Contacts of the helix formed by residues 440 - 444 (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 PRO 440 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348C LYS* 3.1 46.9 - - + +
350C ASN 5.0 1.3 - - - +
433C ARG* 2.5 21.9 + - - -
438C THR 4.7 0.7 - - - +
439C TRP* 1.3 86.9 - - + +
441C LEU* 1.3 61.5 + - - +
442C TRP* 3.2 22.9 - - + +
443C MET* 3.2 33.4 + - - +
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Residues in contact with LEU 441 (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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433C ARG* 3.1 40.4 - - - +
439C TRP 3.8 0.2 + - - -
440C PRO* 1.3 71.2 - - - +
442C TRP* 1.3 54.8 + - - +
444C GLY* 2.7 30.8 + - - -
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Residues in contact with TRP 442 (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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333C ASP* 5.0 3.5 - - - +
336C SER* 4.1 22.7 - - - -
339C LEU* 4.5 6.1 - - + -
340C VAL* 4.4 4.5 - - + -
346C PHE* 3.9 22.2 - + - -
347C SER 3.2 17.7 + - - -
350C ASN 3.0 20.4 + - - -
351C GLU* 3.7 17.0 - - + +
352C SER* 2.8 26.3 + - - -
395C ARG* 3.7 45.5 + - + +
396C ASP* 4.8 4.3 - - - +
399C SER* 5.3 3.8 - - - -
440C PRO* 3.2 20.9 - - + +
441C LEU* 1.3 78.7 - - - +
443C MET* 1.3 91.7 + - + +
444C GLY 3.2 0.8 + - - -
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Residues in contact with MET 443 (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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333C ASP* 3.5 8.9 - - - -
336C SER* 3.2 53.1 + - - +
337C TYR* 3.6 15.7 - - - +
340C VAL* 3.4 31.4 - - + -
348C LYS* 4.9 0.2 - - - -
439C TRP* 3.5 22.4 - - + -
440C PRO* 3.3 37.5 - - + +
441C LEU 2.8 3.4 + - - -
442C TRP* 1.3 96.6 - - + +
444C GLY* 1.4 66.7 + - - +
445C VAL 2.9 4.3 + - - -
446C PRO* 3.6 14.4 - - + -
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Residues in contact with GLY 444 (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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332C LYS* 4.1 9.6 - - - -
333C ASP* 3.8 7.9 - - - -
433C ARG* 3.0 30.4 + - - +
437C LEU* 4.6 0.5 - - - +
440C PRO 4.1 0.6 + - - -
441C LEU* 2.7 17.5 + - - -
442C TRP 3.2 1.4 + - - -
443C MET* 1.4 74.2 - - - +
445C VAL* 1.3 62.7 + - - -
446C PRO* 3.0 11.8 - - - +
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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