Contacts of the helix formed by residues 10 - 20 (chain C) in PDB entry 6CP3
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 VAL 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C PRO 5.2 6.3 - - - +
8C THR* 3.8 1.1 - - - -
9C GLU* 1.3 83.7 - - - +
11C SER* 1.3 66.2 + - - +
12C SER* 4.3 6.1 - - - +
13C ILE* 3.3 34.4 + - + +
14C LEU* 3.2 24.3 + - - +
34C LEU* 4.6 19.1 - - + -
42C ARG* 6.2 1.6 - - - +
54F LEU 5.2 7.0 - - - +
55F GLY* 5.5 1.6 - - - -
56F GLU* 4.9 26.7 - - + +
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Residues in contact with SER 11 (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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9C GLU 3.9 0.8 + - - -
10C VAL* 1.3 74.5 - - - +
12C SER* 1.3 60.4 + - - +
13C ILE 3.5 0.2 + - - -
14C LEU* 4.9 2.7 - - - +
15C GLU* 3.4 23.2 + - - +
56F GLU* 3.1 33.0 + - - +
11Y ARG* 5.6 1.4 + - - -
18Y THR* 3.6 16.7 + - - -
21Y THR* 5.0 8.7 - - - +
22Y ALA* 4.8 6.8 - - - +
25Y GLN* 3.4 24.2 + - - +
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Residues in contact with SER 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 VAL* 3.3 6.4 - - - +
11C SER* 1.3 77.3 - - - +
13C ILE* 1.3 72.7 + - - +
15C GLU* 4.5 9.9 - - - +
16C GLU* 3.1 24.1 + - - +
34C LEU* 5.3 3.6 - - - +
86C GLU* 4.6 13.0 + - - -
56F GLU* 5.3 9.2 - - - +
57F ASN* 5.7 7.0 - - - -
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Residues in contact with ILE 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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8C THR* 4.8 17.9 - - + +
10C VAL* 3.3 27.6 + - + +
12C SER* 1.3 91.5 - - - +
14C LEU* 1.3 65.0 + - + +
15C GLU 3.2 1.8 - - - -
16C GLU* 3.6 11.8 + - + +
17C ARG* 3.5 25.6 + - - +
32C ARG* 5.7 9.0 - - + +
34C LEU* 4.4 13.2 - - + -
44C PHE* 3.5 49.8 - - + -
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Residues in contact with LEU 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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8C THR 3.9 17.5 - - - +
9C GLU* 3.2 30.7 - - - +
10C VAL 3.2 12.5 + - - +
11C SER 4.8 0.2 - - - +
13C ILE* 1.3 75.3 - - + +
15C GLU* 1.3 66.6 + - - +
17C ARG* 3.0 15.7 + - - +
18C ILE* 2.9 28.6 + - + +
18Y THR* 4.5 8.3 - - + +
19Y TYR* 3.5 44.6 - - + +
22Y ALA* 4.0 16.2 - - + -
91Y VAL* 4.7 11.0 - - + -
95Y ASN* 4.6 5.2 - - - +
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Residues in contact with GLU 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 SER 3.4 18.8 + - - +
12C SER* 4.6 9.4 - - - +
14C LEU* 1.3 78.7 - - - +
16C GLU* 1.3 76.5 + - - +
18C ILE* 3.2 22.8 + - - +
19C LYS* 3.4 16.1 + - + +
22Y ALA* 4.2 3.9 - - + +
25Y GLN* 4.0 22.9 + - + +
26Y ALA* 4.4 15.8 - - + +
29Y LYS* 2.9 30.5 + - - +
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Residues in contact with GLU 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 SER 3.1 20.8 - - - +
13C ILE* 3.6 13.5 + - + +
14C LEU 3.2 0.4 - - - -
15C GLU* 1.3 91.7 - - - +
17C ARG* 1.3 61.7 + - - +
19C LYS* 3.4 22.0 + - + +
20C GLY 3.7 4.0 + - - -
21C VAL* 3.8 19.3 + - + +
22C SER* 4.3 2.3 + - - -
23C ASP* 4.1 28.8 - - + +
32C ARG* 4.4 12.5 + - - -
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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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8C THR* 5.1 10.9 + - - -
13C ILE* 3.5 17.8 + - - +
14C LEU* 3.0 18.3 + - + +
16C GLU* 1.3 75.6 - - - +
18C ILE* 1.3 64.3 + - - +
19C LYS 3.2 0.2 - - - -
20C GLY* 3.5 10.4 + - - -
22C SER* 5.2 7.9 - - - +
23C ASP 6.2 0.2 - - - +
24C GLU* 3.6 27.5 + - - +
87Y ASN* 3.7 10.6 - - - +
91Y VAL* 3.8 28.5 - - + +
94Y GLU* 2.8 31.7 + - - +
95Y ASN* 3.5 19.8 + - - +
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Residues in contact with ILE 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 LEU* 2.9 16.0 + - + +
15C GLU* 3.2 7.2 + - - +
17C ARG* 1.3 76.7 - - - +
19C LYS* 1.3 64.8 + - - +
20C GLY 3.4 0.5 + - - -
19Y TYR 4.7 0.4 - - - +
22Y ALA* 3.5 21.1 - - + +
23Y LEU* 3.5 35.7 - - + +
26Y ALA* 3.5 21.1 - - + -
84Y TYR* 3.8 32.7 - - + +
87Y ASN* 3.7 20.5 + - - +
88Y LEU* 3.8 32.1 - - + +
91Y VAL* 5.5 2.9 - - + -
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Residues in contact with LYS 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 GLU* 3.7 12.5 + - + +
16C GLU* 3.4 15.9 + - + +
17C ARG 3.2 0.2 - - - -
18C ILE* 1.3 79.0 - - - +
20C GLY* 1.3 59.4 + - - +
21C VAL* 3.5 20.2 - - + +
26Y ALA* 3.2 31.6 + - - +
29Y LYS* 3.4 30.4 - - - +
30Y ASN* 5.7 2.5 - - - -
84Y TYR* 2.8 38.8 + - - +
87Y ASN* 4.5 1.7 + - - -
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Residues in contact with GLY 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 GLU 3.7 0.4 + - - -
17C ARG 3.5 8.7 + - - -
18C ILE 3.2 4.0 - - - -
19C LYS* 1.3 79.4 - - - +
21C VAL* 1.3 62.6 + - - +
22C SER* 3.2 7.6 + - - -
87Y ASN* 3.9 17.5 - - - -
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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