Contacts of the helix formed by residues 10 - 21 (chain A) in PDB entry 2C3O
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 GLY 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASP* 1.3 71.5 - - - +
11A ASN* 1.3 63.5 + - - +
13A ALA* 3.2 1.6 + - - +
14A THR* 2.9 29.1 + - - +
146A VAL* 3.9 6.4 - - - +
149A ALA* 4.0 18.2 - - - -
171A PHE* 3.8 8.5 - - - -
176A THR 2.9 27.1 + - - -
177A SER* 3.8 2.5 - - - -
179A GLU 3.6 0.6 + - - -
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Residues in contact with ASN 11 (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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9A ASP* 4.0 2.9 - - - +
10A GLY* 1.3 75.3 - - - +
12A THR* 1.3 57.9 + - - +
14A THR* 3.7 0.2 + - - -
15A ALA* 3.0 30.9 + - - +
32A PRO 2.8 20.8 - - - +
35A THR* 3.2 33.5 + - + +
36A MET* 3.2 21.7 - - + +
39A GLU* 4.5 0.4 - - - -
112A THR* 3.4 17.4 - - - +
171A PHE* 3.5 5.1 - - - -
177A SER* 2.9 39.2 + - - +
178A HIS* 3.5 7.8 - - - -
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Residues in contact with THR 12 (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 MET* 5.1 3.6 - - - +
8A THR* 2.8 40.7 - - + -
9A ASP* 3.0 17.6 + - - +
11A ASN* 1.3 74.6 - - - +
13A ALA* 1.3 58.4 + - - +
15A ALA* 3.8 1.6 - - - +
16A HIS* 3.0 30.5 + - - +
35A THR* 4.6 1.1 - - + -
39A GLU* 2.7 28.7 - - - +
43A TRP* 4.1 6.5 - - - -
1206B PRO* 3.8 24.7 - - + -
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Residues in contact with ALA 13 (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 MET* 5.2 3.1 - - - -
8A THR* 4.4 4.5 - - - +
9A ASP 2.9 18.0 + - - +
10A GLY 3.2 4.9 + - - +
12A THR* 1.3 79.0 + - - +
14A THR* 1.3 60.8 + - - +
16A HIS* 3.4 16.8 - - - +
17A VAL* 3.7 4.3 + - - +
146A VAL* 4.0 17.5 - - + +
150A HIS* 3.9 19.9 - - + +
183A ILE* 3.8 28.7 - - + -
185A VAL* 5.8 0.2 - - - -
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Residues in contact with THR 14 (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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10A GLY 2.9 16.7 + - - +
13A ALA* 1.3 72.0 - - - +
15A ALA* 1.3 58.2 + - - +
16A HIS 3.0 1.8 - - - -
17A VAL* 3.0 4.9 + - - +
18A ALA* 2.7 35.1 + - - +
36A MET* 3.1 23.2 - - - -
110A HIS* 4.1 7.1 - - - -
149A ALA* 3.3 33.7 - - + +
153A ALA* 3.9 16.9 - - - +
169A HIS* 3.8 6.3 - - - +
171A PHE* 3.6 20.5 - - + -
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Residues in contact with ALA 15 (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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11A ASN 3.0 17.5 + - - +
12A THR 3.8 4.5 - - - +
14A THR* 1.3 83.0 + - - +
16A HIS* 1.3 60.0 + - - +
18A ALA* 3.7 8.5 - - - +
19A TYR* 3.0 19.6 + - - +
36A MET* 4.0 14.1 - - + +
39A GLU* 4.0 25.8 - - + -
40A ALA* 5.4 0.6 - - + +
43A TRP* 3.3 17.2 - - + -
84A PHE* 4.6 6.0 - - + -
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Residues in contact with HIS 16 (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 MET* 4.4 24.0 - - + -
12A THR 3.0 17.3 + - - +
13A ALA* 3.4 9.0 - - - +
15A ALA* 1.3 79.4 - - - +
17A VAL* 1.3 69.4 + - - +
20A ALA 3.7 2.4 + - - -
43A TRP* 3.8 12.1 - - + -
48A ARG* 3.7 20.4 - - - -
150A HIS* 4.3 4.8 - + + -
185A VAL* 4.0 18.1 - - + +
186A LEU 3.1 29.0 + - - -
188A TYR* 3.0 46.1 + + - -
191A MET* 4.2 3.6 - - + -
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Residues in contact with VAL 17 (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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13A ALA 3.9 4.3 - - - +
14A THR 3.0 7.2 + - - +
16A HIS* 1.3 80.3 - - - +
18A ALA* 1.3 64.4 + - - +
20A ALA* 3.3 2.9 + - - +
21A MET* 3.2 25.0 + - + +
150A HIS* 3.5 49.6 - - + +
153A ALA* 3.7 10.8 - - + +
154A LEU* 3.5 38.1 - - + +
157A HIS* 4.2 5.4 - - + -
191A MET* 4.1 14.1 - - - -
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Residues in contact with ALA 18 (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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14A THR 2.7 20.3 + - - +
15A ALA 3.9 2.5 - - - +
17A VAL* 1.3 74.5 - - - +
19A TYR* 1.3 62.7 + - - +
21A MET 3.5 0.7 + - - -
22A SER* 2.8 30.9 + - - -
56A LEU* 5.9 0.4 - - - -
82A THR* 4.8 2.9 - - - +
84A PHE* 3.7 29.4 - - + -
110A HIS* 3.6 23.3 - - + -
157A HIS* 3.7 12.3 - - - -
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Residues in contact with TYR 19 (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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15A ALA 3.0 18.4 + - - +
18A ALA* 1.3 76.6 - - - +
20A ALA* 1.3 63.2 + - - +
22A SER 3.3 20.3 + - - +
40A ALA* 3.7 34.8 - - + -
43A TRP* 4.1 10.8 - + + -
44A ALA* 3.3 13.3 - - + -
48A ARG* 2.7 53.5 + - + +
49A LYS 3.8 10.5 - - - -
50A ASN* 3.5 5.6 - - - +
56A LEU* 3.2 51.2 + - + +
84A PHE* 5.5 1.3 - - - -
188A TYR* 3.6 24.2 - + - +
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Residues in contact with ALA 20 (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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16A HIS 3.7 1.8 + - - +
17A VAL 3.3 5.9 + - - +
19A TYR* 1.3 79.6 - - - +
21A MET* 1.3 57.6 + - + +
50A ASN* 3.5 5.3 - - - +
51A ILE* 2.9 39.9 + - + +
188A TYR* 3.4 31.0 - - + -
191A MET* 3.3 36.1 - - + -
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Residues in contact with MET 21 (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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17A VAL* 3.2 22.8 + - + +
20A ALA* 1.3 79.2 - - + +
22A SER* 1.3 62.2 + - - +
51A ILE* 4.0 19.5 - - + -
52A PHE* 5.3 2.0 - - - -
80A LEU* 3.9 23.7 - - - +
154A LEU* 4.0 9.4 - - + -
157A HIS* 3.5 43.2 + - + +
158A LEU* 3.5 32.8 - - + +
161A ILE* 5.5 5.6 - - + +
191A MET* 3.9 25.4 - - - +
195A VAL* 3.8 15.3 - - + -
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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