Contacts of the helix formed by residues 13 - 25 (chain B) in PDB entry 2CX6
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 SER 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.7 1.9 - - - +
12B GLU* 1.3 82.4 - - - +
14B GLN* 1.3 66.8 + - - +
15B GLU* 3.1 25.4 - - - +
16B ASP* 2.9 40.8 + - - +
17B PHE 3.1 8.8 + - - -
65B ARG* 4.7 0.9 - - - +
66B PHE* 3.7 10.3 - - - -
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Residues in contact with GLN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER* 1.3 74.9 - - - +
15B GLU* 1.3 66.7 + - - +
17B PHE* 3.2 6.9 + - - +
18B TYR* 2.9 55.7 + - + -
35B LEU* 4.8 5.9 - - - +
65B ARG* 4.0 10.6 + - - +
66B PHE* 3.5 45.0 - - + +
68B ALA* 4.7 12.9 - - - +
69B LEU* 4.0 18.4 - - + +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER* 3.1 32.3 - - - +
14B GLN* 1.3 87.8 + - - +
16B ASP* 1.3 63.1 + - - +
17B PHE 3.1 1.6 - - - -
18B TYR* 3.8 15.6 - - + +
19B ARG* 3.1 38.9 + - + +
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Residues in contact with ASP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU 4.1 6.9 - - - +
11B ILE* 3.8 16.5 - - + +
12B GLU* 2.8 30.1 + - - +
13B SER* 2.9 33.4 + - - +
15B GLU* 1.3 75.6 - - - +
17B PHE* 1.3 58.2 + - - +
19B ARG* 3.5 9.9 + - - +
20B ASP* 3.1 28.2 + - - +
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Residues in contact with PHE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PHE* 3.7 22.4 - + - -
8B PHE* 4.1 13.7 - + - -
11B ILE* 3.9 13.4 - - + +
13B SER 3.1 7.8 + - - +
14B GLN* 3.4 7.9 - - - +
15B GLU 3.1 0.4 - - - -
16B ASP* 1.3 79.1 - - - +
18B TYR* 1.3 72.2 + + - +
20B ASP* 3.3 3.8 + - - +
21B PHE* 2.8 50.5 + + + +
38B LEU* 4.3 6.5 - - + -
55B PHE* 3.5 26.7 - + - -
66B PHE* 4.9 1.6 - - + -
69B LEU* 3.4 30.7 - - + -
73B PHE* 3.7 33.0 - + - -
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Residues in contact with TYR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLN* 2.9 48.6 + - + +
15B GLU* 3.3 14.8 + - + +
17B PHE* 1.3 83.3 - + - +
19B ARG* 1.3 57.3 + - + +
21B PHE* 3.6 3.9 - - - +
22B SER* 2.9 34.6 + - - -
32B VAL* 3.6 30.9 - - + +
33B ARG* 3.4 26.9 - - - -
34B ASP* 3.6 19.0 - - - -
35B LEU* 3.3 32.9 + - - +
38B LEU* 4.4 6.3 - - + -
69B LEU* 4.2 19.3 - - + +
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 3.1 25.4 + - + +
16B ASP* 3.8 8.9 + - - +
18B TYR* 1.3 74.3 - - + +
20B ASP* 1.3 61.6 + - - +
22B SER* 3.2 5.8 + - - -
23B GLN* 2.8 45.2 + - - +
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B THR 5.2 2.8 - - - +
6B PHE* 4.1 17.4 - - + -
10B GLU* 5.3 6.4 - - - +
11B ILE* 4.3 19.3 - - + +
16B ASP 3.1 15.4 + - - +
17B PHE* 3.3 7.8 + - - +
19B ARG* 1.3 79.5 - - - +
21B PHE* 1.3 56.4 + - - +
23B GLN* 3.3 9.7 + - - +
24B THR* 2.9 42.9 + - - -
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Residues in contact with PHE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PHE* 3.6 25.0 - + + -
17B PHE* 2.8 42.4 + + + +
18B TYR* 3.6 5.6 - - - +
20B ASP* 1.3 72.7 - - - +
22B SER* 1.3 62.7 + - - +
24B THR 3.3 0.9 + - - -
25B PHE* 3.1 50.6 + + - +
27B LEU* 4.0 21.5 - - + -
32B VAL* 4.1 17.3 - - + -
38B LEU* 4.0 19.1 - - + -
41B VAL* 4.4 6.7 - - + -
42B LEU* 4.4 2.9 - - + -
47B LEU* 3.8 23.8 - - + -
53B ILE* 4.2 9.9 - - + -
73B PHE* 3.9 17.5 - + - -
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B TYR 2.9 21.4 + - - -
19B ARG* 3.2 6.7 + - - -
21B PHE* 1.3 76.5 - - - +
23B GLN* 1.3 57.9 + - - +
26B GLY* 2.8 24.4 + - - -
27B LEU* 2.9 36.4 + - - +
28B ALA 5.0 3.8 + - - -
32B VAL* 3.6 26.7 + - - +
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 2.8 32.7 + - + +
20B ASP* 3.7 8.6 - - - +
22B SER* 1.3 73.1 - - - +
24B THR* 1.3 69.7 + - - +
26B GLY* 3.0 13.2 + - - -
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR* 3.3 43.3 - - + -
5B THR 5.6 1.6 + - - -
6B PHE* 4.0 8.6 - - + -
20B ASP* 2.9 33.2 + - - -
21B PHE* 3.5 7.6 - - - -
23B GLN* 1.3 80.1 - - - +
25B PHE* 1.3 73.8 + - + +
26B GLY 3.4 0.2 + - - -
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR* 3.4 49.1 - + - -
6B PHE* 4.4 2.2 - + - -
21B PHE* 3.1 51.2 + + - +
24B THR* 1.3 86.9 - - + +
26B GLY* 1.3 63.7 + - - +
27B LEU* 3.3 26.3 + - + +
47B LEU* 3.9 12.3 - - + -
48B PRO* 3.6 32.5 - - + +
51B LEU* 4.1 10.3 - - + -
53B ILE* 4.1 13.2 - - + -
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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