Contacts of the helix formed by residues 22 - 35 (chain V) in PDB entry 1P3Q
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 THR 22 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20V SER 4.5 2.7 - - - +
21V ASP* 1.3 77.1 - - - +
23V ILE* 1.3 65.5 + - - +
24V GLU* 3.5 6.2 + - - +
25V ASN* 2.9 37.7 + - - +
26V VAL* 3.1 22.5 + - - +
52V ASP 3.6 9.4 - - - +
53V GLY* 4.1 14.1 - - - +
54V ARG 3.3 13.2 - - - +
55V THR* 4.3 11.0 - - + -
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Residues in contact with ILE 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V THR* 1.3 73.0 - - - +
24V GLU* 1.3 57.3 + - - +
26V VAL* 3.1 5.5 + - + +
27V LYS* 2.8 53.1 + - - +
43V LEU* 4.1 13.7 - - + -
50V LEU* 3.8 37.0 - - + +
51V GLU 3.0 35.7 - - - +
52V ASP* 3.5 1.8 + - - -
54V ARG 2.9 16.5 + - - +
55V THR 4.8 1.6 - - - -
56V LEU* 4.1 22.9 - - + -
59V TYR* 4.0 15.0 - - + -
67V LEU* 5.4 0.4 - - + -
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Residues in contact with GLU 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V THR* 3.1 7.4 - - - +
23V ILE* 1.3 77.6 - - - +
25V ASN* 1.3 58.8 + - - +
27V LYS* 3.3 8.1 + - - +
28V ALA* 3.0 28.1 + - - +
38V PRO* 5.6 1.2 - - - +
52V ASP* 2.9 52.7 + - + +
53V GLY* 4.1 5.8 + - - -
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Residues in contact with ASN 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V SER 5.1 0.2 - - - +
21V ASP* 3.7 20.1 - - + +
22V THR* 2.9 42.2 + - - +
24V GLU* 1.3 79.9 - - - +
26V VAL* 1.3 63.3 + - - +
28V ALA* 3.3 9.1 + - - +
29V LYS* 3.3 26.3 + - - +
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Residues in contact with VAL 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3V ILE* 4.8 2.0 - - + -
5V VAL* 5.0 0.2 - - + -
15V LEU* 3.8 20.2 - - + -
17V VAL* 4.4 19.1 - - + -
21V ASP* 4.9 3.8 - - + -
22V THR 3.1 13.5 + - - +
23V ILE* 3.4 10.5 - - + +
25V ASN* 1.3 74.1 - - - +
27V LYS* 1.3 66.3 + - - +
29V LYS* 3.2 10.5 + - - +
30V ILE* 3.0 32.0 + - + +
43V LEU* 4.0 13.7 - - + -
56V LEU* 4.1 26.2 - - + -
67V LEU* 4.6 11.7 - - + -
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Residues in contact with LYS 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V ILE* 2.8 31.9 + - - +
24V GLU* 3.3 6.9 + - - +
26V VAL* 1.3 71.4 - - - +
28V ALA* 1.3 62.0 + - - +
30V ILE* 3.1 2.0 + - - -
31V GLN* 3.0 19.9 + - - +
38V PRO* 3.9 30.0 + - + +
41V GLN* 3.0 59.5 + - - +
42V ARG* 4.8 2.2 - - - +
43V LEU* 4.1 20.2 - - + +
50V LEU 4.4 9.0 + - - -
51V GLU* 5.3 1.0 + - - -
52V ASP* 2.7 33.7 + - - +
72V ARG* 4.7 6.9 - - - +
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Residues in contact with ALA 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24V GLU 3.0 12.7 + - - +
25V ASN* 3.4 13.0 - - - +
26V VAL 3.2 0.2 - - - -
27V LYS* 1.3 75.9 - - - +
29V LYS* 1.3 61.7 + - + +
31V GLN* 3.2 20.5 + - - +
32V ASP* 3.2 19.0 + - - +
38V PRO* 4.6 8.7 - - + +
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Residues in contact with LYS 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V LEU* 3.9 28.9 - - + -
16V GLU* 2.7 34.5 + - - +
17V VAL* 4.8 5.3 - - + +
21V ASP* 5.3 3.3 + - - -
25V ASN* 3.3 11.6 + - - +
26V VAL* 3.2 10.6 + - - +
28V ALA* 1.3 75.0 - - + +
30V ILE* 1.3 66.2 + - - +
32V ASP* 3.1 23.4 + - - +
33V LYS* 3.1 21.5 + - - +
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Residues in contact with ILE 30 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5V VAL* 4.2 15.5 - - + -
13V ILE* 4.7 5.8 - - + -
15V LEU* 4.1 12.8 - - + -
26V VAL* 3.0 26.9 + - + +
27V LYS* 3.1 1.3 + - - +
29V LYS* 1.3 73.8 - - - +
31V GLN* 1.3 59.8 + - - +
33V LYS* 4.1 6.5 - - - -
34V GLU* 2.8 47.8 + - + +
36V ILE* 5.1 1.1 - - + +
41V GLN* 3.4 33.7 - - - +
43V LEU* 3.8 27.8 - - + -
69V LEU* 4.0 15.3 - - + -
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Residues in contact with GLN 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V LYS 3.0 11.4 + - - +
28V ALA* 3.4 13.5 - - - +
30V ILE* 1.3 76.6 - - - +
32V ASP* 1.3 68.6 + - - +
35V GLY* 3.1 21.9 + - - -
36V ILE 3.4 26.0 - - - +
37V PRO* 3.6 15.2 - - - +
38V PRO* 3.5 30.4 - - + +
41V GLN* 3.5 1.1 - - - +
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Residues in contact with ASP 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V ALA* 3.2 15.3 + - - +
29V LYS* 3.1 19.0 + - - +
31V GLN* 1.3 84.6 - - - +
33V LYS* 1.3 61.4 + - + +
35V GLY 5.0 0.3 + - - -
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Residues in contact with LYS 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V ILE* 3.6 35.0 - - + -
14V THR 4.0 8.3 - - - +
15V LEU* 3.7 25.1 - - + -
29V LYS* 3.1 14.6 - - - +
30V ILE* 4.0 3.8 - - - +
32V ASP* 1.3 80.5 - - - +
34V GLU* 1.3 70.3 + - - +
35V GLY 3.8 0.2 - - - -
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Residues in contact with GLU 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427R LEU* 3.5 19.2 - - - +
430R ASP* 5.1 7.1 - - - +
7V THR* 3.4 34.1 - - + +
8V LEU* 6.2 0.2 - - - +
11V LYS* 5.3 3.9 - - - +
13V ILE* 3.5 28.0 - - + +
30V ILE* 2.8 39.9 + - + +
33V LYS* 1.3 89.7 - - - +
35V GLY* 1.3 60.6 + - - +
36V ILE* 3.6 16.2 + - + +
69V LEU* 4.7 3.8 - - + +
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Residues in contact with GLY 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427R LEU* 3.9 21.4 - - - +
31V GLN* 3.1 17.1 + - - -
32V ASP 4.9 0.4 + - - -
33V LYS 3.8 0.6 - - - -
34V GLU* 1.3 78.2 - - - +
36V ILE* 1.3 60.8 + - - +
37V PRO* 4.0 6.4 - - - +
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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