Contacts of the helix formed by residues 69 - 86 (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 THR 69 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C SER* 3.3 8.2 + - - -
68C LEU* 1.3 87.1 - - + +
70C PRO* 1.4 63.3 - - - +
71C ALA* 3.2 4.5 - - - -
72C GLU* 3.2 43.9 + - - +
73C VAL* 3.7 4.0 + - - +
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Residues in contact with PRO 70 (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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16C LEU* 5.1 10.3 - - + +
20C GLY 3.5 17.5 - - - +
22C ILE* 3.7 41.1 - - + +
64C VAL* 4.1 17.0 - - + +
67C SER* 3.6 13.9 - - - +
68C LEU 3.4 9.9 - - - +
69C THR* 1.4 85.6 - - - +
71C ALA* 1.3 60.7 + - + +
72C GLU 3.2 0.2 - - - -
73C VAL* 3.0 8.0 + - + +
74C ILE* 2.8 35.5 + - - +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 3.6 35.1 - - + +
16C LEU* 4.3 26.6 - - + +
69C THR* 3.2 2.8 - - - -
70C PRO* 1.3 81.6 - - - +
72C GLU* 1.3 58.3 + - + +
74C ILE* 3.8 3.0 - - - +
75C LEU* 2.8 39.1 + - - +
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C THR* 3.2 35.3 + - - +
71C ALA* 1.3 80.3 - - + +
73C VAL* 1.3 58.1 + - + +
75C LEU* 4.2 5.1 - - - +
76C ALA* 3.1 30.1 + - - +
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ALA* 4.5 1.6 - - - +
62C LYS* 3.6 35.6 + - + +
64C VAL* 3.7 24.9 - - + -
67C SER* 3.4 30.5 - - - +
69C THR* 3.9 6.5 - - - +
70C PRO* 3.0 7.9 + - + +
72C GLU* 1.3 75.8 - - + +
74C ILE* 1.3 60.5 + - - +
76C ALA* 4.0 3.9 - - - +
77C THR* 2.8 34.5 + - - +
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Residues in contact with ILE 74 (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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13C ILE* 6.2 1.8 - - + -
16C LEU* 4.7 4.9 - - + -
22C ILE* 3.8 28.3 - - + -
27C LEU* 5.3 9.4 - - + +
30C THR* 4.6 21.3 - - + -
31C LEU* 4.8 10.1 - - + -
34C ILE* 3.6 30.3 - - + -
55C VAL* 5.3 2.2 - - + -
59C ALA* 5.0 7.9 - - + -
64C VAL* 3.9 15.9 - - + -
70C PRO 2.8 22.8 + - - +
71C ALA* 3.9 2.9 - - - +
73C VAL* 1.3 75.1 - - - +
75C LEU* 1.3 68.8 + - + +
77C THR* 3.1 7.5 + - - -
78C VAL* 3.0 27.6 + - + +
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Residues in contact with LEU 75 (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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5C LEU* 3.6 38.6 - - + -
9C LEU* 4.9 16.4 - - + +
13C ILE* 3.5 33.0 - - + -
34C ILE* 6.5 0.9 - - + -
71C ALA 2.8 21.5 + - - +
72C GLU* 4.2 4.5 - - - +
74C ILE* 1.3 77.3 - - + +
76C ALA* 1.3 55.8 + - - +
78C VAL* 3.4 7.5 + - + +
79C TYR* 3.1 28.5 + - - +
292C LEU* 5.7 0.9 - - - +
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LYS* 4.3 4.9 - - - +
72C GLU 3.1 21.7 + - - +
73C VAL* 4.0 4.9 - - - +
75C LEU* 1.3 73.1 - - - +
77C THR* 1.3 65.7 + - - +
79C TYR* 4.0 5.6 - - - +
80C GLU* 3.2 40.4 + - - +
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Residues in contact with THR 77 (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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55C VAL* 3.2 42.6 - - + +
58C GLU* 3.9 20.5 - - + +
59C ALA* 3.9 7.3 - - - +
62C LYS* 3.2 29.0 + - - +
73C VAL 2.8 22.1 + - - -
74C ILE* 3.1 6.3 + - - -
76C ALA* 1.3 76.4 - - - +
78C VAL* 1.3 58.7 + - - +
80C GLU* 4.0 1.8 - - - +
81C ALA* 2.9 33.6 + - - +
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Residues in contact with VAL 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 6.0 0.7 - - + -
34C ILE* 3.8 40.2 - - + -
51C PHE* 3.7 18.2 - - + -
55C VAL* 3.8 22.4 - - + -
74C ILE 3.0 14.1 + - - +
75C LEU* 3.6 9.4 - - + +
77C THR* 1.3 76.4 - - - +
79C TYR* 1.3 54.8 + - - +
81C ALA 3.6 0.2 - - - -
