Contacts of the helix formed by residues 17 - 26 (chain m) in PDB entry 4PJO
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 SER 17 (chain m).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104 U 2.9 45.3 + - - -
114 G 4.4 2.0 + - - -
15m HIS 3.8 1.2 + - - -
16m ASP* 1.3 94.3 + - - +
18m PRO* 1.3 79.0 - - - +
19m SER* 3.9 11.0 - - - -
20m VAL* 3.9 7.4 - - - +
21m ARG* 3.0 15.3 + - - +
5u HIS* 4.8 5.8 - - - -
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Residues in contact with PRO 18 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17m SER* 1.3 86.1 - - - +
19m SER* 1.3 66.0 + - - +
21m ARG* 3.3 12.1 - - + +
22m LYS* 3.1 40.2 + - - +
37o ASP* 6.1 0.2 - - - +
5u HIS* 3.8 43.5 - - + +
6u PRO* 5.0 8.5 - - + +
8u GLU* 4.9 6.5 - - - +
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Residues in contact with SER 19 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94 C 2.9 30.6 + - - -
104 U 3.7 20.3 + - - -
17m SER* 3.9 3.6 - - - -
18m PRO* 1.3 83.7 - - - +
20m VAL* 1.3 58.0 + - - +
22m LYS* 3.5 7.9 + - - +
23m THR* 2.9 32.3 + - - -
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Residues in contact with VAL 20 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94 C 3.6 19.3 - - + +
104 U 3.4 40.2 - - - +
13m LEU* 3.7 24.2 - - + -
15m HIS 4.0 14.4 - - - +
17m SER* 3.6 14.5 + - - +
18m PRO 3.3 0.6 - - - -
19m SER* 1.3 80.6 + - - +
21m ARG* 1.3 57.8 + - - +
23m THR* 3.4 6.3 + - - -
24m HIS* 3.0 26.7 + - - +
2y G 4.4 13.5 - - - +
3y G 4.7 7.9 + - - +
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Residues in contact with ARG 21 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4m PHE* 3.8 33.6 - - + -
13m LEU* 3.8 16.2 - - + -
16m ASP* 3.2 25.1 + - - +
17m SER 3.0 18.5 + - - +
18m PRO* 3.3 13.9 - - + +
20m VAL* 1.3 76.2 - - - +
22m LYS* 1.3 65.7 + - + +
24m HIS* 3.4 1.4 + - - +
25m CYS* 2.9 36.9 + - - +
3o ILE* 5.5 1.9 - - - +
8o LYS* 5.6 2.0 - - - +
11o HIS* 3.0 54.9 + - - +
14o GLU* 5.4 0.8 + - - -
34o GLU* 5.9 0.4 + - - -
37o ASP* 4.2 13.2 + - - -
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Residues in contact with LYS 22 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18m PRO* 3.1 30.7 + - - +
19m SER* 3.9 6.2 - - - +
21m ARG* 1.3 79.3 - - + +
23m THR* 1.3 64.7 + - - +
25m CYS* 3.2 4.7 + - - +
26m SER* 2.8 34.6 + - - +
34o GLU* 4.2 24.6 + - - +
8u GLU* 3.4 26.9 + - - -
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Residues in contact with THR 23 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94 C 4.6 10.0 + - - -
19m SER* 2.9 21.0 + - - -
20m VAL* 3.5 10.2 - - - -
21m ARG 3.4 0.2 - - - -
22m LYS* 1.3 77.2 - - - +
24m HIS* 1.3 64.3 + - - +
26m SER* 3.3 19.5 + - - +
27m GLY* 3.6 2.8 + - - -
3y G 4.9 9.4 - - - +
4y U 3.6 37.1 + - - +
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Residues in contact with HIS 24 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4m PHE* 6.1 2.2 - + - -
6m CYS* 3.7 7.5 - - + +
9m CYS* 3.3 11.8 - - - -
11m THR* 3.7 20.4 - - + -
13m LEU* 3.7 23.0 - - + +
20m VAL 3.0 15.9 + - - +
21m ARG 3.6 3.8 - - - +
23m THR* 1.3 75.7 - - - +
25m CYS* 1.3 72.7 + - - +
27m GLY 3.2 10.7 + - - -
30m HIS* 3.4 6.7 + + - +
201m ZN 1.8 38.0 - - - -
3y G 3.4 38.0 + - - +
4y U 4.0 8.3 - - - -
102y MG 3.4 9.9 - - - -
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Residues in contact with CYS 25 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4m PHE* 5.9 7.2 - - - -
21m ARG* 2.9 32.0 + - - +
22m LYS* 3.2 6.2 + - - +
24m HIS* 1.3 85.6 - - - +
26m SER* 1.3 56.3 + - - +
27m GLY 3.2 3.0 + - - -
30m HIS* 3.1 41.6 - - + -
31m LYS* 3.9 10.0 - - - +
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Residues in contact with SER 26 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22m LYS* 2.8 20.7 + - - +
23m THR* 3.4 9.7 - - - +
25m CYS* 1.3 74.8 - - - +
27m GLY* 1.3 55.5 + - - +
31m LYS* 4.0 21.9 + - - +
4y U 5.0 1.6 + - - +
5y A 5.2 1.0 + - - +
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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
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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