Contacts of the helix formed by residues 11 - 23 (chain C) in PDB entry 3CWT
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 ASP 11 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C TYR* 1.3 72.5 - - - +
12C TRP* 1.3 60.9 + - - +
13C SER* 3.4 10.6 + - - -
14C TRP* 2.8 42.3 + - + +
15C MET* 3.1 19.1 + - - +
102C ARG* 4.9 16.4 + - + +
104C GLY* 2.9 33.8 + - - +
105C LEU* 4.2 1.8 - - - +
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Residues in contact with TRP 12 (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 TRP* 3.1 52.1 - + - -
10C TYR* 3.2 57.3 + + - -
11C ASP* 1.3 70.3 - - - +
13C SER* 1.3 66.3 + - - +
15C MET* 4.3 2.7 - - + -
16C LEU* 2.8 57.3 + - + +
32C ASP 6.0 0.7 - - - +
52C PRO* 3.5 25.8 - - + -
54C ILE* 4.4 16.6 - - + -
59C LEU* 3.7 22.9 - - + -
82C PHE* 3.7 38.4 - + + -
84C LEU* 4.7 2.0 - - + -
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Residues in contact with SER 13 (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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11C ASP* 3.2 7.4 - - - -
12C TRP* 1.3 77.8 - - - +
14C TRP* 1.3 62.4 + - - +
16C LEU* 4.5 2.5 - - - +
17C GLY* 3.2 19.4 + - - -
32C ASP 5.9 2.5 - - - -
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Residues in contact with TRP 14 (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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11C ASP* 2.8 30.5 + - + +
13C SER* 1.3 76.2 - - - +
15C MET* 1.3 80.0 + - + +
17C GLY* 3.3 1.6 + - - -
18C PHE* 2.9 37.9 + + + +
102C ARG* 3.6 28.3 - - + +
105C LEU* 3.5 29.5 - - + +
106C ARG* 2.9 36.3 - - + -
108C PRO* 3.7 23.6 - - + -
269C LEU* 3.8 12.8 - - + -
273C TYR* 3.2 50.8 - + - -
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Residues in contact with MET 15 (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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10C TYR* 3.4 34.8 - - + +
11C ASP 3.1 13.3 + - - +
12C TRP* 3.9 6.3 - - + +
14C TRP* 1.3 87.1 - - + +
16C LEU* 1.3 64.3 + - + +
18C PHE* 3.1 4.7 + - - +
19C LEU* 2.9 39.2 + - + +
81C LEU 4.3 7.0 - - - +
82C PHE* 3.8 24.0 - - + +
106C ARG* 3.5 34.5 - - + +
107C LEU 4.2 2.2 - - - +
108C PRO* 4.0 32.3 - - + -
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Residues in contact with LEU 16 (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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12C TRP* 2.8 65.6 + - + +
13C SER* 4.5 2.5 - - - +
15C MET* 1.3 76.6 - - + +
17C GLY* 1.3 53.5 + - - +
19C LEU* 4.6 7.0 - - + +
20C ALA* 2.6 37.7 + - - +
30C VAL* 3.3 9.8 - - + +
31C ALA 3.7 17.7 - - - +
32C ASP* 4.6 14.1 - - - +
33C SER 5.6 0.2 - - - -
34C TYR* 3.9 25.1 - - - +
35C TYR* 4.0 20.6 - - + -
52C PRO* 5.0 6.3 - - + -
82C PHE* 5.2 2.5 - - + -
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Residues in contact with GLY 17 (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 SER 3.2 15.0 + - - -
14C TRP 3.7 3.4 - - - -
15C MET 3.1 1.0 - - - -
16C LEU* 1.3 76.5 - - - +
18C PHE* 1.3 64.4 + - - +
20C ALA* 3.6 7.1 - - - +
21C ALA* 3.0 24.9 + - - +
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Residues in contact with PHE 18 (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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14C TRP* 2.9 29.0 + + + +
15C MET* 3.4 11.7 - - - +
17C GLY* 1.3 77.8 - - - +
19C LEU* 1.3 70.0 + - + +
21C ALA* 3.4 5.0 + - - -
22C ARG* 3.1 67.2 + - - +
108C PRO* 3.6 39.3 - - + -
222C TYR* 4.8 1.6 - - - -
226C ARG* 3.5 28.0 - - - -
269C LEU* 4.4 15.3 - - + -
272C TRP* 5.0 7.0 - + - -
273C TYR* 3.6 22.7 - + + +
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Residues in contact with LEU 19 (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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15C MET* 2.9 27.8 + - + +
16C LEU* 3.9 6.7 - - + +
18C PHE* 1.3 87.0 - - + +
20C ALA* 1.3 55.9 + - - +
22C ARG* 2.9 7.6 + - + +
23C ALA* 2.8 34.7 + - - +
28C GLU* 5.1 4.1 - - - +
30C VAL* 4.2 4.2 - - + +
35C TYR* 4.1 32.5 - - + +
81C LEU* 4.3 17.3 - - + -
82C PHE* 3.8 29.4 - - + -
108C PRO* 4.6 6.3 - - + -
226C ARG* 4.2 17.0 - - - +
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Residues in contact with ALA 20 (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 2.6 25.2 + - - +
17C GLY* 3.6 8.5 - - - +
18C PHE 3.3 0.2 - - - -
19C LEU* 1.3 72.1 - - - +
21C ALA* 1.3 60.9 + - - +
23C ALA* 3.3 15.6 + - - +
30C VAL* 3.6 29.5 - - + +
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Residues in contact with ALA 21 (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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17C GLY 3.0 16.9 + - - +
18C PHE* 3.7 5.2 - - - +
19C LEU 3.2 0.4 - - - -
20C ALA* 1.3 76.7 - - - +
22C ARG* 1.3 70.4 + - - +
23C ALA 3.8 0.5 + - - +
128C VAL* 3.4 20.3 - - + +
129C ALA* 5.1 2.1 + - - -
132C ALA* 4.4 8.0 - - - +
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Residues in contact with ARG 22 (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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18C PHE* 3.1 68.6 + - - +
19C LEU* 2.9 10.8 + - + +
21C ALA* 1.3 85.5 - - - +
23C ALA* 1.3 65.6 + - - +
24C VAL* 3.5 3.6 + - - +
28C GLU* 4.3 0.9 - - - -
119C ARG* 3.3 25.6 + - - +
128C VAL* 3.7 33.3 - - + +
132C ALA* 4.4 9.1 - - - +
222C TYR* 4.2 9.8 + - - -
226C ARG* 3.8 12.3 - - - +
272C TRP* 5.4 7.7 - - - -
273C TYR* 3.8 17.6 + - - -
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Residues in contact with ALA 23 (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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19C LEU 2.8 10.2 + - - +
20C ALA* 3.3 16.8 + - - +
21C ALA 3.4 0.9 - - - +
22C ARG* 1.3 79.8 - - - +
24C VAL* 1.3 61.0 + - - +
25C SER* 3.8 3.1 + - - -
28C GLU* 3.3 20.6 - - + +
30C VAL* 3.9 22.7 - - + +
132C ALA* 3.8 13.7 - - - +
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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