Contacts of the strand formed by residues 59 - 68 (chain A) in PDB entry 3PIT
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 GLN 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLU* 3.8 2.3 - - - +
56A ILE 3.0 19.7 + - - +
57A ASP* 3.2 21.2 + - - +
58A ASN* 1.3 83.5 - - + +
60A TRP* 1.3 62.9 + - - +
61A ALA 3.7 0.5 + - - -
176A ARG* 3.0 55.0 + - - +
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Residues in contact with TRP 60 (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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11A LEU* 3.7 16.7 - - + +
12A PRO* 3.5 20.3 - - - +
53A HIS* 3.3 40.8 - + - +
54A THR* 3.4 24.7 - - - -
55A GLU* 3.6 48.8 + - + -
58A ASN 5.3 1.3 - - - -
59A GLN* 1.3 75.1 - - - +
61A ALA* 1.3 59.5 + - - +
176A ARG* 4.3 1.6 + - - -
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Residues in contact with ALA 61 (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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11A LEU* 4.0 3.8 - - - -
12A PRO* 3.6 5.6 - - + -
14A TYR* 3.4 35.9 - - + -
52A LYS 3.7 0.3 - - - +
53A HIS* 3.5 3.8 - - - -
54A THR* 2.8 36.6 + - + +
56A ILE* 5.1 2.5 - - + -
59A GLN 4.4 0.2 - - - +
60A TRP* 1.3 77.2 - - - +
62A ILE* 1.3 65.8 + - - +
63A LEU* 3.9 10.3 + - + -
176A ARG* 3.7 9.4 - - - +
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Residues in contact with ILE 62 (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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11A LEU* 3.9 22.4 - - + +
12A PRO 2.9 8.8 + - - +
13A THR* 3.3 30.7 - - + +
14A TYR* 2.8 27.9 + - - -
51A LEU* 4.6 13.7 - - + -
52A LYS 3.4 7.4 - - - +
53A HIS* 3.6 38.6 - - + -
61A ALA* 1.3 73.0 - - - +
63A LEU* 1.3 71.8 + - - +
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Residues in contact with LEU 63 (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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14A TYR* 3.6 17.3 - - + +
16A LEU* 4.3 12.3 - - + -
33A PHE* 3.8 33.7 - - + -
50A TYR 3.5 1.6 - - - +
51A LEU* 3.3 7.4 - - - +
52A LYS* 2.8 40.7 + - + +
54A THR* 3.7 24.9 - - + -
56A ILE* 4.1 14.4 - - + -
61A ALA* 4.3 3.6 - - + -
62A ILE* 1.3 77.2 - - - +
64A ASP* 1.3 60.3 + - - +
65A VAL* 3.8 11.9 - - + -
168A PHE* 5.4 1.1 - - + +
169A HIS* 5.3 0.2 - - - +
172A VAL* 3.7 26.7 - - + -
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Residues in contact with ASP 64 (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 THR* 4.2 16.5 - - + +
14A TYR 2.9 13.6 + - - +
15A LYS* 3.2 30.4 + - + +
16A LEU 2.9 24.3 + - - +
49A SER* 4.2 14.4 + - - -
50A TYR 3.6 3.6 - - - +
51A LEU* 3.8 22.1 - - + +
62A ILE 3.9 0.8 + - - -
63A LEU* 1.3 70.8 - - - +
65A VAL* 1.3 67.5 + - - +
66A LEU* 3.8 1.7 + - - +
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Residues in contact with VAL 65 (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 LEU* 3.3 27.1 - - + +
18A VAL* 3.9 19.5 - - + -
30A THR* 3.8 24.9 - - + +
33A PHE* 4.8 1.6 - - + -
34A PHE* 3.6 29.8 - - + -
48A ASP 3.8 0.9 - - - +
49A SER* 3.4 4.5 - - - -
50A TYR* 2.8 39.0 + - + +
63A LEU* 4.4 8.1 - - + -
64A ASP* 1.3 75.6 - - - +
66A LEU* 1.3 63.3 + - - +
67A ASP 3.9 0.2 + - - -
168A PHE* 3.9 18.8 - - + -
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Residues in contact with LEU 66 (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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15A LYS* 4.2 22.0 - - - +
16A LEU 2.9 12.2 + - - +
17A VAL* 3.7 9.4 - - + -
18A VAL* 2.9 30.1 + - - +
47A GLU* 3.5 42.2 - - + +
48A ASP 3.6 5.2 - - - +
49A SER* 3.2 24.5 - - - +
64A ASP* 3.8 2.4 + - - +
65A VAL* 1.3 73.2 - - - +
67A ASP* 1.3 60.2 + - - +
68A THR* 3.8 7.1 + - + +
81A TYR* 3.5 36.3 - - + -
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Residues in contact with ASP 67 (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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18A VAL* 4.5 4.6 - - - +
26A LYS* 3.5 22.5 - - - +
27A SER* 2.6 39.9 + - - -
30A THR* 4.2 14.3 + - + +
45A THR* 3.5 12.8 + - - +
47A GLU* 3.6 3.8 - - - +
48A ASP* 2.8 43.1 + - + +
50A TYR* 4.2 18.7 + - + -
65A VAL 3.9 1.0 + - - -
66A LEU* 1.3 71.7 - - - +
68A THR* 1.3 64.9 + - - +
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Residues in contact with THR 68 (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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17A VAL* 3.7 16.6 - - + -
18A VAL 2.6 27.2 + - - +
19A VAL* 3.7 10.4 - - - +
20A GLY 4.7 0.2 + - - -
26A LYS* 3.3 16.1 - - - -
45A THR* 3.8 13.0 - - - -
46A ILE 4.5 2.0 - - - -
47A GLU* 4.9 2.9 - - - +
66A LEU* 3.8 9.9 - - + +
67A ASP* 1.3 82.4 + - - +
69A ALA* 1.3 67.8 + - - +
78A ARG* 5.3 0.2 + - - -
81A TYR* 3.4 47.1 + - + -
179A GNP 4.0 0.9 + - - -
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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