Contacts of the helix formed by residues 25 - 38 (chain C) in PDB entry 4PAR
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 TYR 25 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ARG* 1.3 122.5 + - + +
26C GLU* 1.3 67.1 + - - +
27C ALA 3.4 2.2 - - - -
28C TYR* 3.5 9.9 + + + +
29C VAL* 3.3 25.3 + - + +
73C VAL* 4.7 2.9 - - + -
75C GLU* 3.6 16.5 + - - +
79C PHE* 4.8 0.7 - + - -
125C VAL* 4.1 33.4 - - + -
126C PHE* 3.8 27.1 - + - -
131C GLY 5.0 0.2 + - - -
133C PRO* 3.5 26.4 - - + +
134C GLN 6.1 0.2 - - - -
139C ILE* 5.4 6.7 - - + -
10D THR* 4.4 12.8 + - - -
11D ASP* 4.3 1.7 + - - -
14D ILE* 4.1 29.4 - - + +
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Residues in contact with GLU 26 (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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21C LYS* 4.0 4.9 - - + -
22C ASN* 3.1 31.5 + - - +
23C LYS* 3.5 25.2 + - + +
24C ARG 3.4 1.6 - - - -
25C TYR* 1.3 79.1 - - - +
27C ALA* 1.3 65.5 + - - +
29C VAL* 3.4 1.2 + - - +
30C VAL* 3.0 33.4 + - + +
46C THR* 5.1 2.9 - - - -
47C GLN* 3.5 30.6 + - - +
61C ASP* 3.9 37.0 - - + +
73C VAL* 4.3 11.6 - - - +
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU 5.7 5.6 - - - +
21C LYS* 5.6 12.3 - - + +
23C LYS 5.4 0.4 + - - -
24C ARG 4.8 4.5 + - - +
25C TYR 3.4 0.6 - - - -
26C GLU* 1.3 80.5 - - - +
28C TYR* 1.3 55.6 + - - +
30C VAL* 4.2 3.5 - - - +
31C SER* 2.8 38.7 + - - -
17D LEU 5.8 4.5 - - - +
18D GLY* 6.3 2.2 - - - -
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Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ARG 5.5 0.8 + - - +
25C TYR* 3.5 11.5 + + + +
26C GLU 3.3 0.6 - - - -
27C ALA* 1.3 76.7 - - - +
29C VAL* 1.3 72.9 + - + +
31C SER* 2.8 20.0 + - - -
32C ARG* 2.9 23.3 + - - +
136C LEU* 3.4 22.7 - - + +
139C ILE* 4.9 6.7 - - + -
140C HIS* 2.7 33.9 + + - -
143C ILE* 5.0 1.1 - - + -
13D VAL* 3.6 22.0 - - + -
14D ILE* 4.0 29.8 - - + -
17D LEU* 3.9 18.2 - - + -
35D HIS* 3.2 27.3 + + - -
40D PHE* 3.6 11.7 - + - -
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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
----------------------------------------------------------
25C TYR* 3.3 17.6 + - + +
26C GLU 3.8 4.9 - - - +
28C TYR* 1.3 87.7 - - + +
30C VAL* 1.3 59.0 + - + +
32C ARG* 3.3 1.9 + - - +
33C ILE* 2.9 47.1 + - + +
71C ILE* 4.9 2.9 - - + -
73C VAL* 4.0 25.4 - - + -
123C VAL* 4.1 31.6 - - + -
125C VAL* 4.7 10.1 - - + -
139C ILE* 5.1 3.1 - - + -
143C ILE* 4.2 15.3 - - + -
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.9 22.7 - - + -
26C GLU* 3.0 32.7 + - + +
27C ALA* 4.2 3.4 - - - +
29C VAL* 1.3 80.2 - - + +
31C SER* 1.3 65.5 + - - +
33C ILE* 3.2 8.8 + - + +
34C ILE* 3.0 23.7 + - + +
46C THR* 4.0 15.0 - - + -
61C ASP* 3.9 24.5 - - + +
62C LEU* 4.0 25.1 - - + +
71C ILE* 6.1 1.8 - - + -
73C VAL* 5.4 1.1 - - + -
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.8 13.4 - - - +
27C ALA* 2.8 24.0 + - - -
28C TYR* 2.8 7.6 + - - -
30C VAL* 1.3 78.1 - - - +
32C ARG* 1.3 72.3 + - - +
34C ILE* 3.3 4.5 + - - +
35C HIS* 2.9 46.5 + - - -
31D SER* 4.2 9.8 - - - -
35D HIS* 3.2 12.6 - - - -
