Contacts of the helix formed by residues 11 - 22 (chain C) in PDB entry 6MOL
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 PHE 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 LYS* 1.3 78.6 - - + +
12C GLU* 1.3 80.3 + - + +
14C LYS* 3.3 4.8 + - - +
15C ALA* 3.0 25.0 + - + +
29C PHE* 3.4 30.3 - + - -
31C GLU* 3.9 18.7 + - - +
37C VAL* 3.9 19.1 - - + -
39C PHE* 4.9 2.9 - + + -
80C ARG* 4.5 13.7 - - - -
82C TRP* 4.4 42.4 - + + -
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Residues in contact with GLU 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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10C LYS 3.2 4.8 - - - +
11C PHE* 1.3 90.5 - - + +
13C SER* 1.3 63.0 + - - +
15C ALA* 3.3 1.7 + - - -
16C ALA* 3.1 25.8 + - + +
74C THR* 3.4 19.2 + - - -
80C ARG* 3.3 32.9 + - - +
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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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10C LYS* 2.8 33.3 + - - +
12C GLU* 1.3 79.4 - - - +
14C LYS* 1.3 63.7 + - - +
16C ALA* 3.6 6.9 + - - +
17C LEU* 3.6 16.3 + - - +
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Residues in contact with LYS 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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10C LYS 3.4 10.1 + - - +
11C PHE 3.3 8.4 + - - +
12C GLU 3.2 0.6 - - - -
13C SER* 1.3 82.2 + - - +
15C ALA* 1.3 63.8 + - - +
17C LEU* 3.3 15.1 + - - +
18C LEU* 3.4 16.5 + - - +
29C PHE* 4.3 10.1 - - + -
31C GLU* 3.5 29.7 - - + +
120C LEU* 2.8 48.6 + - + +
121C LEU 3.3 23.9 + - - -
122C ASP* 3.5 27.7 + - - +
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Residues in contact with ALA 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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11C PHE* 3.0 26.2 + - + +
12C GLU 3.8 0.4 - - - +
14C LYS* 1.3 77.1 - - - +
16C ALA* 1.3 63.0 + - - +
18C LEU* 3.3 1.8 + - - -
19C ALA* 3.0 22.9 + - - +
29C PHE* 4.9 1.5 - - - -
39C PHE* 3.4 35.9 - - + -
80C ARG* 3.4 28.5 - - - +
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Residues in contact with ALA 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 GLU* 3.1 19.9 + - + +
13C SER* 3.9 8.1 - - - +
14C LYS 3.2 0.4 - - - -
15C ALA* 1.3 77.9 - - - +
17C LEU* 1.3 61.6 + - - +
19C ALA* 3.5 4.4 + - - +
20C ALA* 3.2 23.0 + - - +
80C ARG* 4.2 11.8 - - - +
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Residues in contact with LEU 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 3.6 8.2 + - - +
14C LYS* 3.3 10.6 + - - +
15C ALA 3.3 0.6 - - - -
16C ALA* 1.3 78.6 - - - +
18C LEU* 1.3 78.0 + - + +
20C ALA* 3.4 6.9 + - - +
21C ARG* 3.2 31.6 + - + +
120C LEU* 4.9 8.5 - - + -
208C PHE* 5.5 3.4 - - + -
209C TRP 4.8 15.7 - - - +
210C SER 5.7 0.7 - - - -
211C ALA* 5.6 13.0 - - + +
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Residues in contact with LEU 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 LYS 3.4 9.4 + - - +
15C ALA 3.3 7.4 + - - +
17C LEU* 1.3 85.2 - - + +
19C ALA* 1.3 66.1 + - - +
21C ARG* 3.1 11.0 + - + +
22C GLY 3.1 19.1 + - - -
27C LEU* 3.4 30.8 - - + +
28C CYS 5.2 0.4 - - - +
29C PHE* 3.8 42.6 - - + -
39C PHE* 4.1 8.1 - - + -
120C LEU* 4.0 12.3 - - + -
208C PHE* 3.7 42.0 - - + -
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Residues in contact with ALA 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 ALA 3.0 16.5 + - - +
16C ALA* 3.9 6.3 - - - +
17C LEU 3.3 0.2 - - - -
18C LEU* 1.3 77.6 - - - +
20C ALA* 1.3 61.7 + - - +
22C GLY 4.6 0.9 - - - -
23C PRO* 3.2 32.0 - - + +
27C LEU* 3.8 10.7 - - + +
39C PHE* 4.5 6.5 - - + -
41C GLU* 3.9 31.4 - - + +
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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 ALA 3.2 17.4 + - - +
17C LEU* 3.7 7.2 - - - +
18C LEU 3.2 0.2 - - - -
19C ALA* 1.3 77.7 - - - +
21C ARG* 1.3 62.4 + - - +
23C PRO* 4.3 4.7 - - - +
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Residues in contact with ARG 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 LEU* 3.2 27.6 + - + +
18C LEU* 3.1 15.8 + - + +
20C ALA* 1.3 80.4 - - - +
22C GLY* 1.3 57.6 + - - +
23C PRO* 3.9 3.6 - - - +
27C LEU* 6.1 0.7 - - + -
197C ARG* 5.4 7.7 - - - +
208C PHE* 6.1 6.6 - - - +
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Residues in contact with GLY 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 LEU 3.1 7.5 + - - -
19C ALA 3.6 3.4 - - - -
21C ARG* 1.3 79.9 - - - +
23C PRO* 1.3 68.2 - - - +
25C GLU* 3.9 21.0 + - - +
27C LEU* 3.6 25.5 - - - +
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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