Contacts of the helix formed by residues 399 - 412 (chain A) in PDB entry 2YD0
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 TYR 399 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A LEU* 3.6 30.3 - - + -
349A MET* 6.1 1.1 - - + -
384A PHE* 4.3 6.9 - + + -
394A LEU 3.5 26.3 + - - -
395A LYS* 4.2 4.0 - - - +
396A VAL* 2.9 30.5 + - + +
398A ASP* 1.4 83.3 + - + +
400A PHE* 1.3 68.8 + - - +
401A PHE 3.5 1.6 - - - -
402A GLY* 3.1 14.7 + - - -
403A LYS* 4.1 6.5 + - - +
670A ILE* 4.2 19.7 - - + -
671A MET* 3.7 24.6 - - + +
722A VAL* 4.3 1.6 - - - +
723A SER* 4.0 18.1 + - - -
726A MET* 3.4 25.4 - - + +
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Residues in contact with PHE 400 (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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381A PHE* 4.1 14.6 - + - -
384A PHE* 3.6 46.9 - + + -
396A VAL 3.5 3.4 + - - -
397A GLY* 3.3 15.8 + - - +
398A ASP 3.5 0.2 - - - -
399A TYR* 1.3 72.5 - - - +
401A PHE* 1.3 71.8 + - - +
402A GLY 2.8 1.7 + - - -
403A LYS* 3.0 22.9 + - + +
404A CYS* 3.7 19.8 + - - -
442A ALA* 3.7 37.2 - - + -
443A CYS* 4.1 5.8 - - - -
446A ASN* 3.6 35.7 - - + -
604A MET 5.3 3.8 - - - -
605A ASN* 5.5 1.1 - - - -
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Residues in contact with PHE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A GLY 4.9 0.6 + - - -
398A ASP 5.0 3.1 - - - +
400A PHE* 1.3 80.7 - - - +
402A GLY* 1.3 54.9 + - - +
404A CYS* 2.6 37.2 + - - +
405A PHE* 3.3 18.5 + - + -
603A GLY 5.1 0.6 + - - +
604A MET* 4.2 34.3 + - + +
634A ASN* 4.4 21.1 - - + +
637A ALA* 6.0 1.3 - - + -
671A MET* 5.1 7.0 - - + -
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Residues in contact with GLY 402 (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 TYR 3.1 11.0 + - - -
400A PHE 2.8 6.5 + - - -
401A PHE* 1.3 75.2 - - - +
403A LYS* 1.3 59.9 + - - -
405A PHE* 3.4 14.5 + - - +
406A ASP* 3.2 26.6 + - - +
671A MET* 4.8 9.8 - - - -
675A GLN* 5.3 3.1 - - - -
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Residues in contact with LYS 403 (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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380A LYS* 4.6 19.5 - - + +
383A GLU* 5.5 1.1 - - - -
384A PHE* 4.1 29.6 - - + -
399A TYR* 4.5 4.0 - - - +
400A PHE* 3.0 16.1 + - + +
401A PHE 2.9 0.2 + - - -
402A GLY* 1.3 75.5 - - - +
404A CYS* 1.3 64.1 + - - +
406A ASP* 2.9 26.8 + - - +
407A ALA 3.0 10.7 + - - -
439A ASP* 3.7 39.1 - - + +
442A ALA* 6.1 0.9 - - + -
443A CYS* 4.8 4.5 - - - -
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Residues in contact with CYS 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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400A PHE* 3.7 22.9 - - - -
401A PHE* 2.6 20.2 + - - +
403A LYS* 1.3 70.4 - - - +
405A PHE* 1.3 61.7 + - - +
407A ALA* 3.1 7.7 + - - +
408A MET* 3.1 25.2 + - + +
443A CYS* 2.1 50.9 - - + -
604A MET* 3.6 24.9 - - + -
605A ASN 6.5 0.4 - - - -
606A GLY 5.5 2.5 - - - +
607A TYR* 3.8 9.8 - - + -
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Residues in contact with PHE 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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401A PHE* 3.3 21.7 + - + -
402A GLY* 3.7 11.0 - - - +
404A CYS* 1.3 73.5 - - - +
406A ASP* 1.3 68.9 + - - +
408A MET* 3.2 23.4 + - - +
409A GLU* 3.3 10.2 + - - +
604A MET* 3.6 32.3 - - + -
609A ILE* 5.9 0.2 - - + -
637A ALA* 4.3 10.3 - - + -
638A SER* 3.8 18.2 - - - -
641A ASN* 3.4 45.4 + - + +
