Contacts of the helix formed by residues 401 - 411 (chain F) in PDB entry 2Y1M
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 CYS 401 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381F CYS* 3.3 10.3 - - + -
384F CYS* 4.1 0.2 - - - -
387F ASN* 3.2 30.5 - - + -
388F ASP 3.3 23.8 - - - +
390F ASP* 3.8 5.6 - - - +
391F VAL* 4.2 1.3 - - - -
400F MET* 1.3 82.7 - - - +
402F THR* 1.3 61.5 + - + +
403F SER* 3.5 7.2 - - - -
404F CYS* 3.3 17.3 - - - +
405F LEU* 3.3 16.1 + - - +
1436F ZN 2.4 33.0 - - - -
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Residues in contact with THR 402 (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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390F ASP* 3.0 31.0 + - - +
391F VAL* 4.3 11.0 - - - -
401F CYS* 1.3 72.4 - - - +
403F SER* 1.3 66.7 + - - +
405F LEU* 3.4 10.1 + - - +
406F THR* 2.8 35.4 + - - -
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Residues in contact with SER 403 (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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387F ASN* 3.7 11.7 + - - -
401F CYS* 3.5 13.6 - - - -
402F THR* 1.3 82.3 - - - +
404F CYS* 1.3 58.2 + - - +
406F THR* 3.3 5.1 + - - -
407F SER* 3.0 31.6 + - - -
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Residues in contact with CYS 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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381F CYS* 4.7 0.2 - - - -
383F ILE* 3.5 39.5 - - + -
384F CYS* 3.6 13.2 - - - -
400F MET* 5.2 1.3 - - + -
401F CYS* 3.3 7.6 - - - +
403F SER* 1.3 77.2 - - - +
405F LEU* 1.3 67.5 + - - +
407F SER* 3.2 7.3 + - - -
408F TRP* 3.0 26.7 + - - +
417F PRO* 5.1 2.5 - - + -
1436F ZN 2.3 35.9 - - - -
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Residues in contact with LEU 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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391F VAL* 4.4 13.7 - - + -
393F ILE* 3.8 19.1 - - + -
400F MET* 3.6 25.4 - - + -
401F CYS 3.3 12.1 + - - +
402F THR* 3.7 11.4 - - - +
403F SER 3.4 0.4 - - - -
404F CYS* 1.3 77.0 - - - +
406F THR* 1.3 51.9 + - - +
408F TRP* 3.7 4.7 - - - +
409F GLN* 2.6 50.2 + - + +
415F GLY 4.9 0.7 - - - +
417F PRO* 3.9 10.8 - - + -
423F ILE* 3.7 27.1 - - + -
426F THR* 4.1 16.4 - - + -
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Residues in contact with THR 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 THR* 2.8 22.7 + - - -
403F SER* 3.8 5.6 - - - -
405F LEU* 1.3 73.3 - - - +
407F SER* 1.3 67.5 + - - +
408F TRP 3.1 1.6 - - - -
409F GLN* 2.9 10.6 + - + -
410F GLU* 2.8 50.1 + - + +
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Residues in contact with SER 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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403F SER* 3.0 18.1 + - - -
404F CYS* 3.6 11.1 - - - -
406F THR* 1.3 75.2 - - - +
408F TRP* 1.3 53.5 + - - +
410F GLU* 3.2 10.2 + - - +
411F SER* 2.8 38.5 + - - -
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Residues in contact with TRP 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 CYS 3.0 14.2 + - - +
405F LEU* 3.7 4.3 - - + +
407F SER* 1.3 78.7 - - - +
409F GLN* 1.3 67.6 + - + +
411F SER* 3.1 27.1 + - - -
412F GLU 5.3 1.6 - - - -
413F GLY* 3.2 35.0 + - - -
414F GLN* 3.5 13.1 - - + +
415F GLY 3.0 30.9 + - - -
417F PRO* 3.6 32.2 - - + -
420F ARG* 3.7 42.2 - - - -
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Residues in contact with GLN 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 LEU* 2.6 49.2 + - + +
406F THR* 2.9 15.0 + - + +
408F TRP* 1.3 77.9 - - + +
410F GLU* 1.3 63.0 + - + +
412F GLU* 3.6 8.1 + - - -
413F GLY* 3.8 7.6 + - - +
415F GLY* 5.2 6.3 + - - -
423F ILE* 4.5 15.8 - - - +
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Residues in contact with GLU 410 (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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406F THR* 2.8 44.7 + - + +
407F SER* 3.7 6.5 - - - +
409F GLN* 1.3 71.3 - - + +
411F SER* 1.3 58.3 + - - +
412F GLU 3.0 10.7 + - - -
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Residues in contact with SER 411 (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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407F SER 2.8 16.1 + - - -
408F TRP* 3.1 27.9 + - - -
410F GLU* 1.3 74.3 - - - +
412F GLU* 1.3 78.9 + - - +
413F GLY* 3.2 2.3 + - - -
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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