Contacts of the helix formed by residues 9 - 29 (chain C) in PDB entry 4PKO
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 9 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE* 1.3 76.1 - - - +
10C ASN* 1.3 54.2 + - - -
12C ALA* 2.7 28.1 + - - +
13C ARG* 2.9 34.7 + - - +
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Residues in contact with ASN 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE 3.7 0.2 + - - -
9C GLY* 1.3 71.4 - - - -
11C ASP* 1.3 61.5 + - - +
13C ARG* 3.0 27.8 + - - +
14C VAL* 3.0 47.6 + - - +
104C LEU 5.3 0.3 - - - +
108C ALA* 3.8 25.6 - - - +
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Residues in contact with ASP 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 3.4 37.6 + - + +
8C PHE 3.2 14.4 - - - +
9C GLY 3.0 0.2 - - - -
10C ASN* 1.3 80.1 - - - +
12C ALA* 1.3 60.0 + - - +
14C VAL* 3.7 4.4 + - - +
15C LYS* 3.6 21.1 + - - +
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Residues in contact with ALA 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 3.9 31.0 - - + +
8C PHE 3.3 5.4 + - - +
9C GLY 2.7 14.7 + - - +
11C ASP* 1.3 74.3 - - - +
13C ARG* 1.3 58.4 + - - +
15C LYS* 3.1 9.3 + - - +
16C MET* 2.8 29.2 + - - +
66C PHE* 5.6 5.3 - - + +
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLY* 2.9 24.9 + - - +
10C ASN* 3.0 42.9 + - - +
12C ALA* 1.3 75.7 - - + +
14C VAL* 1.3 58.8 + - + +
16C MET* 3.1 12.2 + - + +
17C LEU* 2.8 32.9 + - - +
104C LEU* 3.8 40.9 + - + +
107C VAL* 3.8 35.9 + - - +
108C ALA* 5.2 1.8 - - - +
113C PRO* 5.8 0.8 - - - +
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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
----------------------------------------------------------
10C ASN* 3.0 40.8 + - - +
11C ASP* 3.9 5.4 - - - +
12C ALA 3.2 0.2 - - - -
13C ARG* 1.3 76.6 - - + +
15C LYS* 1.3 64.8 + - + +
17C LEU* 3.8 6.4 - - + +
18C ARG* 3.0 44.9 + - + +
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 4.8 14.4 - - + +
11C ASP* 3.6 17.2 + - - +
12C ALA* 3.1 11.3 + - - +
14C VAL* 1.3 81.9 - - + +
16C MET* 1.3 62.2 + - - +
18C ARG* 4.6 4.9 - - - +
19C GLY 3.4 4.3 + - - -
64C ASP* 3.2 34.2 + - - +
66C PHE* 3.7 29.2 - - + -
67C GLU* 3.3 48.1 + - + +
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Residues in contact with MET 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA 2.8 13.3 + - - +
13C ARG* 3.1 13.7 + - + +
15C LYS* 1.3 77.4 - - - +
17C LEU* 1.3 62.7 + - - +
19C GLY* 3.1 5.0 + - - -
20C VAL* 3.0 27.9 + - + +
66C PHE* 4.5 5.6 - - - +
70C GLY* 3.6 25.2 - - - +
73C MET* 4.0 19.7 - - + +
100C ILE* 4.8 11.0 - - + -
104C LEU* 4.1 34.5 - - + -
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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 ARG 2.8 19.8 + - - +
14C VAL* 3.8 7.2 - - + +
16C MET* 1.3 72.9 - - - +
18C ARG* 1.3 58.7 + - + +
20C VAL* 3.0 12.8 + - + +
21C ASN* 2.8 50.3 + - - +
97C GLN* 5.5 0.7 - - + +
100C ILE* 3.8 25.1 - - + -
101C THR* 4.2 26.0 - - + +
104C LEU* 3.8 17.9 - - + +
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Residues in contact with ARG 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 VAL* 3.0 39.2 + - + +
15C LYS* 3.7 10.3 - - - +
16C MET 3.3 0.2 - - - -
17C LEU* 1.3 75.8 - - + +
19C GLY* 1.3 62.7 + - - +
21C ASN* 3.5 11.3 + - - +
22C VAL* 3.3 32.8 + - - +
67C GLU* 2.8 50.2 + - + -
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Residues in contact with GLY 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 LYS 3.4 3.8 + - - -
16C MET 3.1 4.7 + - - -
17C LEU 3.1 0.6 - - - -
18C ARG* 1.3 77.5 - - - +
20C VAL* 1.3 63.9 + - - +
22C VAL* 3.0 13.5 + - - +
23C LEU 3.2 10.2 + - - -
62C LEU* 3.5 14.1 - - - -
67C GLU* 3.1 26.6 - - - +
71C ALA* 3.4 14.5 - - - +
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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
