Contacts of the helix formed by residues 360 - 368 (chain C) in PDB entry 3COG
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 LEU 360 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C ASN* 5.2 1.2 + - - -
122C ARG* 3.7 45.1 - - - +
358C SER 3.8 2.8 + - - +
359C VAL* 1.3 75.5 - - - +
361C LYS* 1.3 62.3 + - - +
362C ASN* 4.4 4.5 - - + +
363C ASP* 3.0 30.4 + - - +
364C ARG* 2.9 25.1 + - - +
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Residues in contact with LYS 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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359C VAL 3.4 2.2 + - - -
360C LEU* 1.3 72.8 - - - +
362C ASN* 1.3 62.6 + - - +
364C ARG* 3.3 36.9 + - - +
365C ASP* 2.9 62.5 + - - +
369C ILE 5.8 0.8 + - - -
370C SER* 6.1 1.6 - - - +
371C ASP* 4.9 14.2 + - - +
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Residues in contact with ASN 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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360C LEU* 3.3 4.3 - - + +
361C LYS* 1.3 79.9 - - - +
363C ASP* 1.3 63.2 + - - +
365C ASP* 3.4 11.0 + - - +
366C VAL* 3.0 36.2 + - + +
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Residues in contact with ASP 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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118C ASN* 4.8 7.9 + - - +
122C ARG* 4.5 9.2 - - - -
134C PHE* 5.8 3.6 - - - -
359C VAL* 3.6 14.8 - - + +
360C LEU* 3.0 37.3 + - - +
362C ASN* 1.3 79.7 - - - +
364C ARG* 1.3 59.3 + - - +
366C VAL* 3.3 8.5 + - - +
367C LEU* 2.9 40.1 + - + +
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Residues in contact with ARG 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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352C ALA* 3.5 42.2 + - - +
356C HIS* 3.5 14.8 + - - -
357C ALA* 3.7 13.9 + - - +
359C VAL* 2.7 43.2 + - + +
360C LEU 2.9 17.1 + - - +
361C LYS* 3.4 46.0 - - - +
363C ASP* 1.3 76.2 - - - +
365C ASP* 1.3 58.4 + - - +
367C LEU* 3.2 3.3 + - - -
368C GLY 2.9 9.0 + - - -
369C ILE* 2.8 53.0 + - + +
371C ASP* 5.4 2.2 + - - -
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Residues in contact with ASP 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 LYS* 2.9 59.0 + - - +
362C ASN* 3.7 11.2 - - - +
364C ARG* 1.3 78.5 - - - +
366C VAL* 1.3 62.5 + - + +
368C GLY* 3.3 11.0 + - - -
369C ILE 4.8 5.6 - - - +
370C SER* 5.3 5.1 - - - +
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Residues in contact with VAL 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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111C ASP* 5.7 2.0 - - - +
362C ASN* 3.0 23.5 + - + +
363C ASP* 3.6 9.0 - - - +
364C ARG 3.3 0.2 - - - -
365C ASP* 1.3 77.9 - - + +
367C LEU* 1.3 68.2 + - + +
368C GLY 3.4 0.9 + - - -
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Residues in contact with LEU 367 (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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111C ASP* 3.4 57.4 - - + +
112C ASP* 3.8 23.6 - - + +
113C VAL 5.5 0.4 - - - +
118C ASN* 5.5 1.1 - - - +
163C THR* 3.7 16.1 + - - +
165C LYS* 4.4 7.8 + - - +
317C TYR* 5.0 0.3 + - - -
359C VAL* 4.4 12.8 - - + -
363C ASP* 2.9 32.4 + - + +
364C ARG 3.2 4.4 + - - +
366C VAL* 1.3 82.3 - - + +
368C GLY* 1.3 59.8 + - - +
369C ILE* 4.0 18.6 - - + -
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Residues in contact with GLY 368 (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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163C THR* 4.6 0.2 - - - -
317C TYR* 2.6 34.6 + - - -
364C ARG 2.9 4.3 + - - -
365C ASP* 3.3 7.7 + - - -
366C VAL 3.3 4.8 + - - -
367C LEU* 1.3 78.1 - - - +
369C ILE* 1.3 60.8 + - - +
370C SER* 3.0 11.6 + - - -
373C LEU* 3.7 3.5 - - - +
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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