Contacts of the helix formed by residues 11 - 22 (chain C) in PDB entry 1M6X
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 PRO 11 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B GLN* 3.2 20.0 - - - +
127B PHE* 3.5 24.9 - - + -
9C LYS 3.6 4.9 - - - +
10C THR* 1.3 91.4 - - + +
12C PRO* 1.3 62.7 - - + +
13C LYS* 4.7 1.8 - - + -
14C VAL* 2.7 47.3 + - + +
15C LEU* 3.0 9.8 + - - +
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Residues in contact with PRO 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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120B VAL* 3.8 10.5 - - + +
123B LEU* 3.4 22.7 - - + +
124B GLN* 3.2 40.8 - - + +
127B PHE* 3.5 25.8 - - + -
10C THR 3.6 2.8 - - - +
11C PRO* 1.3 78.9 - - + -
13C LYS* 1.3 64.3 + - - +
15C LEU* 2.9 20.8 + - + +
16C VAL* 3.1 14.4 + - - +
40C TYR* 3.9 17.5 - - + +
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Residues in contact with LYS 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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120B VAL* 3.8 12.5 - - + +
121B SER* 6.1 0.4 - - - -
124B GLN* 2.9 52.5 + - + +
128B GLU* 5.2 4.0 + - - -
11C PRO* 5.2 0.9 - - - -
12C PRO* 1.3 73.5 - - - +
14C VAL* 1.3 70.0 + - + +
16C VAL* 3.5 2.6 + - - +
17C ARG* 2.8 57.3 + - - +
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Residues in contact with VAL 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 THR* 3.5 19.7 - - + -
11C PRO* 2.7 44.1 + - + +
13C LYS* 1.3 81.0 - - + +
15C LEU* 1.3 53.1 + - - +
17C ARG* 3.0 11.1 - - + +
18C GLN* 2.8 57.7 + - + +
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Residues in contact with LEU 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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7C LEU* 3.8 29.4 - - + +
10C THR* 3.4 40.6 - - + +
11C PRO 3.0 6.7 + - - +
12C PRO* 2.9 10.4 + - + +
14C VAL* 1.3 77.6 - - - +
16C VAL* 1.3 64.9 + - + +
18C GLN* 3.1 12.9 + - - +
19C PHE* 2.8 23.5 + - - +
37C GLU* 3.9 19.0 - - + +
40C TYR* 3.5 45.5 - - + +
41C LEU* 5.9 2.0 - - + -
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Residues in contact with VAL 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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117B THR* 5.9 2.2 - - + -
120B VAL* 3.1 46.9 - - + -
12C PRO 3.1 5.1 + - - +
13C LYS* 3.8 5.8 - - - +
15C LEU* 1.3 75.2 - - + +
17C ARG* 1.3 66.4 + - - +
19C PHE* 3.3 8.1 + - - +
20C VAL* 3.0 29.1 + - + +
40C TYR* 5.6 2.7 - - + -
41C LEU* 4.2 16.4 - - + +
96C LEU* 3.8 36.6 - - + -
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Residues in contact with ARG 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 LYS* 2.8 51.5 + - - +
14C VAL* 3.0 17.1 - - + +
16C VAL* 1.3 74.1 - - - +
18C GLN* 1.3 56.4 + - + +
20C VAL* 2.8 30.1 + - - +
21C GLU* 3.2 30.1 + - + +
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Residues in contact with GLN 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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10C THR* 4.0 16.0 + - - +
14C VAL* 2.8 42.3 + - + +
15C LEU* 3.5 11.1 - - - +
17C ARG* 1.3 74.0 - - + +
19C PHE* 1.3 61.5 + - - +
21C GLU* 3.6 18.9 + - - +
22C ARG* 3.3 28.1 + - - +
37C GLU* 3.4 20.1 - - - +
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Residues in contact with PHE 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 LEU 2.8 11.8 + - - +
16C VAL* 3.5 10.5 - - - +
17C ARG 3.0 0.2 + - - -
18C GLN* 1.3 76.3 - - - +
20C VAL* 1.3 60.6 + - - +
22C ARG* 3.4 6.2 - - - +
23C PHE* 3.1 46.5 - + - -
34C CYS* 3.5 33.0 - - + -
37C GLU* 3.0 25.7 + - + +
38C LEU* 3.9 28.7 - - + -
41C LEU* 3.4 27.4 - - + -
77C LEU* 6.0 0.2 - - + -
93C LEU* 4.6 7.2 - - + -
96C LEU* 4.0 16.8 - - + -
97C ILE* 3.6 19.5 - - + -
102C PHE* 4.7 8.1 - + - -
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Residues in contact with VAL 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 VAL* 3.0 21.3 - - + +
17C ARG* 2.8 9.4 + - - +
19C PHE* 1.3 73.7 - - + +
21C GLU* 1.3 56.0 + - - +
22C ARG 3.0 2.0 - - - -
23C PHE* 2.7 30.8 + - + +
24C GLU* 3.4 20.7 + - + +
96C LEU* 4.4 35.4 - - + +
97C ILE* 4.4 13.2 - - + -
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Residues in contact with GLU 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 ARG* 3.2 31.3 + - + +
18C GLN* 3.6 22.9 + - - +
19C PHE 3.5 0.2 - - - -
20C VAL* 1.3 77.7 - - + +
22C ARG* 1.3 62.8 + - - +
24C GLU* 3.1 30.8 + - - +
30C LYS* 3.3 16.2 + - - -
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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 GLN* 3.3 14.2 + - - +
19C PHE 3.4 10.5 - - - +
20C VAL 2.9 0.2 + - - -
21C GLU* 1.3 78.1 - - + +
23C PHE* 1.3 67.7 + - + +
26C PRO* 4.2 4.3 - - - +
30C LYS* 2.9 63.9 + - + +
31C ILE* 3.2 14.6 - - + +
33C SER* 3.6 27.8 + - - -
34C CYS* 3.6 24.6 - - - +
37C GLU* 2.7 41.3 + - - -
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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