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Residues in contact with ARG 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 2.9 18.6 + - - +
29C VAL* 3.6 4.5 - - - +
31C SER* 1.3 81.4 + - - +
33C ILE* 1.3 64.4 + - - +
35C HIS* 3.8 0.5 - - - +
36C LEU* 2.9 51.9 + - + +
140C HIS* 3.5 40.0 + - - +
143C ILE* 3.7 33.0 - - + +
144C ASP* 4.8 4.2 + - - -
35D HIS* 3.2 56.3 + - + +
38D ASN* 3.0 36.5 + - - +
40D PHE* 4.9 0.8 - - - -
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Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 2.9 28.1 + - + +
30C VAL* 3.5 7.9 - - + +
32C ARG* 1.3 75.5 - - - +
34C ILE* 1.3 65.5 + - - +
36C LEU 3.4 0.2 + - - -
37C LEU* 2.9 24.2 + - + +
62C LEU* 4.1 18.4 - - + -
64C PHE* 4.7 5.4 - - + -
71C ILE* 3.7 43.3 - - + -
143C ILE* 3.7 22.9 - - + -
146C ILE* 4.3 11.7 - - + -
147C ILE* 3.8 21.9 - - + +
150C ILE* 4.5 8.3 - - + -
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.1 19.1 - - + -
30C VAL 3.0 17.7 + - - +
31C SER* 3.7 8.1 - - - +
33C ILE* 1.3 78.0 - - - +
35C HIS* 1.3 69.0 + - + +
37C LEU* 3.2 6.1 + - + +
38C ASN* 3.0 21.3 + - - -
39C ASP 4.9 0.3 + - - -
40C PHE* 4.1 29.0 - - + -
44C PHE* 3.5 53.6 - - + -
62C LEU* 4.3 7.6 - - + -
64C PHE* 4.2 17.3 - - + -
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Residues in contact with HIS 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.7 6.2 - - + +
31C SER* 2.9 39.0 + - - +
32C ARG 3.9 2.5 - - - +
34C ILE* 1.3 77.2 - - + +
36C LEU* 1.3 61.5 + - - +
38C ASN* 3.6 15.4 + - - +
40C PHE* 5.7 0.9 - - - -
28D TYR* 3.3 40.3 + + - -
31D SER* 2.9 29.1 + - - -
32D ARG* 3.5 49.8 + - + +
35D HIS* 4.0 8.3 - - + -
36D LEU* 3.7 24.4 - - + +
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Residues in contact with LEU 36 (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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32C ARG* 2.9 58.1 + - + +
35C HIS* 1.3 75.0 - - - +
37C LEU* 1.3 67.0 + - - +
38C ASN* 4.0 3.6 - - - +
143C ILE* 4.6 0.4 - - + -
144C ASP* 3.8 19.3 - - - +
147C ILE* 3.5 19.2 - - + +
151C LYS* 5.2 4.3 + - - -
35D HIS* 3.7 27.4 - - + +
36D LEU* 4.4 11.7 - - + -
38D ASN* 6.0 0.4 - - - -
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Residues in contact with LEU 37 (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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33C ILE* 2.9 19.3 + - + +
34C ILE* 3.5 7.9 - - + +
36C LEU* 1.3 79.8 - - - +
38C ASN* 1.3 64.8 + - - +
39C ASP* 3.0 31.2 + - + +
42C LEU* 4.0 13.7 - - + -
64C PHE* 3.8 33.9 - - + -
147C ILE* 4.1 21.0 - - + +
150C ILE* 4.0 21.1 - - + -
151C LYS* 4.3 33.8 + - + +
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Residues in contact with ASN 38 (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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34C ILE 3.0 15.4 + - - -
35C HIS 3.6 9.6 - - - +
36C LEU 4.0 3.6 - - - +
37C LEU* 1.3 76.5 - - - +
39C ASP* 1.3 58.7 + - - +
40C PHE* 3.9 19.4 + - - -
32D ARG* 2.6 39.0 + - - +
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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
------------------------------------------------------------
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