Contacts of the helix formed by residues 335 - 341 (chain C) in PDB entry 1C2O
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 GLY 335 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295C PHE* 5.8 0.2 - - - -
333C ASP 3.2 1.2 + - - -
334C GLU* 1.3 77.8 - - - +
336C SER* 1.3 63.5 + - - +
337C TYR 3.5 0.2 - - - -
338C PHE* 3.4 16.0 + - - +
339C LEU* 3.5 14.2 + - - +
399C SER* 3.4 23.4 + - - -
402C VAL* 3.9 10.4 - - - +
403C GLY* 3.3 17.6 - - - -
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Residues in contact with SER 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ASP* 2.5 27.5 + - - -
334C GLU 3.1 0.2 + - - -
335C GLY* 1.3 71.0 - - - +
337C TYR* 1.3 68.5 + - - +
339C LEU* 2.8 21.6 + - - +
399C SER* 3.3 19.4 + - - -
442C TRP* 4.1 8.9 - - - -
443C MET* 3.2 50.8 + - - +
446C PRO* 3.6 7.3 - - - +
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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
----------------------------------------------------------
83C THR* 4.9 1.6 - - - +
86C TRP* 3.7 31.7 - + - +
124C TYR* 5.8 0.2 + - - -
334C GLU 4.0 2.4 + - - +
336C SER* 1.3 79.5 + - - +
338C PHE* 1.3 90.8 + + + +
339C LEU 2.9 6.8 + - - -
340C VAL* 3.0 25.8 - - - +
341C TYR* 3.8 27.1 + + - -
439C TRP* 3.2 45.3 - + - -
443C MET* 3.6 10.5 - - - +
446C PRO* 4.4 12.3 - - + +
447C HIS* 4.5 13.0 - + + +
449C TYR* 4.5 8.3 - + - -
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Residues in contact with PHE 338 (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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203C SER* 5.4 0.9 - - - -
294C ILE* 3.5 26.8 - - + +
295C PHE* 3.1 63.0 - + + -
297C PHE* 4.5 12.3 - + - -
334C GLU 3.7 22.4 - - - -
335C GLY* 3.8 9.6 - - - +
336C SER 3.3 0.6 - - - -
337C TYR* 1.3 88.3 - + - +
339C LEU* 1.3 63.5 + - - +
340C VAL 3.3 0.7 - - - -
341C TYR* 3.5 16.6 + + + +
402C VAL* 4.3 11.4 - - + -
447C HIS* 3.6 32.8 - + + -
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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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294C ILE* 3.9 10.1 - - + -
335C GLY 3.5 9.9 - - - +
336C SER* 2.8 12.9 + - - +
338C PHE* 1.3 78.0 - - - +
340C VAL* 1.3 62.8 + - - +
341C TYR 3.2 0.3 + - - -
343C VAL* 3.0 36.8 + - + +
346C PHE* 3.6 43.0 - - + +
395C ARG 4.6 0.2 - - - +
398C MET* 4.0 11.9 - - + +
399C SER* 3.5 37.0 - - - +
402C VAL* 3.6 30.5 - - + -
442C TRP* 4.5 5.2 - - + -
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Residues in contact with VAL 340 (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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76C LEU* 4.0 16.5 - - + +
77C TYR* 4.4 12.6 + - + +
337C TYR 3.0 20.0 - - - +
339C LEU* 1.3 76.6 - - - +
341C TYR* 1.3 79.3 + - + +
342C GLY 3.1 6.2 + - - -
343C VAL 4.8 0.2 + - - -
346C PHE* 4.4 14.4 - - - +
347C SER* 4.1 4.9 - - - -
348C LYS* 4.0 22.2 - - + +
439C TRP* 4.4 14.4 - - + -
442C TRP* 4.4 5.2 - - + -
443C MET* 3.4 26.9 - - + -
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Residues in contact with TYR 341 (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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74C ASP* 3.0 38.8 + - - -
76C LEU* 3.3 24.0 - - + -
83C THR* 3.2 16.6 - - - +
124C TYR* 5.8 2.9 - - - -
293C SER 4.9 1.2 - - - +
294C ILE* 3.5 13.9 - - + +
337C TYR* 3.8 39.5 + + - -
338C PHE* 3.8 17.0 - + + +
339C LEU 3.1 2.3 - - - -
340C VAL* 1.3 109.0 - - + +
342C GLY* 1.3 55.0 + - - -
439C TRP* 4.6 2.7 - + - -
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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