6 - - + +
441A LEU* 4.2 15.8 - - - +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A SER* 3.0 28.2 + - - +
408A ALA* 4.0 2.5 - - - +
410A GLN* 1.3 76.1 - - + +
412A TYR* 1.3 67.6 + - - +
414A LEU* 3.3 9.5 + - + +
415A SER* 3.1 17.3 + - - -
437A ILE* 5.2 3.4 - - + -
441A LEU* 3.7 31.6 - - + -
500A LEU* 4.7 7.6 - - + -
506A ARG* 3.8 18.6 - - - +
509A TRP* 3.9 13.7 - - + +
510A PHE* 3.3 38.6 - - + +
517A PHE* 3.4 22.3 - - + -
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Residues in contact with TYR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ALA 2.9 19.1 + - - +
409A THR 4.1 2.7 - - - +
411A LEU* 1.3 77.4 - - - +
413A ARG* 1.3 63.9 + - - +
415A SER* 3.0 26.8 + - - -
416A ILE* 3.3 26.4 + - + +
514A ARG* 4.1 6.5 + - + -
517A PHE* 3.4 39.4 - - + -
518A GLU* 2.6 36.2 + - + +
525A ILE 5.7 0.2 - - - +
528A ALA* 3.9 14.8 - - + -
529A VAL* 3.6 27.8 - - + +
532A MET* 3.6 39.7 - - + -
533A PRO* 5.6 0.7 - - + -
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Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR 3.0 20.0 + - - +
410A GLN 3.7 4.5 - - - +
412A TYR* 1.3 78.3 - - - +
414A LEU* 1.3 62.7 + - - +
416A ILE* 3.1 11.1 + - - +
417A GLU* 2.9 50.1 + - - +
420A LYS* 5.4 1.0 - - - +
426A GLU* 3.6 20.9 + - - +
429A TYR* 3.5 27.4 - - + +
532A MET* 3.9 14.9 - - + +
536A LEU* 3.4 28.3 - - - +
539A GLU* 2.9 40.2 + - - -
806A GOL 3.0 28.1 + - - +
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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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410A GLN* 2.9 15.0 + - + +
411A LEU* 3.6 11.7 - - + +
412A TYR 3.3 0.2 - - - -
413A ARG* 1.3 78.0 - - - +
415A SER* 1.3 53.6 + - - +
417A GLU* 3.1 2.3 + - - -
418A ARG* 2.8 72.3 + - + +
429A TYR* 3.8 38.8 - - + +
434A LEU* 3.9 18.2 - - + -
437A ILE* 4.5 11.4 - - + -
510A PHE* 3.7 30.7 - - + +
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Residues in contact with SER 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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411A LEU 3.1 6.6 + - - -
412A TYR* 3.0 19.6 + - - -
414A LEU* 1.3 76.2 - - - +
416A ILE* 1.3 59.0 + - - +
418A ARG* 3.7 12.7 + - - +
419A GLU* 3.5 19.1 - - - +
512A ALA 3.8 9.0 - - - -
513A ASP* 4.5 1.0 - - - +
514A ARG* 3.3 31.1 + - - +
517A PHE* 3.4 35.1 - - - -
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Residues in contact with ILE 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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412A TYR* 3.3 43.3 + - + +
413A ARG* 3.1 13.1 + - - +
415A SER* 1.3 77.4 + - - +
417A GLU* 1.3 77.6 + - - +
419A GLU* 3.2 18.5 + - - +
420A LYS* 4.1 12.9 + - - +
514A ARG* 4.0 39.5 + - - +
532A MET* 4.0 16.2 - - + -
536A LEU* 4.8 13.5 - - + -
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Residues in contact with GLU 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 ARG* 2.9 45.9 + - - +
414A LEU 3.7 5.6 - - - +
416A ILE* 1.3 81.7 - - - +
418A ARG* 1.3 63.0 + - - +
420A LYS* 3.0 42.1 + - - +
425A ARG* 3.2 27.7 - - + +
426A GLU* 2.9 28.1 + - - -
429A TYR* 3.8 31.6 - - + +
536A LEU* 5.2 0.7 - - - +
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Residues in contact with ARG 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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414A LEU* 2.8 46.8 + - + +
415A SER* 4.0 11.8 - - - +
416A ILE 3.2 1.0 - - - -
417A GLU* 1.3 77.2 - - - +
419A GLU* 1.3 59.8 + - + +
420A LYS 3.2 8.6 - - - +
425A ARG* 3.5 27.2 + - - +
434A LEU* 4.0 22.2 - - + +
510A PHE* 2.7 51.3 + - - -
511A ALA* 4.3 11.3 + - - +
512A ALA 5.1 5.5 + - - -
513A ASP* 6.5 0.2 - - - +
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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
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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