Contacts of the helix formed by residues 44 - 53 (chain A) in PDB entry 2PY2
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 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PHE* 5.0 1.9 - - - -
42A ILE* 3.7 2.3 - - - +
43A HIS* 1.3 80.5 - - - +
45A LEU* 1.3 60.2 + - - +
46A GLU* 3.4 17.6 + - - +
47A GLU* 3.0 25.2 + - - +
48A SER* 2.9 27.0 + - - -
85A TYR* 3.6 17.3 - - - -
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Residues in contact with LEU 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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44A SER* 1.3 73.9 - - - +
46A GLU* 1.3 74.7 + - - +
48A SER* 3.2 7.2 + - - +
49A THR* 2.8 45.9 + - - +
52A LYS* 6.3 0.9 - - - +
85A TYR* 3.5 27.4 - - + +
87A ASP* 6.0 1.8 - - - +
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Residues in contact with GLU 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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11A PHE* 3.8 19.2 - - + -
44A SER* 3.1 14.2 - - - +
45A LEU* 1.3 103.1 + - - +
47A GLU* 1.3 61.5 + - - +
49A THR* 3.5 6.2 + - - -
50A PHE* 3.1 21.8 + - - +
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Residues in contact with GLU 47 (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 PHE* 3.5 33.1 - - + -
12A ASN* 4.7 3.6 - - - +
14A ARG* 2.8 40.2 + - - -
16A PHE* 3.8 11.9 - - + -
41A SER 4.3 0.9 - - - -
42A ILE* 3.6 6.6 - - + -
43A HIS* 2.8 38.0 + - - +
44A SER* 3.0 21.5 + - - +
46A GLU* 1.3 74.8 - - - +
48A SER* 1.3 66.8 + - - +
50A PHE* 3.2 2.7 + - - +
51A VAL* 2.9 31.4 + - + +
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Residues in contact with SER 48 (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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42A ILE* 3.8 14.6 - - - +
44A SER 2.9 13.0 + - - -
45A LEU* 3.4 13.4 - - - +
47A GLU* 1.3 78.0 - - - +
49A THR* 1.3 56.4 + - - +
51A VAL* 2.8 27.9 - - - +
52A LYS* 2.9 32.2 + - - +
85A TYR* 3.7 18.6 + - - -
87A ASP* 4.4 7.6 + - - -
104A MET* 5.0 2.6 - - - +
112A TRP* 5.2 3.5 + - - -
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Residues in contact with THR 49 (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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45A LEU* 2.8 32.8 + - - +
46A GLU* 3.8 6.9 - - - -
48A SER* 1.3 77.2 - - - +
50A PHE* 1.3 62.7 + - - +
52A LYS* 3.2 11.7 + - + +
53A GLU* 3.0 42.8 + - + +
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Residues in contact with PHE 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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9A LYS* 3.7 23.6 - - + -
10A MET 3.5 24.0 - - - -
11A PHE* 3.6 38.6 - + + -
16A PHE* 3.6 24.7 - + - -
46A GLU 3.1 14.9 + - - +
47A GLU 3.2 7.2 + - - +
49A THR* 1.3 77.2 - - - +
51A VAL* 1.3 70.0 + - + +
53A GLU* 3.2 31.9 + - + +
54A LEU* 3.6 22.2 + - + +
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Residues in contact with VAL 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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16A PHE* 3.9 35.2 - - + -
40A ALA* 5.5 0.2 - - + -
42A ILE* 3.7 25.1 - - + -
47A GLU* 2.9 18.3 + - + +
48A SER* 2.8 31.0 - - - +
50A PHE* 1.3 78.9 - - + +
52A LYS* 1.3 66.9 + - - +
54A LEU* 2.8 24.5 + - + +
55A THR* 3.6 10.6 - - - +
104A MET* 3.8 13.7 - - + -
124A ILE* 4.5 16.4 - - + +
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Residues in contact with LYS 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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45A LEU* 6.3 0.8 - - - +
48A SER* 2.9 35.5 + - - +
49A THR* 3.2 10.7 + - + +
51A VAL* 1.3 77.0 - - - +
53A GLU* 1.3 57.4 + - + +
54A LEU 3.0 0.2 - - - -
55A THR* 2.7 31.6 + - - -
56A SER 4.3 1.2 + - - +
59A LEU* 3.4 26.1 - - + +
87A ASP* 4.1 9.8 + - - -
104A MET* 3.6 17.5 - - + -
105A ASN* 3.6 16.8 - - - +
109A GLY 4.6 2.4 + - - -
110A LYS* 3.0 34.6 + - - +
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Residues in contact with GLU 53 (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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49A THR* 3.0 24.8 + - + +
50A PHE* 3.4 29.1 - - + +
51A VAL 3.1 0.6 - - - -
52A LYS* 1.3 74.9 - - + +
54A LEU* 1.3 63.2 + - + +
55A THR 3.4 0.4 - - - -
56A SER* 4.4 5.9 + - - -
59A LEU* 5.5 0.2 - - - -
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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