Contacts of the helix formed by residues 410 - 419 (chain A) in PDB entry 2WSK
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 PRO 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A ARG* 5.3 1.6 - - - +
408A ASP 4.0 5.6 - - - +
409A LEU* 1.3 99.0 - - + +
411A LEU* 1.3 66.0 + - - +
412A GLY* 4.2 2.9 - - - +
413A ALA* 3.0 27.0 + - + +
414A PHE* 3.3 10.2 + - - +
592A TRP 4.7 2.9 - - - +
593A GLN* 4.7 17.0 - - - +
597A LYS* 4.5 5.6 - - - +
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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
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403A PHE* 3.9 23.6 - - + -
409A LEU 3.5 3.6 + - - -
410A PRO* 1.3 71.3 - - - +
412A GLY* 1.3 61.8 + - - +
414A PHE* 3.5 2.6 + - + +
415A ALA* 3.1 17.5 + - - +
587A LEU* 3.9 26.2 - - + -
591A GLU 4.0 14.6 - - - +
592A TRP* 3.5 27.3 + - + +
593A GLN 5.1 1.0 + - - -
595A GLY 5.1 1.3 - - - +
596A PRO 3.9 19.1 - - - +
597A LYS* 4.2 21.6 - - + +
598A GLN 3.9 10.8 - - - +
599A LEU* 3.5 28.5 - - + -
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Residues in contact with GLY 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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410A PRO* 3.0 2.9 - - - +
411A LEU* 1.3 77.1 - - - +
413A ALA* 1.3 65.5 + - - +
415A ALA* 3.3 3.3 + - - +
416A GLY* 3.0 18.9 + - - -
592A TRP* 3.5 31.8 + - - -
593A GLN* 6.0 1.8 - - - -
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Residues in contact with ALA 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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399A ALA* 6.0 0.7 - - + -
409A LEU* 4.0 23.1 - - + -
410A PRO* 3.0 22.9 + - + +
412A GLY* 1.3 75.4 - - - +
414A PHE* 1.3 63.0 + - - +
416A GLY* 3.1 4.7 + - - -
417A ARG* 3.0 30.3 + - + +
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Residues in contact with PHE 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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399A ALA* 5.8 0.7 - - - -
400A ALA* 5.2 5.6 - - + -
403A PHE* 3.3 65.1 - + + -
404A TRP* 4.0 9.9 - + - -
409A LEU* 4.1 9.3 - - + +
410A PRO 3.3 3.3 + - - +
411A LEU* 3.8 8.1 - - + +
412A GLY 3.2 0.6 - - - -
413A ALA* 1.3 74.7 - - - +
415A ALA* 1.3 72.3 + - + +
416A GLY 2.9 1.3 - - - -
417A ARG* 3.0 10.6 + - + +
418A PHE* 2.9 36.8 + + + +
502A THR* 3.7 32.1 - - + -
599A LEU* 4.9 11.2 - - + -
601A ILE* 4.3 22.2 - - + -
611A ILE* 5.2 6.1 - - + -
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Residues in contact with ALA 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 4.0 + - - +
412A GLY 3.3 5.4 + - - +
414A PHE* 1.3 85.7 - - + +
416A GLY* 1.3 61.5 + - - +
418A PHE* 3.5 1.5 + - - -
419A ALA* 3.1 24.1 + - - +
579A TRP* 3.6 29.6 - - + -
592A TRP* 3.5 39.0 - - + -
599A LEU* 5.1 1.1 - - + -
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Residues in contact with GLY 416 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A GLY 3.0 13.3 + - - -
413A ALA* 3.4 5.2 - - - -
414A PHE 2.9 1.2 - - - -
415A ALA* 1.3 75.4 - - - +
417A ARG* 1.3 64.9 + - - +
419A ALA* 3.3 12.0 + - - +
421A SER* 3.1 23.3 + - - -
422A SER* 4.4 2.0 + - - -
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Residues in contact with ARG 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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393A ASN* 4.2 4.6 + - - -
395A HIS* 4.0 36.5 + - - +
396A PHE* 3.4 36.6 - - + +
399A ALA* 3.6 28.3 - - + +
400A ALA* 5.9 1.3 - - + +
413A ALA* 3.0 15.8 + - - +
414A PHE* 3.0 11.1 + - + +
416A GLY* 1.3 76.3 - - - +
418A PHE* 1.3 63.3 + - - +
419A ALA 3.4 0.3 + - - -
420A ALA* 3.5 10.4 + - - -
421A SER* 3.1 34.9 + - - +
424A VAL* 4.2 16.4 - - - +
437A ASN* 4.6 1.6 + - - +
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Residues in contact with PHE 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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396A PHE* 4.6 0.4 - - - -
414A PHE* 2.9 34.8 + + + +
415A ALA* 3.7 6.7 - - - +
417A ARG* 1.3 78.6 - - - +
419A ALA* 1.3 57.4 + - - +
420A ALA 3.1 1.4 + - - -
502A THR* 4.6 5.8 - - + -
505A LEU* 3.1 32.8 - - + -
506A SER* 3.0 26.5 - - - -
507A GLN* 2.8 30.1 + - - +
570A TRP* 3.9 20.9 - + - -
579A TRP* 4.0 16.4 - + + -
601A ILE* 3.9 31.4 - - + -
603A LEU* 4.3 7.2 - - + -
609A ILE* 4.1 22.2 - - + -
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Residues in contact with ALA 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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415A ALA 3.1 16.7 + - - +
416A GLY* 3.3 5.4 + - - +
417A ARG 3.2 0.6 - - - -
418A PHE* 1.3 73.6 - - - +
420A ALA* 1.3 67.7 + - - +
421A SER 3.2 3.2 + - - -
422A SER* 3.6 12.8 + - - +
507A GLN* 3.3 18.6 - - - +
569A TRP* 3.6 6.4 - - - -
570A TRP* 4.3 17.7 - - + -
579A TRP* 4.5 8.7 - - + -
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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