Contacts of the helix formed by residues 403 - 409 (chain F) in PDB entry 5YWB
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 403 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401F HIS 3.4 0.6 + - - -
402F LEU* 1.3 89.5 - - - +
404F THR* 1.3 60.8 + - - +
405F SER* 3.1 10.5 - - - -
406F ASN* 3.0 25.8 + - - +
407F LEU 3.4 0.7 + - - -
617F ALA* 3.5 10.6 + - - -
618F GLU 2.6 29.7 + - - -
619F ILE* 3.8 16.2 - - - +
729F GLU* 5.0 2.9 - - - -
1215F ARG* 4.2 4.5 - - - +
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Residues in contact with THR 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402F LEU* 4.0 1.2 + - - -
403F SER* 1.3 70.0 - - - +
405F SER* 1.3 58.2 + - - +
406F ASN 3.2 0.2 - - - -
407F LEU* 3.1 30.5 + - + -
408F SER* 2.9 29.0 + - - +
688F TRP* 5.1 7.0 - - - -
724F LEU* 5.8 2.1 - - - +
729F GLU* 4.2 15.6 + - - +
1211F LEU* 5.3 2.0 - - + +
1212F THR* 4.2 17.5 - - + +
1215F ARG* 3.8 15.6 + - - +
1480F GLU* 3.9 26.0 - - - +
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Residues in contact with SER 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403F SER* 3.1 8.7 - - - -
404F THR* 1.3 78.1 - - - +
406F ASN* 1.3 59.8 + - - +
408F SER* 2.7 23.4 + - - -
409F MET* 3.2 13.2 - - - +
617F ALA* 6.4 0.7 - - - -
686F PHE* 5.9 0.7 - - - -
688F TRP* 3.3 51.3 - - - +
689F THR* 5.2 2.5 - - - -
730F MET* 5.2 3.6 - - - +
2501F ADP 5.0 0.2 - - - -
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Residues in contact with ASN 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402F LEU* 4.3 7.4 - - + +
403F SER* 3.0 13.6 + - - +
405F SER* 1.3 78.3 + - - +
407F LEU* 1.3 60.1 - - - +
408F SER 3.1 0.2 - - - -
409F MET* 2.8 36.0 + - - +
411F GLU* 5.4 2.5 - - + +
412F MET* 3.3 19.9 + - + +
616F SER* 4.0 10.6 - - - +
617F ALA* 3.1 50.5 + - - +
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Residues in contact with LEU 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402F LEU* 4.4 14.8 - - + +
403F SER 3.4 3.9 + - - +
404F THR* 3.1 35.5 + - + +
406F ASN* 1.3 78.0 - - - +
408F SER* 1.3 62.2 + - - +
409F MET 3.3 6.9 - - - +
412F MET* 3.3 27.7 - - - +
413F THR* 4.8 2.3 + - - -
414F ALA* 5.0 3.6 - - + +
417F ILE* 5.0 1.3 - - + -
1208F VAL* 3.9 36.8 - - + +
1209F GLU* 4.7 9.9 - - - +
1211F LEU* 4.8 10.1 - - + -
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Residues in contact with SER 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404F THR* 2.9 12.0 + - - +
405F SER* 2.7 26.7 + - - -
407F LEU* 1.3 77.8 - - - +
409F MET* 1.3 69.0 + - - +
1476F THR* 3.0 28.2 + - - +
1479F GLY* 4.9 9.7 - - - -
1480F GLU* 3.9 27.1 - - - -
1481F ASN* 4.5 8.5 + - - +
2501F ADP 4.3 10.1 + - - -
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Residues in contact with MET 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F SER 3.2 16.4 - - - +
406F ASN* 2.8 23.6 + - - +
407F LEU 3.3 6.8 - - - +
408F SER* 1.3 95.0 - - - +
410F GLY* 1.3 66.0 + - - +
411F GLU* 3.2 10.3 + - + +
412F MET 3.5 3.3 + - - -
413F THR* 3.8 5.0 + - - -
1476F THR* 4.4 5.8 - - + -
1481F ASN* 5.4 7.9 - - - +
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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