Contacts of the helix formed by residues 359 - 366 (chain C) in PDB entry 2AYN
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 THR 359 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251C GLU* 3.6 35.9 + - + +
315C LYS* 3.6 31.0 - - + +
316C ILE 3.6 5.1 + - - -
317C SER* 3.9 9.2 + - - +
358C CYS* 1.3 76.7 - - - +
360C PRO* 1.3 74.9 - - + +
361C GLU* 4.0 11.3 - - - +
362C LEU* 2.9 31.4 + - - +
363C GLN* 2.9 11.8 + - - +
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Residues in contact with PRO 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C LYS* 4.2 22.7 - - + +
358C CYS 4.1 2.7 - - - +
359C THR* 1.3 84.4 - - + +
361C GLU* 1.3 76.5 + - + +
362C LEU 2.9 1.4 + - - -
363C GLN* 3.0 21.9 + - + +
364C GLU* 3.0 32.8 + - + +
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Residues in contact with GLU 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C GLU* 4.6 14.4 - - - +
359C THR* 4.0 14.4 - - - +
360C PRO* 1.3 89.7 - - + +
362C LEU* 1.3 58.1 + - - +
364C GLU* 4.1 16.6 - - - +
365C LYS* 3.5 24.3 + - - +
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Residues in contact with LEU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C ILE 2.7 26.2 - - - +
317C SER 3.4 18.6 - - - +
318C ARG* 4.1 7.6 - - - +
319C LEU* 4.3 8.1 - - + +
358C CYS* 3.6 15.9 - - + -
359C THR* 2.9 18.8 + - - +
361C GLU* 1.3 76.3 - - - +
363C GLN* 1.3 57.0 + - - +
364C GLU 3.0 1.6 - - - -
365C LYS* 2.6 38.0 + - + +
366C MET* 2.8 44.9 + - + +
407C ASP* 5.8 3.8 - - - +
413C ASN 5.7 3.1 - - - +
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Residues in contact with GLN 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C TYR* 3.2 63.7 + - + +
356C GLU* 4.0 9.3 + - - +
358C CYS* 3.8 19.9 + - + -
359C THR 2.9 15.7 + - - +
360C PRO* 3.0 31.8 - - - +
362C LEU* 1.3 74.7 - - - +
364C GLU* 1.3 63.0 + - + +
366C MET* 2.9 15.5 + - - -
367C VAL* 2.8 24.4 + - - +
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Residues in contact with GLU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C PRO* 3.0 22.9 + - + +
361C GLU* 4.1 20.2 - - - +
363C GLN* 1.3 77.6 - - + +
365C LYS* 1.3 66.3 + - + +
366C MET 3.1 0.9 + - - -
367C VAL* 3.2 19.7 + - - +
368C SER* 4.2 3.3 + - - -
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Residues in contact with LYS 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C GLU 3.5 17.0 - - - +
362C LEU* 2.6 20.6 + - + +
364C GLU* 1.3 78.7 - - + +
366C MET* 1.3 54.4 + - + -
368C SER* 3.5 17.8 + - - -
369C PHE* 4.2 9.7 - - - -
407C ASP* 4.9 15.4 - - - +
409C ILE* 3.9 26.4 - - + +
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Residues in contact with MET 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C LEU* 4.6 10.8 - - + -
355C TYR* 3.7 30.5 - - + -
358C CYS* 3.9 18.8 - - + -
362C LEU* 2.8 34.3 + - + +
363C GLN* 2.9 10.7 + - - +
365C LYS* 1.3 77.8 - - - +
367C VAL* 1.3 57.7 + - - +
368C SER 3.7 0.2 - - - -
369C PHE* 4.7 2.0 - - - -
370C ARG* 2.7 36.2 + - - +
407C ASP* 5.8 1.6 - - - +
413C ASN 4.9 1.3 - - - +
414C CYS* 4.0 17.7 - - + -
415C GLY* 3.2 39.9 - - - +
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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