Contacts of the helix formed by residues 412 - 417 (chain C) in PDB entry 1CX2
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 SER 412 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C ASN* 3.3 3.2 + - - -
411C ASN* 1.3 79.9 - - - +
413C ILE* 1.3 58.0 + - - +
415C LEU* 4.2 9.6 - - - +
416C GLU* 2.6 69.7 + - - +
681C NAG 4.1 16.2 - - - -
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Residues in contact with ILE 413 (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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296C PRO* 4.7 2.9 - - + -
397C ILE* 5.3 0.4 - - + -
402C TYR* 3.9 17.3 - - + -
406C GLN 3.3 26.9 - - - +
407C PHE* 3.6 33.0 - - + +
410C ASN* 3.3 19.1 + - + +
411C ASN 3.0 2.0 + - - -
412C SER* 1.3 78.4 - - - +
414C LEU* 1.3 58.6 + - - +
416C GLU* 3.8 0.6 - - - +
417C HIS* 2.9 41.9 + - + +
422C PHE* 3.8 21.3 - - + -
681C NAG 3.0 34.0 + - - +
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Residues in contact with LEU 414 (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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262C TYR* 4.3 19.7 + - + -
285C PHE* 5.0 5.2 - - + -
296C PRO* 4.3 9.1 - - + +
299C MET* 3.9 38.8 - - + +
300C MET* 4.0 14.4 - - + +
303C THR* 4.6 1.6 - - - +
410C ASN 4.6 2.8 + - - +
411C ASN 3.3 7.6 + - - +
413C ILE* 1.3 76.0 - - - +
415C LEU* 1.3 62.5 + - + +
418C GLY* 2.9 31.6 + - - +
419C LEU* 3.6 25.8 - - + -
422C PHE* 3.6 36.3 - - + -
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Residues in contact with LEU 415 (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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257C ILE* 3.5 40.7 - - + +
262C TYR* 3.9 28.0 + - + -
282C ASN 5.5 1.3 - - - +
285C PHE* 3.7 19.3 - - + -
411C ASN* 3.1 45.0 + - - +
412C SER* 3.4 8.9 + - - +
414C LEU* 1.3 80.0 - - + +
416C GLU* 1.3 66.1 + - - +
418C GLY* 4.3 3.3 + - - -
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Residues in contact with GLU 416 (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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412C SER* 2.6 53.4 + - - +
413C ILE* 3.8 2.2 - - - +
415C LEU* 1.3 78.3 - - - +
417C HIS* 1.3 71.9 + - + +
418C GLY* 4.3 0.5 - - - -
681C NAG 4.7 9.0 - - - +
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Residues in contact with HIS 417 (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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397C ILE* 3.0 33.9 + - + +
398C GLU 5.3 2.2 + - - -
400C GLN* 4.0 10.5 + - + +
402C TYR* 2.7 46.5 + + - -
413C ILE* 2.9 27.7 + - + +
416C GLU* 1.3 80.8 - - + +
418C GLY* 1.3 59.7 + - - +
421C GLN* 3.2 38.2 + - + +
422C PHE* 4.0 4.0 - - + -
681C NAG 5.0 0.4 - - - -
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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