Contacts of the helix formed by residues 25 - 37 (chain U) in PDB entry 1P9D
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 VAL 25 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19U MET* 4.0 5.8 - - + -
23U GLU* 3.3 2.0 - - - +
24U THR* 1.3 69.0 - - - +
26U LYS* 1.3 58.5 + - - +
27U VAL 3.5 1.3 - - - +
28U LEU* 3.2 8.4 - - + +
29U LYS* 2.8 47.1 - - - +
48U LEU* 4.6 8.3 - - + -
55U LEU* 3.9 17.0 - - + +
57U ASP* 3.6 5.4 - - - -
59U VAL* 2.5 47.1 - - + +
60U PRO 3.5 0.2 - - - -
61U ILE* 2.8 46.0 - - + +
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Residues in contact with LYS 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U THR* 2.6 17.3 + - - +
25U VAL* 1.3 70.1 - - - +
27U VAL* 1.3 62.2 + - - +
28U LEU 2.9 1.3 - - - -
29U LYS* 2.7 35.4 + - - +
30U GLU* 3.0 14.4 + - + +
43U VAL* 3.3 33.5 + - - +
44U ALA* 4.7 0.6 - - - +
57U ASP* 2.8 52.9 + - - +
58U ASP* 5.0 3.1 - - - +
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Residues in contact with VAL 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U MET* 4.2 17.9 - - + -
23U GLU* 3.0 42.6 - - + +
24U THR* 4.5 2.0 - - - +
25U VAL* 4.6 1.3 - - - +
26U LYS* 1.3 78.3 - - - +
28U LEU* 1.3 64.2 + - - +
30U GLU* 3.0 41.6 - - - +
31U LYS* 3.2 17.9 + - + +
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Residues in contact with LEU 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U ILE* 3.6 21.1 - - + -
7U LEU* 4.3 0.2 - - + -
17U ILE* 2.8 39.5 - - + -
19U MET* 2.8 42.2 - - + -
25U VAL* 3.2 11.7 - - - +
27U VAL* 1.3 80.0 - - - +
29U LYS* 1.3 61.4 + - + +
31U LYS* 2.9 5.8 + - - +
32U ILE* 2.8 42.5 + - + +
48U LEU* 3.1 36.3 - - + -
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Residues in contact with LYS 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25U VAL* 2.8 38.7 - - - +
26U LYS* 2.7 13.3 + - - +
28U LEU* 1.3 76.3 - - + +
30U GLU* 1.3 50.7 + - - +
32U ILE* 4.9 0.7 - - + -
33U GLU* 2.6 41.8 + - - +
43U VAL* 3.0 19.3 - - + -
46U GLN* 3.1 49.0 + - + +
47U LYS* 3.7 2.2 - - - +
48U LEU* 2.8 37.9 - - + -
57U ASP* 2.9 26.7 - - + +
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Residues in contact with GLU 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U LYS* 3.5 14.5 - - + +
27U VAL* 3.0 36.4 + - - +
29U LYS* 1.3 79.0 - - - +
31U LYS* 1.3 60.6 + - + +
33U GLU* 3.9 5.2 - - - +
34U ALA* 3.1 28.4 + - - +
43U VAL* 3.8 14.4 - - + -
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Residues in contact with LYS 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17U ILE* 3.5 30.3 - - + -
18U ARG* 4.9 23.1 + - + +
19U MET* 5.7 0.2 - - + -
27U VAL* 3.2 21.8 + - + +
28U LEU* 2.9 8.4 + - - +
30U GLU* 1.3 81.6 - - - +
32U ILE* 1.3 60.8 + - - +
34U ALA* 2.8 22.3 + - - +
35U GLU* 2.8 14.4 + - - +
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Residues in contact with ILE 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7U LEU* 4.0 11.4 - - + -
15U PHE* 4.3 2.9 - - + -
17U ILE* 3.0 32.5 - - + -
28U LEU* 2.8 52.8 + - + +
29U LYS* 4.9 1.1 - - + +
31U LYS* 1.3 73.8 - - - +
33U GLU* 1.3 57.3 + - - +
35U GLU* 3.6 9.9 - - - +
36U LYS* 2.9 25.6 + - - +
41U PHE* 3.1 32.4 - - + -
46U GLN* 3.6 5.2 - - - +
48U LEU* 4.7 3.8 - - + -
74U VAL* 3.5 24.0 - - + -
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Residues in contact with GLU 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U LYS 2.6 23.9 + - - +
30U GLU* 3.9 6.2 - - - +
32U ILE* 1.3 77.5 - - - +
34U ALA* 1.3 62.2 + - - +
37U GLY* 2.8 24.6 + - - +
38U ARG* 2.7 35.8 + - - +
41U PHE* 2.6 40.2 - - - +
42U PRO* 3.6 7.2 - - + +
43U VAL* 3.9 9.2 + - + +
46U GLN* 3.4 0.4 - - - +
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Residues in contact with ALA 34 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30U GLU 3.1 19.2 + - - +
31U LYS* 2.8 9.9 + - - +
33U GLU* 1.3 82.8 - - - +
35U GLU* 1.3 59.0 + - - +
36U LYS 5.1 0.3 - - - -
37U GLY* 4.7 1.0 + - - -
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Residues in contact with GLU 35 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274S GLY 5.0 2.4 - - - +
9U THR* 4.0 0.7 - - - +
13U GLN* 6.0 1.8 - - - -
15U PHE* 2.6 56.0 - - - -
16U LYS 4.9 0.3 - - - +
17U ILE* 4.1 6.9 - - + +
31U LYS 2.8 13.1 + - - +
32U ILE* 3.2 8.2 + - - +
34U ALA* 1.3 79.9 - - - +
36U LYS* 1.3 84.2 + - + +
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Residues in contact with LYS 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274S GLY* 3.3 34.1 + - - -
275S LEU* 4.0 5.2 - - - +
276S PRO* 3.5 38.4 - - + +
9U THR* 4.0 10.5 - - + +
11U GLN* 5.1 5.5 - - - +
13U GLN* 4.3 22.0 + - - +
32U ILE 2.9 5.6 + - - +
34U ALA 5.0 0.2 - - - -
35U GLU* 1.3 103.7 - - - +
37U GLY* 1.3 55.4 + - - +
40U ALA* 5.4 6.2 - - + +
41U PHE* 2.8 47.6 - - + -
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Residues in contact with GLY 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U GLU* 2.8 20.2 + - - +
34U ALA 5.4 0.7 - - - -
36U LYS* 1.3 77.6 - - - +
38U ARG* 1.3 56.2 + - - -
39U ASP* 3.0 9.2 - - - -
40U ALA* 4.5 6.1 - - - -
41U PHE* 2.8 33.2 + - - +
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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