642A ASN* 4.4 5.8 - - - -
645A GLN* 5.5 0.2 + - - -
671A MET* 6.4 0.4 - - + -
675A GLN* 3.2 35.0 - - + +
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Residues in contact with ASP 406 (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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402A GLY 3.2 19.8 + - - +
403A LYS* 2.9 23.4 + - - +
405A PHE* 1.3 75.8 - - - +
407A ALA* 1.3 64.7 + - - +
409A GLU* 3.0 22.9 + - - +
410A VAL* 3.8 2.8 + - - +
435A ASP* 5.0 11.1 - - - +
439A ASP* 4.1 12.4 - - - +
678A ASN* 5.3 6.9 + - - -
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Residues in contact with ALA 407 (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 LYS 3.0 10.0 + - - +
404A CYS 3.1 8.5 + - - +
406A ASP* 1.3 77.0 - - - +
408A MET* 1.3 50.9 + - - +
410A VAL* 3.3 7.2 + - + +
411A ASP* 2.7 36.3 + - + +
435A ASP* 3.9 20.9 - - - +
436A VAL* 5.4 0.9 - - + -
439A ASP* 4.0 2.6 - - + +
440A LYS* 3.9 26.0 - - + +
607A TYR* 3.6 16.8 - - + +
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Residues in contact with MET 408 (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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404A CYS 3.1 14.9 + - - +
405A PHE* 3.5 24.7 - - - +
406A ASP 3.1 0.4 - - - -
407A ALA* 1.3 75.6 - - - +
409A GLU* 1.3 64.8 + - - +
412A ALA* 3.0 27.0 + - - +
530A PHE* 3.7 24.1 - - + -
604A MET* 5.1 5.4 - - + -
606A GLY 4.5 2.7 - - - +
607A TYR* 3.6 31.6 - - + -
608A TYR* 3.3 40.8 - - - +
609A ILE* 3.8 9.2 - - + -
645A GLN* 3.7 31.4 - - - +
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Residues in contact with GLU 409 (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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405A PHE 3.3 8.4 + - - +
406A ASP* 3.0 13.9 + - - +
408A MET* 1.3 78.1 - - - +
410A VAL* 1.3 62.6 + - - +
412A ALA* 3.8 6.1 + - - +
413A LEU* 3.9 14.8 - - - +
551A LYS* 5.7 4.6 - - - +
645A GLN* 5.8 0.7 - - - -
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Residues in contact with VAL 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 ASP 3.8 3.0 + - - +
407A ALA* 3.3 15.2 + - - +
409A GLU* 1.3 79.2 - - - +
411A ASP* 1.3 70.3 + - - +
412A ALA 3.1 1.4 + - - -
413A LEU* 3.1 24.4 + - + +
416A SER* 3.6 11.4 - - - +
434A ASP* 6.0 0.9 - - - +
435A ASP* 4.8 12.1 - - + +
436A VAL* 4.0 23.1 - - + -
876A MET* 5.6 5.2 - - + -
910A GLN* 3.3 46.4 - - + +
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Residues in contact with ASP 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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407A ALA* 2.7 23.8 + - + +
408A MET* 4.2 2.5 - - - -
409A GLU 3.5 0.2 - - - -
410A VAL* 1.3 76.3 - - + +
412A ALA* 1.3 59.6 + - - +
413A LEU 3.2 7.4 + - - +
416A SER* 2.6 29.5 + - - +
417A HIS 4.2 4.2 - - - +
436A VAL* 4.5 4.4 - - + +
440A LYS* 2.9 29.7 + - - +
528A LYS* 5.4 0.9 - - - +
529A GLY* 3.2 38.4 + - - +
530A PHE* 4.2 4.3 - - + -
548A HIS* 5.5 0.5 + - - -
549A TYR 5.1 0.5 - - - +
550A MET* 6.2 0.2 - - - +
607A TYR* 2.9 23.0 + - - +
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Residues in contact with ALA 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 MET 3.0 18.9 + - - +
409A GLU 4.2 4.7 - - - +
410A VAL 3.1 0.8 + - - -
411A ASP* 1.3 75.7 - - - +
413A LEU* 1.3 59.8 + - + +
530A PHE* 4.0 8.9 - - + -
549A TYR* 3.6 35.0 - - + -
550A MET* 3.5 9.6 - - - +
551A LYS* 3.1 38.1 + - + +
645A GLN* 4.7 1.3 - - - +
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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