Contacts of the helix formed by residues 7 - 19 (chain C) in PDB entry 4NL3
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 GLY 7 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C GLY* 3.5 4.8 + - - -
6C GLN* 1.3 75.7 - - - +
8C LEU* 1.3 67.3 + - - +
9C GLN 3.2 1.1 + - - -
10C ASP* 3.3 3.7 + - - +
11C TYR* 3.0 26.3 + - - +
41K ASP* 3.6 2.2 + - - +
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Residues in contact with LEU 8 (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 GLY* 1.3 77.2 - - - +
9C GLN* 1.3 55.6 + - - +
11C TYR* 4.1 7.5 - - + +
12C TYR* 3.2 31.3 + - + +
39K SER* 3.8 30.3 - - - +
40K PHE* 3.5 30.3 - - - +
41K ASP* 3.6 12.3 + - + +
44K THR* 3.2 28.3 - - - +
46K LEU* 4.0 24.5 - - + +
55K LEU* 4.5 6.3 - - + -
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Residues in contact with GLN 9 (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 GLN* 4.5 5.6 - - - +
8C LEU* 1.3 76.2 - - - +
10C ASP* 1.3 72.6 + - - +
12C TYR* 4.0 2.6 - - - +
13C LEU* 3.1 36.2 + - + +
58C LYS* 2.4 40.3 + - - +
41K ASP* 3.1 17.3 + - - +
43K PHE* 3.6 34.6 - - - +
44K THR* 3.4 21.2 - - + +
55K LEU* 5.1 3.8 - - + -
57K PHE* 3.8 9.9 - - + -
31Z U 3.5 10.5 + - - +
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Residues in contact with ASP 10 (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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3C GLN 5.6 0.9 - - - +
6C GLN* 3.3 43.1 - - - +
7C GLY* 3.3 4.5 + - - +
9C GLN* 1.3 85.3 - - - +
11C TYR* 1.3 58.9 + - - +
13C LEU* 5.6 0.2 - - - -
14C ASN* 3.1 27.5 + - - +
40C PHE* 3.7 20.0 - - + -
42C ASN* 5.7 0.2 - - - +
58C LYS* 5.1 2.9 + - - -
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Residues in contact with TYR 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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7C GLY 3.0 17.5 + - - +
8C LEU* 4.1 7.0 - - + +
10C ASP* 1.3 76.3 - - - +
12C TYR* 1.3 64.9 + + + +
14C ASN* 3.2 8.9 + - + +
15C GLN* 2.9 69.8 + - + +
70C VAL* 4.6 2.7 - - + -
71C ALA* 3.7 28.9 + - - +
72C LEU 5.0 1.1 + - - -
73C ASN* 5.0 23.7 + - + +
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Residues in contact with TYR 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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8C LEU* 3.2 21.8 + - + +
9C GLN 4.0 2.9 - - - +
11C TYR* 1.3 85.4 - + + +
13C LEU* 1.3 57.2 - - - +
15C GLN* 3.3 6.3 + - - +
16C LEU* 3.0 56.2 + - + +
64C PHE* 4.9 2.0 - - + -
66C PRO* 3.3 25.3 - - + +
70C VAL* 3.6 22.0 - - + +
46K LEU* 3.5 31.9 - - + +
53K GLN* 2.8 37.7 + - - +
55K LEU* 3.5 34.6 - - + +
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Residues in contact with LEU 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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9C GLN* 3.1 40.2 + - + +
12C TYR* 1.3 79.8 - - - +
14C ASN* 1.3 61.2 + - - +
16C LEU* 3.8 15.2 - - + +
17C ARG* 3.2 17.7 + - - +
37C VAL* 3.8 9.7 - - + +
40C PHE* 3.3 44.3 - - + -
45C VAL* 4.5 9.0 - - + -
58C LYS* 4.4 9.6 - - - -
64C PHE* 3.8 40.4 - - + -
55K LEU* 4.5 7.4 - - + -
57K PHE* 5.0 2.0 - - + -
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Residues in contact with ASN 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 ASP 3.1 21.0 + - - +
11C TYR* 3.2 10.7 + - + +
12C TYR 3.1 0.4 - - - -
13C LEU* 1.3 74.9 - - - +
15C GLN* 1.3 57.0 + - + +
17C ARG* 2.3 35.7 + - - +
18C LYS* 2.7 58.5 + - - +
40C PHE* 3.5 12.4 - - + -
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Residues in contact with GLN 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 TYR* 2.9 61.1 + - + +
12C TYR 3.7 1.3 - - - +
14C ASN* 1.3 75.9 + - - +
16C LEU* 1.3 58.8 + - - +
18C LYS* 4.3 22.6 + - - +
19C GLU* 2.7 68.1 + - + +
21C ILE* 5.1 0.7 - - - -
70C VAL* 3.7 23.7 - - + +
71C ALA* 5.2 4.8 - - - +
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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 TYR* 3.0 40.5 + - + +
13C LEU* 3.8 21.3 - - + +
15C GLN* 1.3 76.2 - - - +
17C ARG* 1.3 59.9 + - - +
20C LYS* 3.4 2.9 + - - -
21C ILE* 3.1 57.5 + - + +
23C ALA* 4.7 8.3 - - + -
37C VAL* 4.0 19.5 + - + +
64C PHE* 4.2 18.2 - - + -
66C PRO* 3.9 11.4 - - + -
70C VAL* 3.6 22.7 - - + -
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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 LEU 3.2 11.5 + - - +
14C ASN* 2.3 41.9 + - - +
16C LEU* 1.3 78.7 - - - +
18C LYS* 1.3 88.9 + - - +
20C LYS* 3.4 17.2 + - - +
37C VAL* 3.5 24.1 - - + +
38C VAL 3.3 29.8 + - - +
39C SER* 4.4 8.0 - - - +
40C PHE* 4.4 8.5 - - - -
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Residues in contact with LYS 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 ASN* 2.7 42.1 + - - +
15C GLN* 4.0 20.1 + - - +
17C ARG* 1.3 91.8 - - - +
19C GLU* 1.3 60.2 + - + +
20C LYS* 3.0 16.7 + - - +
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Residues in contact with GLU 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 GLN* 2.7 51.2 + - - +
18C LYS* 1.3 73.6 - - + +
20C LYS* 1.3 70.0 + - - +
21C ILE* 3.0 31.1 + - + +
68C LYS* 4.4 17.2 + - - +
69C ASN 5.9 1.3 - - - -
70C VAL* 5.2 3.1 - - - +
71C ALA* 4.7 14.7 + - - +
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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