82C LEU* 2.7 38.8 + - + +
292C LEU* 3.8 28.5 - - + -
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Residues in contact with TYR 79 (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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75C LEU 3.1 16.9 + - - +
76C ALA* 4.0 6.5 - - - +
77C THR 3.5 0.2 - - - -
78C VAL* 1.3 76.4 - - - +
80C GLU* 1.3 70.4 + - + +
82C LEU* 3.7 1.4 - - - +
83C LYS* 2.9 42.3 + - + +
285C GLU* 2.8 41.2 + - + +
288C ALA* 4.5 4.7 - - + +
289C GLY* 4.6 19.5 - - - -
292C LEU* 4.1 24.6 - - + +
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Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LYS* 3.4 22.0 + - - -
76C ALA* 3.2 25.6 + - - +
77C THR* 4.1 2.0 - - - +
79C TYR* 1.3 87.5 - - + +
81C ALA* 1.3 59.3 + - - +
83C LYS* 3.9 8.4 - - + +
84C GLU* 3.0 29.8 + - - +
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Residues in contact with ALA 81 (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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51C PHE* 3.6 19.2 - - + -
54C ARG* 3.4 21.3 + - - +
55C VAL* 4.2 7.6 - - + -
58C GLU* 3.6 21.0 + - - +
77C THR 2.9 21.1 + - - +
78C VAL 3.7 0.7 - - - +
80C GLU* 1.3 73.4 - - - +
82C LEU* 1.3 60.0 + - - +
84C GLU 3.5 0.2 + - - -
85C ALA* 2.9 31.9 + - - +
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Residues in contact with LEU 82 (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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38C LEU* 4.7 3.6 - - + -
51C PHE* 3.5 14.3 - - + -
78C VAL* 2.7 21.8 + - + +
79C TYR 3.7 4.0 - - - +
81C ALA* 1.3 70.0 - - - +
83C LYS* 1.3 65.1 - - - +
85C ALA* 3.1 1.8 + - - -
86C LEU* 3.0 40.8 + - + +
257C LEU* 4.0 32.5 - - + -
288C ALA* 3.5 36.3 - - + +
291C ILE* 3.8 21.5 - - + -
292C LEU* 3.6 23.6 - - + -
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Residues in contact with LYS 83 (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* 2.9 31.4 + - + +
80C GLU* 3.9 8.1 - - + +
82C LEU* 1.3 72.5 - - - +
84C GLU* 1.3 55.1 + - - +
86C LEU 3.4 0.9 + - - -
87C GLY 3.4 4.5 + - - -
88C GLY* 2.8 52.9 + - - +
89C GLU* 2.8 30.7 + - - -
284C PRO* 3.4 8.6 - - - +
285C GLU* 3.8 40.4 - - + +
288C ALA* 3.9 16.8 - - + +
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Residues in contact with GLU 84 (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 ARG* 3.4 25.4 - - - +
80C GLU 3.0 20.0 + - - +
81C ALA 3.8 3.8 - - - +
83C LYS* 1.3 78.9 - - - +
85C ALA* 1.3 57.1 + - - +
87C GLY* 2.8 24.6 + - - -
88C GLY* 3.4 15.2 + - - +
260C ARG* 4.3 4.9 + - - -
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PHE* 4.6 7.2 - - + -
54C ARG* 3.5 16.2 - - - +
81C ALA 2.9 21.7 + - - +
82C LEU 3.1 2.4 + - - +
84C GLU* 1.3 73.2 - - - +
86C LEU* 1.3 54.6 + - - +
87C GLY 3.3 1.1 - - - -
257C LEU* 3.8 24.8 - - + +
260C ARG* 2.8 33.0 + - - +
261C HIS* 5.2 4.5 + - + -
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Residues in contact with LEU 86 (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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82C LEU* 3.0 36.0 + - + +
83C LYS 3.9 4.7 - - - +
85C ALA* 1.3 77.1 - - - +
87C GLY* 1.3 56.2 + - - +
88C GLY 3.7 1.3 - - - -
256C ALA* 4.0 7.9 - - + +
257C LEU* 3.7 40.8 - - + +
260C ARG* 3.6 14.5 + - - +
267C ILE* 4.2 8.7 + - + +
282C PHE* 3.7 13.2 - - + -
284C PRO* 3.6 25.0 - - + +
287C LEU* 4.1 23.6 - - + -
288C ALA* 3.8 25.8 - - - +
291C ILE* 4.1 3.1 - - + -
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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
------------------------------------------------------------
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