----------------------------------------------------------
16C MET* 3.0 22.9 + - + +
17C LEU* 3.0 19.8 + - + +
19C GLY* 1.3 76.0 - - - +
21C ASN* 1.3 58.7 + - - +
23C LEU* 3.4 2.8 + - - +
24C ALA* 2.9 27.5 + - + +
70C GLY* 3.7 20.9 - - - +
71C ALA* 4.0 1.2 - - - +
74C VAL* 3.8 32.9 - - + +
97C GLN* 4.6 18.4 - - + -
100C ILE* 3.9 21.5 - - + -
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Residues in contact with ASN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 2.8 47.6 + - - +
18C ARG* 3.7 9.0 - - - +
19C GLY 3.2 0.2 - - - -
20C VAL* 1.3 73.7 - - - +
22C VAL* 1.3 54.4 + - + +
25C ASP* 2.5 50.7 + - - +
97C GLN* 2.8 30.4 + - - +
101C THR* 4.5 3.3 + - - -
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.0 29.8 - - + -
8B PHE* 4.9 2.6 - - - -
18C ARG* 3.4 23.8 - - - +
19C GLY 3.0 8.7 + - - +
21C ASN* 1.3 77.8 - - + +
23C LEU* 1.3 64.0 + - - +
25C ASP* 4.0 4.1 - - - +
26C ALA* 3.1 24.9 + - - +
60C ILE* 4.3 6.7 - - + +
62C LEU* 3.9 33.2 - - + -
67C GLU* 5.5 0.7 - - - +
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Residues in contact with LEU 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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19C GLY 3.2 2.8 + - - -
20C VAL 3.7 6.3 - - - +
22C VAL* 1.3 79.8 - - - +
24C ALA* 1.3 67.4 + - - +
26C ALA* 3.7 2.4 + - - +
27C VAL* 3.1 30.6 + - + +
57C ALA* 3.2 37.7 - - + +
60C ILE* 3.2 39.2 - - + +
71C ALA* 3.9 24.5 - - + +
74C VAL* 3.9 25.1 - - + +
75C LYS* 4.4 11.2 - - + +
93C THR* 4.4 10.8 - - + +
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 2.9 19.3 + - + +
23C LEU* 1.3 74.2 - - + +
25C ASP* 1.3 54.6 + - - +
26C ALA 3.1 2.0 - - - -
27C VAL* 2.8 7.1 + - - +
28C LYS* 2.7 39.0 + - + +
74C VAL* 6.0 0.7 - - + -
93C THR* 4.0 20.9 - - + +
97C GLN* 3.3 39.3 - - + +
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Residues in contact with ASP 25 (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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8B PHE* 3.7 19.3 - - + -
21C ASN* 2.5 35.5 + - - +
22C VAL* 4.1 3.1 - - - +
24C ALA* 1.3 71.0 - - - +
26C ALA* 1.3 60.1 + - - +
28C LYS* 3.3 28.4 + - - +
29C VAL* 3.3 22.3 - - - +
97C GLN* 2.9 28.1 + - - -
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.9 3.4 - - + -
8B PHE* 3.6 21.0 - - + -
519B CYS* 4.2 11.0 - - - -
521B VAL* 5.2 0.7 - - + -
22C VAL 3.1 16.1 + - - +
23C LEU 4.0 4.0 - - - +
24C ALA 3.1 0.6 - - - -
25C ASP* 1.3 78.1 - - - +
27C VAL* 1.3 60.8 + - - +
29C VAL* 3.5 7.1 - - - +
38C VAL* 3.5 25.6 - - - +
56C VAL* 4.1 14.5 - - + +
60C ILE* 4.5 13.5 - - + -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.1 20.4 + - + +
24C ALA 2.8 7.4 + - - +
26C ALA* 1.3 76.0 - - - +
28C LYS* 1.3 64.7 + - - +
29C VAL 3.0 3.7 + - - -
30C THR* 3.2 21.8 + - - +
53C GLY* 3.9 22.4 - - - +
56C VAL* 3.5 23.8 - - + -
57C ALA* 3.9 15.3 - - + +
90C THR* 3.7 23.9 - - + +
93C THR* 3.8 25.4 - - + +
94C VAL* 5.9 0.2 - - + -
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Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ALA* 2.7 25.0 + - + +
25C ASP* 3.3 35.8 + - - +
26C ALA 3.5 0.4 - - - -
27C VAL* 1.3 73.2 - - - +
29C VAL* 1.3 64.0 + - + +
30C THR 3.0 2.0 + - - -
31C LEU* 3.0 21.0 + - - +
90C THR* 4.7 0.9 - - - -
93C THR* 5.7 0.4 - - + -
94C VAL* 4.2 29.4 - - + -
97C GLN* 3.3 23.9 + - - +
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 4.6 11.0 - - + -
518B GLU* 4.2 33.4 - - + -
519B CYS* 4.7 2.5 - - + -
25C ASP 3.3 20.6 - - - +
26C ALA 3.5 15.3 - - - +
27C VAL 3.0 0.6 + - - -
28C LYS* 1.3 76.1 - - + +
30C THR* 1.3 54.2 + - + +
31C LEU 3.3 2.5 + - - -
35C GLY* 3.6 3.6 - - - -
36C ARG* 2.7 34.8 + - - +
38C VAL* 3.6 20.0 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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