Contacts of the helix formed by residues 422 - 432 (chain D) in PDB entry 5SUY
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 422 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420D HIS 3.7 2.0 + - - -
421D THR* 1.3 76.6 - - - +
423D MET* 1.3 64.5 + - - +
424D ALA* 3.4 11.6 + - - +
425D SER* 2.7 42.3 + - - -
426D VAL* 3.3 17.9 + - - +
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Residues in contact with MET 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C TYR* 3.7 60.6 - - + +
481C GLY* 4.1 23.1 - - - +
482C LEU* 4.0 11.7 - - + +
485C ALA* 5.1 4.0 - - - -
487C LEU* 3.8 17.0 - - + -
421D THR 3.5 2.1 + - - +
422D ASP* 1.3 73.0 - - - +
424D ALA* 1.3 63.2 + - - +
426D VAL* 3.3 3.8 + - - +
427D THR* 3.0 27.6 + - - -
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Residues in contact with ALA 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C LEU* 3.8 28.2 - - + +
422D ASP* 3.2 9.5 + - - +
423D MET* 1.3 77.7 - - - +
425D SER* 1.3 58.2 + - - +
427D THR* 3.4 2.4 + - - -
428D LYS* 3.0 46.9 + - - +
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Residues in contact with SER 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D LEU* 5.2 2.4 - - - +
421D THR* 4.3 10.3 - - - -
422D ASP* 2.7 33.6 + - - -
424D ALA* 1.3 74.3 - - - +
426D VAL* 1.3 58.7 + - - +
428D LYS* 3.4 10.3 + - - +
429D ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C TRP* 4.3 5.0 - - + -
462C LEU* 3.8 27.1 - - + -
466C VAL* 4.0 13.9 - - + -
478C TYR* 3.4 30.3 - - + +
482C LEU* 5.7 0.7 - - + -
417D LEU* 4.4 13.7 - - + -
418D SER 4.4 5.4 - - - +
421D THR* 3.7 25.3 - - + +
422D ASP 3.3 12.0 + - - +
423D MET 3.6 3.8 - - - +
425D SER* 1.3 73.3 - - - +
427D THR* 1.3 59.6 + - - +
429D ALA* 3.3 9.1 + - - +
430D MET* 2.9 26.7 + - + +
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Residues in contact with THR 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C LEU* 3.4 24.5 - - + +
487C LEU* 3.7 29.1 - - + +
488C ILE* 4.8 2.5 - - + -
505C PHE* 3.6 28.2 - - + -
508C LEU* 4.2 8.5 - - + -
423D MET 3.0 17.6 + - - -
424D ALA 3.7 5.4 - - - -
426D VAL* 1.3 76.3 - - - +
428D LYS* 1.3 53.5 + - - +
430D MET* 3.1 14.7 + - + +
431D ALA* 2.8 34.1 + - - +
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Residues in contact with LYS 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508C LEU* 3.6 47.7 + - + +
509C SER 4.6 7.7 + - - -
424D ALA* 3.0 35.6 + - - +
425D SER* 3.7 8.3 - - - +
427D THR* 1.3 73.2 - - - +
429D ALA* 1.3 63.6 + - - +
431D ALA* 3.3 8.6 + - - +
432D ALA* 3.2 21.1 + - - +
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Residues in contact with ALA 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C TRP* 4.4 4.8 - - + -
417D LEU* 4.0 26.5 - - + -
425D SER 2.9 14.8 + - - +
426D VAL 3.5 8.3 - - - +
428D LYS* 1.3 73.3 - - - +
430D MET* 1.3 62.7 + - - +
432D ALA* 3.2 17.5 + - - +
435D SER* 3.3 13.9 - - - -
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Residues in contact with MET 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453C PHE* 5.0 0.4 - - + -
458C VAL* 4.1 36.1 - - + +
461C TRP* 3.7 45.9 - - + -
462C LEU* 4.7 5.4 - - - -
482C LEU* 4.6 9.4 - - + -
488C ILE* 4.5 10.5 - - + -
505C PHE* 3.6 25.6 - - + -
426D VAL 2.9 14.0 + - - +
427D THR* 3.1 9.6 + - + +
429D ALA* 1.3 76.6 - - - +
431D ALA* 1.3 58.0 + - - +
432D ALA 4.0 0.3 - - - +
435D SER* 2.9 19.3 + - - -
437D LEU* 3.9 31.7 - - + +
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Residues in contact with ALA 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C PHE* 3.4 29.2 - - + -
508C LEU* 3.6 23.8 - - + -
427D THR 2.8 15.8 + - - +
428D LYS 3.7 5.8 - - - +
429D ALA 3.2 0.4 - - - -
430D MET* 1.3 74.7 - - - +
432D ALA* 1.3 63.5 + - - +
433D PRO* 3.9 1.9 - - - +
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Residues in contact with ALA 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D LYS 3.2 10.2 + - - +
429D ALA* 3.2 17.1 + - - +
430D MET 4.0 0.2 - - - +
431D ALA* 1.3 79.7 - - - +
433D PRO* 1.4 80.1 - - + +
434D GLU 3.5 0.5 + - - -
435D SER* 3.2 20.4 + - - -
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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