Contacts of the helix formed by residues 335 - 344 (chain C) in PDB entry 6O81
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 335 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C ILE* 6.3 0.7 - - + -
331C ASN* 3.3 33.7 - - + -
332C ALA* 3.5 21.5 - - + +
333C PRO 3.2 0.8 - - - -
334C SER* 1.3 79.2 - - - +
336C ILE* 1.3 61.5 + - - +
337C TYR* 3.2 8.7 - + - -
338C ARG* 2.9 50.5 + - + +
339C LEU* 3.7 15.6 + - + +
342C GLU* 4.5 3.5 + - - -
510E SER 5.1 0.4 - - - +
513E PRO* 3.7 38.3 + - + +
514E VAL* 3.6 30.5 - - + -
517E ARG* 4.1 16.3 + - - +
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Residues in contact with ILE 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ILE* 4.2 6.7 - - + -
240C LEU 3.9 12.3 - - - +
241C ALA 4.5 2.9 - - - +
242C ASN 5.3 0.2 - - - -
243C GLY* 4.0 14.8 - - - +
274C LEU* 3.7 29.2 - - + -
324C PHE* 3.7 29.4 - - + -
331C ASN* 4.7 3.6 - - + -
332C ALA 3.5 14.6 - - - +
333C PRO* 3.6 23.6 + - + +
334C SER 3.9 0.2 - - - -
335C TYR* 1.3 76.3 - - - +
337C TYR* 1.3 57.0 + - - +
339C LEU* 3.0 28.0 + - + +
340C MET* 2.8 25.0 + - + +
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Residues in contact with TYR 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ALA 4.3 10.7 + - - +
334C SER 3.2 25.0 + - - -
335C TYR* 3.8 11.4 - - - -
336C ILE* 1.3 78.3 - - - +
338C ARG* 1.3 67.2 + - + +
340C MET* 3.0 14.8 + - + +
341C SER* 2.7 34.1 + - - -
510E SER 5.0 0.9 + - - -
511E SER* 5.5 0.2 - - - -
514E VAL* 3.7 14.4 - - + +
291G LEU* 5.8 3.8 - - + -
292G THR* 4.5 18.3 + - - +
294G SER* 3.2 28.7 + - - -
295G ALA* 3.6 33.7 - - + -
298G ASP* 3.3 34.0 + - + +
299G GLU* 6.1 0.7 - - - -
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Residues in contact with ARG 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C TYR* 2.9 35.1 + - + +
337C TYR* 1.3 85.9 - - + +
339C LEU* 1.3 61.8 + - - +
341C SER* 3.0 29.8 + - - +
342C GLU* 2.8 54.7 + - - +
517E ARG* 3.3 51.5 - - - +
298G ASP* 3.7 11.2 + - - +
302G LYS* 3.8 25.5 - - - +
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Residues in contact with LEU 339 (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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271C MET* 3.9 23.3 - - + -
274C LEU* 3.7 21.1 - - + -
326C SER* 5.4 0.4 - - - +
328C ILE* 4.5 7.0 - - + -
331C ASN* 3.8 29.4 - - + +
335C TYR* 4.1 17.9 - - + +
336C ILE* 3.0 32.7 + - + +
338C ARG* 1.3 75.6 - - - +
340C MET* 1.3 57.9 + - - +
342C GLU* 3.9 19.7 - - - +
343C LEU* 2.8 42.8 + - + +
344C TYR* 4.4 0.2 - - - -
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Residues in contact with MET 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ALA* 3.8 27.6 - - + +
274C LEU* 3.8 25.4 - - + -
275C SER 3.4 24.2 - - - +
276C PRO* 3.6 22.4 - - + -
336C ILE* 2.8 8.5 + - + +
337C TYR* 3.0 19.7 + - - +
339C LEU* 1.3 76.7 - - - +
341C SER* 1.3 55.8 + - - +
342C GLU 3.4 0.2 - - - -
344C TYR* 3.0 47.6 + - - +
346C PRO* 5.8 0.9 - - - +
349C HIS* 4.6 11.9 + - + +
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Residues in contact with SER 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LYS* 3.0 16.2 + - - -
337C TYR* 2.7 15.6 + - - -
338C ARG* 3.0 39.7 + - - -
340C MET* 1.3 73.0 - - - +
342C GLU* 1.3 59.3 + - - +
344C TYR 4.3 3.0 - - - +
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Residues in contact with GLU 342 (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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84C ARG* 5.3 1.2 + - - -
87C LYS* 3.2 15.0 + - - +
328C ILE* 5.6 2.4 - - - +
335C TYR* 4.5 3.7 + - - -
338C ARG* 2.8 46.5 + - - +
339C LEU* 3.0 23.8 + - + +
341C SER* 1.3 79.8 - - - +
343C LEU* 1.3 70.4 + - + +
517E ARG* 3.4 17.5 - - - +
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ARG* 3.3 59.4 - - - +
87C LYS* 3.5 15.7 - - - +
271C MET* 3.8 39.5 - - + +
274C LEU* 4.0 18.4 - - + -
339C LEU* 2.8 16.2 + - + +
342C GLU* 1.3 91.8 - - + +
344C TYR* 1.3 77.2 + - + +
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Residues in contact with TYR 344 (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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80C ASN* 3.2 39.0 + - + +
81C MET* 4.5 5.1 - - + +
83C ARG* 3.6 32.3 - - + -
84C ARG* 4.2 5.6 - - + -
87C LYS* 3.4 21.1 + - - +
271C MET 3.9 11.3 + - - -
274C LEU* 2.5 46.8 + - + -
275C SER 4.8 0.2 - - - -
276C PRO* 4.6 3.4 - - + -
339C LEU 4.4 3.8 - - - -
340C MET* 3.0 46.7 + - - +
341C SER* 4.3 2.9 - - - +
343C LEU* 1.3 100.2 - - + +
345C HIS* 1.3 62.5 + - - +
346C PRO* 4.4 2.6 - - - +
349C HIS* 4.8 3.1 - - - +
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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
------------------------------------------------------------
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