Contacts of the helix formed by residues 283 - 293 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ALA* 3.7 25.4 - - + -
280A GLU* 4.9 2.9 - - + -
281A PRO* 3.2 42.1 - - + +
282A PHE* 1.3 78.8 - - - +
284A PRO* 1.4 69.1 - - - +
285A GLU* 3.3 9.9 - - + +
286A ARG* 2.9 58.0 + - + +
287A LEU* 3.3 10.7 + - - +
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Residues in contact with PRO 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LYS* 3.4 24.9 - - - +
86A LEU* 3.4 28.2 - - + +
87A GLY* 3.9 0.9 - - - -
88A GLY 3.7 15.7 - - - +
89A GLU 3.8 28.9 - - - +
90A ALA* 3.8 1.1 - - - +
282A PHE* 3.5 25.8 - - + +
283A TYR* 1.4 80.5 - - - +
285A GLU* 1.3 57.9 + - - +
287A LEU* 3.1 5.0 + - - +
288A ALA* 2.9 29.8 + - - +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TYR* 6.0 0.3 - - - -
83A LYS* 3.6 34.2 - - + +
88A GLY 4.7 0.2 + - - -
283A TYR* 3.3 10.1 - - + +
284A PRO* 1.3 78.4 - - - +
286A ARG* 1.3 76.1 + - - +
288A ALA* 3.4 6.1 + - - +
289A GLY* 3.1 19.9 + - - -
56C ARG* 3.1 42.6 + - - +
57C GLU* 5.9 0.2 - - - +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLN* 5.3 2.3 + - - -
272A VAL* 5.0 5.7 - - - +
280A GLU* 2.8 35.2 + - - -
283A TYR* 2.9 49.1 + - + +
285A GLU* 1.3 88.2 + - - +
287A LEU* 1.3 57.5 + - - +
289A GLY* 3.7 1.7 + - - -
290A ARG* 3.3 21.5 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.7 13.9 - - + -
244A LEU* 4.0 7.0 - - + -
247A LEU* 3.7 30.3 - - + -
252A ARG 4.1 6.7 - - - +
253A GLY* 3.9 7.4 - - - +
256A ALA* 3.6 27.8 - - + -
282A PHE* 3.4 38.8 - - + -
283A TYR 3.3 1.4 + - - +
284A PRO 3.1 3.9 + - - +
286A ARG* 1.3 75.2 - - - +
288A ALA* 1.3 61.1 + - - +
289A GLY 3.2 1.3 - - - -
290A ARG* 3.4 17.2 - - - +
291A ILE* 2.8 35.6 + - + +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TYR* 4.5 12.1 - - + +
82A LEU* 3.5 30.2 - - + +
83A LYS* 3.9 18.6 - - + +
86A LEU* 3.8 2.6 - - + +
284A PRO 2.9 12.6 + - - +
285A GLU* 3.4 12.1 - - - +
287A LEU* 1.3 77.1 - - - +
289A GLY* 1.3 59.8 + - - +
291A ILE 3.4 0.3 + - - -
292A LEU* 3.2 31.6 + - - +
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Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLN* 3.8 30.1 - - - +
79A TYR* 4.2 15.1 + - - -
285A GLU 3.1 12.0 + - - -
286A ARG 4.1 2.5 - - - -
288A ALA* 1.3 77.9 - - - +
290A ARG* 1.3 58.3 + - - +
292A LEU* 3.4 1.8 + - - +
293A GLY* 2.9 27.5 + - - -
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLN* 4.4 3.1 - - - +
220A ALA* 5.3 0.8 - - - +
246A LYS 4.7 1.4 + - - -
247A LEU* 2.9 44.1 + - - +
249A GLY 3.0 28.1 + - - -
250A ASP* 3.9 1.6 - - - +
251A ALA* 2.6 30.1 + - - +
252A ARG* 2.8 60.7 + - - +
286A ARG 3.3 15.9 + - - +
287A LEU* 3.2 23.9 + - - +
289A GLY* 1.3 77.2 - - - +
291A ILE* 1.3 62.4 + - - +
293A GLY 3.3 5.0 + - - -
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER* 5.8 0.2 - - - -
37A ALA* 4.8 3.1 - - - +
38A LEU* 3.9 25.5 - - + +
41A ALA* 3.6 27.5 - - + +
43A VAL* 4.6 6.3 - - + -
82A LEU* 4.0 14.1 - - + -
86A LEU* 4.1 17.3 - - + -
252A ARG* 3.6 23.7 - - - +
253A GLY 3.9 15.9 - - - +
254A GLY* 4.1 14.1 - - - +
257A LEU* 5.0 4.0 - - + -
287A LEU* 2.8 36.6 + - + +
288A ALA 3.8 3.8 - - - +
290A ARG* 1.3 74.6 - - - +
292A LEU* 1.3 60.1 + - - +
293A GLY 3.6 4.7 + - - +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.5 19.0 - - + +
6A SER* 3.0 25.3 + - - -
9A LEU* 3.8 23.6 - - + +
34A ILE* 5.0 1.6 - - + -
37A ALA* 5.9 0.2 - - + -
38A LEU* 4.3 16.6 - - + -
75A LEU* 5.5 1.6 - - + -
78A VAL* 3.8 30.7 - - + -
79A TYR* 3.7 39.0 - - + +
82A LEU* 3.6 19.5 - - + -
288A ALA 3.2 18.1 + - - +
289A GLY 3.7 3.4 - - - +
291A ILE* 1.3 75.5 - - - +
293A GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 3.1 28.9 - - - -
5A LEU* 3.8 1.1 - - - -
6A SER* 3.3 27.9 - - - -
252A ARG* 3.8 34.0 - - - -
289A GLY 2.9 16.1 + - - -
290A ARG 3.3 2.9 + - - -
291A ILE 4.0 2.3 - - - +
292A LEU* 1.3 79.4 - - - +
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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