Contacts of the helix formed by residues 48 - 62 (chain A) in PDB entry 2P1Q
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A SER* 4.0 0.9 - - - -
11A SER* 3.4 12.9 + - - -
12A ASP* 3.7 12.0 + - - +
46A ASN 4.2 0.4 - - - -
47A VAL* 1.3 77.9 - - - +
49A SER* 1.3 50.9 + - - +
50A LYS* 3.3 17.0 - - + +
51A ILE* 3.1 27.9 - - + +
52A LEU* 2.7 35.0 + - - +
100A GLU* 3.3 27.6 + - - +
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 2.5 32.1 + - - -
12A ASP* 3.0 17.6 + - - +
14A GLU* 2.9 30.9 + - - +
16A PHE* 3.6 14.1 - - - -
48A THR* 1.3 68.7 - - - +
50A LYS* 1.3 68.5 + - - +
52A LEU* 4.3 0.2 - - - -
53A ALA* 2.8 26.6 + - - +
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Residues in contact with LYS 50 (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 ASP* 4.7 0.8 + - - -
48A THR* 3.3 11.0 - - + +
49A SER* 1.3 80.3 - - - +
51A ILE* 1.3 78.0 + - + +
53A ALA* 3.3 16.7 - - - +
54A LYS* 3.3 8.8 + - - +
94A ASP* 5.7 0.2 + - - -
96A ALA* 6.2 0.8 - - - +
97A THR* 3.2 32.9 + - - +
100A GLU* 5.1 4.8 + - - -
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Residues in contact with ILE 51 (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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47A VAL* 4.5 3.4 - - + -
48A THR* 3.1 19.4 - - + +
50A LYS* 1.3 101.5 - - + +
52A LEU* 1.3 59.2 + - - +
54A LYS* 3.2 6.5 + - + +
55A VAL* 2.9 28.0 + - - +
97A THR* 4.5 11.4 - - + +
100A GLU* 3.4 57.2 - - + +
101A LEU* 4.0 15.7 - - + +
104A ALA* 3.5 31.2 - - + -
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Residues in contact with LEU 52 (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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8A LEU* 4.1 26.7 - - + -
10A SER* 4.0 15.9 - - - +
16A PHE* 3.5 30.7 - - + -
29A ILE* 5.6 0.2 - - + -
44A LEU* 3.8 26.0 - - + -
47A VAL* 3.6 16.4 - - + +
48A THR 2.7 22.0 + - - +
49A SER* 3.9 5.8 - - - +
51A ILE* 1.3 70.8 - - - +
53A ALA* 1.3 64.8 + - - +
55A VAL* 3.3 6.2 + - + +
56A ILE* 2.9 42.6 + - + +
108A LEU* 4.5 12.6 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.9 20.1 - - + -
49A SER 2.8 23.3 + - - +
50A LYS* 3.3 7.6 - - - +
52A LEU* 1.3 72.0 - - - +
54A LYS* 1.3 57.6 - - - +
56A ILE* 3.4 5.0 + - - +
57A GLU* 3.0 37.3 + - + +
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Residues in contact with LYS 54 (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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50A LYS 3.3 8.6 + - - +
51A ILE* 3.2 12.7 + - + +
53A ALA* 1.3 76.0 - - - +
55A VAL* 1.3 67.0 + - - +
57A GLU* 3.2 32.9 + - - +
58A TYR 3.1 17.7 + - - -
90A PHE* 3.1 62.6 + - + +
92A LYS 5.4 0.4 + - - -
93A ILE* 3.3 23.2 - - + +
97A THR* 4.7 10.3 - - + -
101A LEU* 4.0 21.1 - - + -
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Residues in contact with VAL 55 (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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51A ILE 2.9 21.2 + - - +
52A LEU* 3.3 11.6 + - + +
54A LYS* 1.3 76.5 - - - +
56A ILE* 1.3 60.0 + - + +
58A TYR* 3.3 8.4 + - - +
59A CYS* 2.9 32.1 + - - -
101A LEU* 3.8 19.5 - - + -
104A ALA* 4.1 19.3 - - + -
108A LEU* 4.0 13.9 - - + -
110A ILE* 3.4 30.3 - - + -
113A LEU* 3.9 12.1 - - + -
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Residues in contact with ILE 56 (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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8A LEU* 4.2 9.2 - - + -
16A PHE* 3.5 38.6 - - + -
18A VAL* 3.6 32.1 - - + -
22A VAL* 4.6 4.7 - - + -
52A LEU* 2.9 33.5 + - + +
53A ALA* 3.7 5.2 - - - +
55A VAL* 1.3 74.4 - - + +
57A GLU* 1.3 66.4 + - - +
59A CYS* 3.3 5.6 + - - +
60A LYS* 2.8 59.5 + - + +
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Residues in contact with GLU 57 (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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53A ALA* 3.0 24.9 + - + +
54A LYS* 3.3 39.5 + - - +
56A ILE* 1.3 76.4 - - - +
58A TYR* 1.3 63.5 + - - +
60A LYS* 3.5 12.6 + - - +
61A ARG* 3.1 34.4 + - - +
90A PHE* 4.1 8.9 - - + -
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Residues in contact with TYR 58 (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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54A LYS 3.1 2.7 + - - +
55A VAL* 3.4 10.3 - - - +
57A GLU* 1.3 80.9 - - - +
59A CYS* 1.3 70.3 + - - +
61A ARG* 3.4 11.2 + - - +
62A HIS* 2.9 70.9 + + + +
90A PHE* 3.6 36.8 - + + -
110A ILE* 4.6 0.9 - - + -
112A ASN* 3.1 57.7 + - - +
113A LEU* 3.7 26.7 - - + -
116A LEU* 3.8 22.4 - - + +
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Residues in contact with CYS 59 (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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22A VAL* 3.7 34.2 - - + +
25A GLU* 3.9 29.0 - - + +
26A SER* 6.2 0.2 - - - -
55A VAL* 2.9 33.8 + - - +
56A ILE* 4.0 1.1 - - - +
58A TYR* 1.3 82.6 - - - +
60A LYS* 1.3 67.0 + - - +
62A HIS* 3.6 16.9 - - - -
110A ILE* 4.0 23.1 - - - -
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Residues in contact with LYS 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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17A GLU 5.7 2.5 - - - -
18A VAL* 5.4 5.8 - - - +
22A VAL* 4.0 22.9 - - + +
56A ILE* 2.8 48.6 + - + +
57A GLU* 3.7 10.7 - - - +
59A CYS* 1.3 79.4 - - - +
61A ARG* 1.3 64.2 + - - +
62A HIS 4.1 3.1 - - - -
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Residues in contact with ARG 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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57A GLU* 3.1 23.9 + - - +
58A TYR* 3.7 17.9 - - - +
60A LYS* 1.3 77.7 - - - +
62A HIS* 1.3 80.4 + - - +
90A PHE* 3.5 41.3 - - - +
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Residues in contact with HIS 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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25A GLU* 5.5 8.1 - - + +
58A TYR* 2.9 67.6 + + + +
59A CYS* 3.6 15.5 - - - +
60A LYS 3.3 3.3 - - - -
61A ARG* 1.3 99.3 + - - +
112A ASN* 4.0 21.1 - - + +
116A LEU* 5.7 1.3 - - + -
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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