Contacts of the helix formed by residues 53 - 61 (chain C) in PDB entry 5NC5
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 ASP 53 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B GLN* 5.1 1.2 + - - -
235B ILE* 3.9 28.9 - - + +
238B THR* 4.7 7.1 - - - +
52C ALA* 1.3 77.7 - - - +
54C ALA* 1.3 70.9 + - - +
55C LYS* 2.8 18.5 + - - +
56C THR* 2.5 39.3 + - - -
57C VAL* 2.9 10.5 + - - +
83C ASP 4.1 2.2 - - - -
84C SER* 4.1 7.9 - - - +
726C GLN* 4.3 17.0 + - - +
813C SER 5.9 0.2 - - - +
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASP* 1.3 74.4 + - - +
55C LYS* 1.3 58.1 + - - +
57C VAL* 3.7 2.8 - - - +
58C GLN* 2.8 31.0 + - - +
82C SER* 3.4 23.2 - - - +
83C ASP* 3.7 22.2 + - - -
84C SER* 3.7 6.1 - - - +
813C SER 3.2 27.4 + - - +
815C ARG 4.2 1.6 - - - +
816C LEU* 3.8 13.4 - - + +
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Residues in contact with LYS 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B GLY* 4.8 7.1 - - - -
53C ASP* 3.1 10.8 + - - +
54C ALA* 1.3 80.7 - - - +
56C THR* 1.3 62.1 + - - +
58C GLN* 4.4 4.6 - - + +
59C ASP* 3.0 51.5 + - - +
813C SER 5.1 0.2 + - - -
816C LEU* 3.8 17.9 - - + -
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLN* 3.8 24.7 + - - +
238B THR* 4.4 9.2 - - + +
239B ARG* 4.0 17.0 - - - +
763B ILE* 5.2 4.7 - - + -
49C TYR* 4.6 7.2 - - + -
52C ALA* 4.5 1.6 - - + -
53C ASP* 2.5 35.1 + - - -
55C LYS* 1.3 78.4 - - - +
57C VAL* 1.3 61.6 + - - +
59C ASP* 3.4 3.2 + - - -
60C THR* 3.0 37.3 + - + +
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C TYR* 3.8 12.1 - - + -
52C ALA* 3.6 26.5 - - + -
53C ASP 2.9 13.4 + - - +
54C ALA* 3.7 4.5 - - - +
56C THR* 1.3 74.3 - - - +
58C GLN* 1.3 61.7 + - - +
60C THR* 4.1 5.4 - - - -
61C VAL* 2.8 29.6 + - + +
62C THR 3.2 4.2 + - - -
82C SER* 4.1 10.5 - - - -
83C ASP 4.3 1.3 - - - +
86C GLY* 3.6 21.5 - - - +
87C THR 4.5 6.5 - - - +
88C VAL* 3.1 35.2 - - + -
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Residues in contact with GLN 58 (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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54C ALA 2.8 21.0 + - - +
55C LYS* 4.0 8.8 - - - +
56C THR 3.3 0.2 - - - -
57C VAL* 1.3 75.1 - - - +
59C ASP* 1.3 65.3 + - - +
62C THR* 3.4 16.8 + - - -
63C GLN* 3.0 43.9 + - - +
82C SER* 4.0 8.6 + - - -
816C LEU* 3.6 35.1 - - + +
817C GLU 4.3 1.4 - - - +
818C ARG* 3.4 43.5 + - - +
823C PRO* 6.1 0.4 - - - +
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Residues in contact with ASP 59 (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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763B ILE* 4.3 20.3 - - + +
766B GLY* 3.3 30.2 - - - +
767B ARG* 4.7 0.2 - - - -
768B VAL* 4.0 19.2 + - - +
55C LYS* 3.0 47.8 + - - +
56C THR* 3.9 3.7 - - - +
58C GLN* 1.3 82.7 + - - +
60C THR* 1.3 59.6 + - - +
63C GLN* 3.5 25.5 + - - +
64C VAL* 4.4 5.2 - - - +
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Residues in contact with THR 60 (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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239B ARG* 4.1 18.8 - - - +
763B ILE* 3.4 31.2 - - + -
768B VAL* 4.2 15.7 - - + +
49C TYR* 3.6 15.2 - - - -
56C THR* 3.0 24.3 + - + +
57C VAL 4.0 0.3 + - - -
59C ASP* 1.3 79.3 - - - +
61C VAL* 1.3 72.2 + - - +
64C VAL* 3.2 21.1 - - - +
117C LEU 4.3 3.6 - - - +
118C LEU* 4.4 0.7 - - - +
119C PRO* 3.7 19.7 - - - +
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA* 4.3 14.6 - - + -
48C SER 6.4 0.4 - - - -
49C TYR* 4.4 7.6 - - + -
57C VAL* 2.8 17.8 + - + +
60C THR* 1.3 90.6 - - - +
62C THR* 1.3 66.5 + - - +
63C GLN 3.4 0.9 - - - -
64C VAL* 3.2 4.9 + - - +
65C ILE* 3.0 41.3 + - + +
88C VAL* 4.0 20.0 - - + -
118C LEU* 4.4 8.5 - - + +
119C PRO* 3.9 6.5 - - + -
122C VAL* 3.8 30.7 - - + -
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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