Contacts of the helix formed by residues 35 - 46 (chain A) in PDB entry 3PPA
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 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL 3.3 4.2 + - - -
34A ASP* 1.3 72.3 + - - +
36A ARG* 1.4 58.8 + - - +
37A TRP 3.5 0.2 - - - -
38A PHE* 3.8 8.2 - - - +
39A LYS* 2.9 31.4 + - - +
86A GLU 3.9 12.6 - - - -
87A LEU 2.9 24.4 + - - -
88A ASP* 3.1 22.2 + - - -
89A TYR* 4.1 4.9 - - - -
90A ILE* 5.5 3.8 - - - -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP* 3.1 20.6 + - - +
35A SER* 1.4 76.9 - - - +
37A TRP* 1.4 65.1 + - - +
39A LYS* 3.6 5.5 + - - +
40A GLN* 3.5 24.4 + - - +
69A GLY* 6.2 1.8 - - - -
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Residues in contact with TRP 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.6 18.2 - - + -
34A ASP* 3.2 9.7 + - + +
36A ARG* 1.4 78.2 - - - +
38A PHE* 1.3 69.8 + + - +
40A GLN* 3.4 8.0 + - - +
41A TRP* 3.1 46.8 + + + -
62A PRO* 3.3 29.7 + - + +
63A GLY 3.0 26.7 + - - -
64A PRO 3.5 14.4 + - - -
65A ILE* 3.6 27.1 - - + +
66A ASP* 3.8 30.1 - - + +
100A LEU* 3.8 27.1 - - + -
104A TYR* 3.8 19.3 - + - -
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Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.8 21.1 - - + -
20A LEU* 3.9 17.7 - - + -
33A VAL* 4.3 7.6 - - + -
34A ASP 3.0 15.8 + - - +
35A SER* 4.0 9.0 - - - +
37A TRP* 1.3 92.4 - + - +
39A LYS* 1.4 59.2 + - - +
41A TRP* 3.3 30.0 + + - +
42A LYS* 3.0 52.0 + - + +
47A PHE* 5.5 1.6 - + - -
90A ILE* 3.8 42.0 - - + -
92A LEU* 4.0 8.7 - - + -
100A LEU* 4.6 3.1 - - + -
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER 2.9 20.3 + - - +
36A ARG* 3.9 7.2 - - - +
37A TRP 3.4 0.4 - - - -
38A PHE* 1.4 75.8 - - - +
40A GLN* 1.3 60.6 + - + +
42A LYS* 3.5 13.1 - - - +
43A LYS* 3.4 37.4 + - - +
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Residues in contact with GLN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG 3.5 11.6 + - - +
37A TRP* 3.4 10.0 + - - +
38A PHE 3.2 0.2 - - - -
39A LYS* 1.3 75.6 - - + +
41A TRP* 1.3 65.4 + - - +
42A LYS 3.2 0.4 + - - -
43A LYS* 3.4 29.8 + - - +
44A TYR* 3.1 17.7 + - - +
59A ASN 3.9 6.1 - - - +
60A VAL* 3.2 40.8 - - - +
61A TYR 4.5 2.8 - - - +
62A PRO* 4.0 14.6 - - + -
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Residues in contact with TRP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLN* 3.4 48.4 + - + +
13A ARG* 4.3 2.7 - - - -
16A ILE* 3.6 26.7 - - + -
37A TRP* 3.1 36.1 + + + +
38A PHE* 3.5 34.5 - + - +
40A GLN* 1.3 75.2 - - - +
42A LYS* 1.4 83.7 + - + +
44A TYR* 3.5 2.3 + - - +
45A VAL* 3.1 28.7 + - + +
47A PHE* 3.6 32.5 - + + -
62A PRO* 3.8 12.0 - - + +
100A LEU* 4.1 8.2 - - + +
104A TYR* 3.3 34.8 - + - -
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.0 34.6 + - + +
39A LYS* 3.5 15.0 - - - +
40A GLN 3.2 0.4 - - - -
41A TRP* 1.4 92.5 - - + +
43A LYS* 1.4 57.4 + - + +
45A VAL 3.3 1.9 + - - -
46A GLY 2.9 10.0 + - - -
47A PHE* 2.9 60.4 + - + +
48A ASP* 4.0 15.5 - - - +
51A ASP 5.5 0.4 - - - -
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 3.4 21.0 + - - +
40A GLN* 3.4 32.3 + - - +
42A LYS* 1.4 76.9 - - + +
44A TYR* 1.3 60.0 + - - +
46A GLY* 3.4 10.2 + - - -
51A ASP* 3.6 37.6 + - - +
52A LYS 5.0 0.2 - - - +
54A GLN* 3.6 29.6 + - + +
55A MET 3.5 18.0 + - - -
60A VAL* 4.2 10.8 - - + -
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Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.9 23.5 - - + +
40A GLN 3.1 6.8 + - - +
41A TRP 3.7 4.5 - - - +
42A LYS 3.3 0.2 - - - -
43A LYS* 1.3 78.4 - - - +
45A VAL* 1.3 57.8 + - + +
46A GLY 3.5 0.4 - - - -
54A GLN 4.1 5.4 - - - -
55A MET* 3.7 2.4 - - - +
56A GLY* 3.0 49.4 + - - -
57A ASP 3.3 28.5 - - - -
58A GLN* 4.5 1.1 - - - -
60A VAL* 3.3 18.5 - - - +
61A TYR* 3.4 41.0 - + + -
62A PRO* 4.0 7.4 - - + -
104A TYR* 3.7 22.7 - - - -
322A CIT 5.5 1.9 + - - -
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.1 29.8 - - + +
10A ASP* 5.1 1.6 - - - +
12A GLN* 4.8 4.7 - - + +
13A ARG* 4.0 19.3 - - + +
41A TRP* 3.1 40.7 + - + +
42A LYS* 4.2 1.8 - - - +
44A TYR* 1.3 76.6 - - + +
46A GLY* 1.3 63.7 - - - +
47A PHE 3.4 1.3 + - - +
55A MET* 3.6 16.5 - - - +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.6 6.3 - - - -
42A LYS 2.9 5.7 + - - -
43A LYS 3.4 6.8 + - - -
44A TYR 3.5 0.4 - - - -
45A VAL* 1.3 78.9 - - - +
47A PHE* 1.4 63.0 + - - +
48A ASP 3.4 2.9 - - - -
51A ASP 3.9 14.8 - - - -
52A LYS* 3.4 26.8 + - - +
55A MET* 3.5 21.5 - - - +
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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