Contacts of the helix formed by residues 283 - 292 (chain C) in PDB entry 2CNW
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 TYR 283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C ALA* 3.6 28.3 - - + -
280C GLU* 5.4 6.5 - - + -
281C PRO* 3.5 45.1 - - + +
282C PHE* 1.3 78.4 - - - +
284C PRO* 1.4 70.0 - - + +
285C GLU* 3.2 4.9 - - + +
286C ARG* 2.9 36.9 + - + +
287C LEU* 3.3 11.3 + - - +
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Residues in contact with PRO 284 (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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83C LYS* 3.4 25.3 - - - +
86C LEU* 3.6 28.5 - - + +
87C GLY* 3.8 3.6 - - - -
88C GLY 3.5 22.9 - - - +
89C GLU 3.8 5.2 - - - +
90C ALA* 3.7 17.0 - - - +
282C PHE* 3.6 25.5 - - + +
283C TYR* 1.4 82.4 - - - +
285C GLU* 1.3 63.2 + - - +
287C LEU 3.4 0.9 + - - -
288C ALA* 3.0 24.2 + - - +
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Residues in contact with GLU 285 (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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79C TYR* 2.8 31.4 + - - +
83C LYS* 3.8 37.6 - - - +
88C GLY 4.4 1.2 + - - +
283C TYR* 3.2 3.9 - - + -
284C PRO* 1.3 78.6 - - - +
286C ARG* 1.3 70.8 + - + +
288C ALA* 3.2 6.9 + - - +
289C GLY* 3.1 18.7 + - - -
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Residues in contact with ARG 286 (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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280C GLU* 5.8 1.8 + - - -
283C TYR* 2.9 30.4 + - + +
285C GLU* 1.3 85.2 - - + +
287C LEU* 1.3 57.8 + - - +
289C GLY* 3.6 2.2 + - - +
290C ARG* 2.9 32.6 + - - +
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Residues in contact with LEU 287 (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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86C LEU* 4.1 9.2 - - + -
244C LEU* 3.8 6.3 - - + -
247C LEU* 3.9 21.8 - - + -
252C ARG 4.2 3.1 - - - +
253C GLY* 3.8 9.9 - - - +
256C ALA* 3.6 31.2 - - + -
282C PHE* 3.7 32.8 - - + -
283C TYR 3.3 5.7 + - - -
284C PRO 4.0 2.7 - - - +
286C ARG* 1.3 74.1 - - - +
288C ALA* 1.3 56.2 + - - +
290C ARG* 3.6 27.4 - - - +
291C ILE* 2.6 47.9 + - + +
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Residues in contact with ALA 288 (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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79C TYR* 4.5 11.9 - - + +
82C LEU* 3.5 20.6 - - + +
83C LYS* 3.9 27.6 - - + +
86C LEU* 3.8 2.3 - - + +
284C PRO 3.0 14.3 + - - +
285C GLU* 3.2 11.9 + - - +
287C LEU* 1.3 75.6 - - - +
289C GLY* 1.3 55.7 + - - +
291C ILE 3.5 0.2 + - - -
292C LEU* 3.1 37.4 + - - +
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Residues in contact with GLY 289 (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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4C GLN* 4.9 10.5 - - - +
79C TYR* 4.6 12.5 - - - -
285C GLU 3.1 9.7 + - - -
286C ARG* 3.8 3.4 - - - -
288C ALA* 1.3 76.4 - - - +
290C ARG* 1.3 61.0 + - - +
292C LEU* 3.5 5.0 + - - -
293C GLY* 2.8 26.0 + - - -
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Residues in contact with ARG 290 (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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220C ALA* 5.4 0.2 - - - +
246C LYS 4.8 0.8 + - - -
247C LEU* 2.9 42.4 + - - +
249C GLY 2.6 31.7 + - - -
250C ASP* 3.9 2.8 - - - +
251C ALA* 2.8 28.5 + - - +
252C ARG* 2.7 59.2 + - - +
286C ARG* 2.9 26.4 + - - +
287C LEU* 3.1 21.7 + - - +
289C GLY* 1.3 74.3 - - - +
291C ILE* 1.3 65.6 + - - +
293C GLY 3.0 2.9 + - - -
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Residues in contact with ILE 291 (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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6C SER* 5.7 0.5 + - - -
37C ALA 4.9 2.8 - - - +
38C LEU* 3.8 29.2 - - + -
41C ALA* 3.7 22.7 - - + +
43C VAL* 4.7 3.6 - - + -
82C LEU* 3.8 16.4 - - + -
86C LEU* 4.1 14.4 - - + -
252C ARG* 3.6 25.7 - - + +
253C GLY 3.9 15.7 - - - +
254C GLY* 4.0 15.7 - - - +
257C LEU* 4.7 9.0 - - + -
287C LEU* 2.6 34.4 + - + +
288C ALA 3.9 3.4 - - - +
290C ARG* 1.3 73.8 - - - +
292C LEU* 1.3 60.3 + - - +
293C GLY 3.4 1.7 + - - -
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Residues in contact with LEU 292 (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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4C GLN 4.6 0.2 - - - -
5C LEU* 3.5 18.6 - - + -
6C SER* 2.9 26.7 + - - -
9C LEU* 3.8 29.1 - - + +
34C ILE* 5.7 1.1 - - + -
37C ALA* 6.3 0.2 - - + -
38C LEU* 4.3 14.8 - - + -
75C LEU 5.7 0.4 - - - +
78C VAL* 3.8 21.3 - - + -
79C TYR* 4.1 39.5 - - + +
82C LEU* 3.6 19.3 - - + -
288C ALA 3.1 18.8 + - - +
289C GLY* 3.6 4.9 - - - +
291C ILE* 1.3 73.9 - - - +
293C GLY* 1.3 58.6 + - - +
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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