Contacts of the helix formed by residues 12 - 24 (chain C) in PDB entry 1NZ0
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 ARG 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C LEU* 1.3 75.7 - - - +
13C LEU* 1.3 53.8 - - - +
14C ARG 3.3 2.2 - - - +
15C ARG* 2.8 26.9 + - - +
16C ASP* 2.8 19.3 + - - +
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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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14A ARG 5.3 0.2 - - - +
18A LEU* 3.7 17.5 - - + +
11C LEU* 3.1 37.9 + - + +
12C ARG* 1.3 69.9 - - - +
14C ARG* 1.3 66.0 + - - +
16C ASP 4.2 1.6 - - - +
17C PHE* 2.9 44.0 + - + +
47C GLY* 3.5 28.3 - - - -
48C ILE 3.8 15.5 - - - +
49C VAL* 4.2 13.2 - - + -
68C ARG* 5.7 2.2 - - - +
85C VAL* 3.7 21.1 - - + -
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Residues in contact with ARG 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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14A ARG* 3.0 28.4 - - - +
15A ARG* 4.4 7.8 - - - +
18A LEU* 4.1 14.1 - - - +
12C ARG* 3.3 1.2 - - - +
13C LEU* 1.3 76.8 - - - +
15C ARG* 1.3 57.4 + - - +
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Residues in contact with ARG 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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14A ARG* 3.2 32.0 + - - +
12C ARG* 2.8 16.7 + - - +
13C LEU 3.7 0.4 - - - -
14C ARG* 1.3 80.6 - - - +
16C ASP* 1.3 67.8 + - - +
17C PHE 3.7 0.4 - - - -
18C LEU* 5.2 2.7 + - - +
19C LEU* 5.3 2.8 + - - +
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Residues in contact with ASP 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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14A ARG* 3.9 11.3 + - - -
11C LEU* 4.9 6.8 - - + +
12C ARG* 2.8 20.6 + - - +
13C LEU* 4.9 0.9 - - - -
15C ARG* 1.3 83.0 - - - +
17C PHE* 1.3 64.4 + - - +
18C LEU 3.4 2.2 - - - -
19C LEU* 3.2 27.6 + - - +
20C ILE* 3.0 38.8 + - + +
83C ASP* 4.0 14.2 - - - +
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Residues in contact with PHE 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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14A ARG 5.9 1.1 + - - +
17A PHE* 3.4 35.0 - + + -
18A LEU* 3.7 33.9 - - + -
21A PHE* 3.9 37.7 - + - -
13C LEU* 2.9 31.3 + - + +
15C ARG 3.7 0.6 - - - -
16C ASP* 1.3 76.0 - - - +
18C LEU* 1.3 61.3 + - - +
20C ILE* 3.3 4.1 + - - +
21C PHE* 2.9 28.9 + + - +
35C LEU* 4.2 15.0 - - + -
49C VAL* 4.1 23.1 - - + -
85C VAL* 4.1 19.1 - - + -
87C ILE* 4.5 3.1 - - + -
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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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13A LEU* 3.9 31.2 - - + +
14A ARG* 3.9 24.2 + - + +
17A PHE* 3.6 31.4 - - + -
49A VAL* 3.9 23.1 - - + -
15C ARG 5.2 2.4 + - - +
16C ASP 3.4 0.6 - - - -
17C PHE* 1.3 76.9 - - - +
19C LEU* 1.3 56.8 + - - +
21C PHE* 3.2 1.7 + - - +
22C LYS* 2.9 56.1 + - + +
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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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14A ARG* 6.0 2.0 - - - +
15C ARG 5.3 1.5 + - - +
16C ASP* 3.2 37.0 + - + +
18C LEU* 1.3 77.2 - - - +
20C ILE* 1.3 60.9 + - + +
22C LYS* 3.8 4.4 - - + -
23C GLU* 2.9 32.2 + - - +
24C GLY 3.9 0.2 + - - -
37C ARG* 3.9 44.4 - - - +
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Residues in contact with ILE 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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11C LEU* 3.8 29.2 - - + -
16C ASP* 3.0 29.8 + - + +
17C PHE 3.9 3.4 - - - +
19C LEU* 1.3 77.4 - - + +
21C PHE* 1.3 59.2 + - - +
24C GLY* 2.9 29.0 + - - +
25C LYS 5.1 0.2 - - - +
35C LEU* 3.8 28.7 - - + +
36C PHE* 3.9 21.3 - - - +
37C ARG* 4.2 18.4 - - + +
83C ASP* 3.9 17.5 - - + +
85C VAL* 3.9 14.1 - - + -
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Residues in contact with PHE 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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17A PHE* 3.8 24.9 - + + -
21A PHE* 4.6 14.1 - + - -
49A VAL* 3.8 30.7 - - + -
51A LYS* 3.9 41.0 - - + +
87A ILE* 4.1 27.4 - - + -
17C PHE* 2.9 24.6 + + + +
18C LEU 3.6 3.8 - - - +
20C ILE* 1.3 79.7 - - - +
22C LYS* 1.3 60.1 + - - +
24C GLY 4.5 4.0 + - - +
35C LEU* 4.0 31.4 - - + +
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Residues in contact with LYS 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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48A ILE 5.2 5.3 + - - -
49A VAL* 3.6 26.7 - - + -
50A VAL 3.5 24.9 - - - +
51A LYS* 3.6 8.7 - - - +
52A ARG* 2.9 39.9 + - - +
53A LYS 4.8 0.5 + - - -
5009A SO4 2.6 38.2 + - - -
18C LEU* 2.9 41.7 + - + +
19C LEU* 4.0 4.9 - - + +
21C PHE* 1.3 79.9 - - - +
23C GLU* 1.3 58.0 + - - +
24C GLY 4.8 1.6 - - - +
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Residues in contact with GLU 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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52A ARG* 4.4 13.3 - - - +
19C LEU* 2.9 18.6 + - - -
22C LYS* 1.3 74.4 - - - +
24C GLY* 1.3 66.3 + - - +
25C LYS* 5.5 0.3 - - - +
37C ARG* 4.5 14.5 + - - +
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Residues in contact with GLY 24 (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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53A LYS* 6.0 1.6 + - - -
19C LEU 3.9 0.6 + - - -
20C ILE* 2.9 21.1 + - - +
21C PHE 4.8 3.6 - - - +
22C LYS 3.7 2.5 - - - +
23C GLU* 1.3 82.4 + - - +
25C LYS* 1.3 67.1 + - - +
36C PHE 3.2 14.1 - - - -
37C ARG* 4.1 10.7 - - - +
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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