Contacts of the helix formed by residues 49 - 62 (chain A) in PDB entry 2IAG
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 ASP 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ASP 3.2 7.1 + - - +
48A LYS* 1.3 101.8 + - - +
50A ALA* 1.3 62.2 + - - +
51A ALA* 3.9 0.5 - - - +
52A SER* 2.6 39.4 + - - -
53A PHE* 3.1 19.4 + - - +
478A LEU* 3.5 31.8 - - + +
481A TYR* 3.2 16.9 + - - -
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Residues in contact with ALA 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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46A PHE* 3.1 39.3 + - + +
47A GLY 5.1 0.2 + - - -
48A LYS 4.2 0.2 - - - -
49A ASP* 1.3 71.3 + - - +
51A ALA* 1.3 56.7 + - - +
53A PHE* 3.9 0.4 - - - +
54A LEU* 3.0 37.0 + - + +
356A PHE* 4.1 28.0 - - + -
386A PHE* 4.6 1.6 - - + -
478A LEU 4.6 0.4 + - - -
481A TYR* 3.7 18.3 - - + +
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Residues in contact with ALA 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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49A ASP* 3.3 1.6 + - - +
50A ALA* 1.3 75.9 - - - +
52A SER* 1.3 60.8 + - - +
54A LEU 4.0 0.2 - - - -
55A THR* 2.7 35.5 + - - -
386A PHE* 3.9 15.2 - - + -
388A PHE* 3.9 15.5 - - + -
389A LEU* 3.8 8.1 - - + +
481A TYR* 3.4 37.6 - - + +
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Residues in contact with SER 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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49A ASP* 2.6 35.7 + - - -
51A ALA* 1.3 71.6 - - - +
53A PHE* 1.3 68.5 + - - +
55A THR* 3.3 8.0 + - - -
56A ARG* 3.2 40.1 + - - +
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Residues in contact with PHE 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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42A TYR* 3.4 52.0 - + + -
45A ASP* 3.7 26.2 - - + +
46A PHE* 4.0 20.6 - + - -
49A ASP 3.1 17.4 + - - +
50A ALA 3.9 2.0 - - - +
52A SER* 1.3 75.1 - - - +
54A LEU* 1.3 77.3 + - + +
56A ARG* 3.0 39.5 + - - +
57A MET* 3.1 38.4 + - + +
67A ILE* 3.6 26.0 - - + -
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Residues in contact with LEU 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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46A PHE* 4.1 22.2 - - + -
50A ALA* 3.0 20.2 + - + +
53A PHE* 1.3 95.0 - - + +
55A THR* 1.3 59.2 + - - +
57A MET* 3.5 4.6 + - - +
58A LYS* 3.0 27.7 + - - +
65A PHE* 4.0 13.4 - - + -
67A ILE* 4.4 0.7 - - + -
76A VAL* 3.9 30.5 - - + -
78A LEU* 4.1 4.6 - - + +
356A PHE* 5.3 0.2 - - + -
384A LEU* 4.3 9.4 - - + -
386A PHE* 3.7 33.2 - - + -
389A LEU* 3.7 16.4 - - + +
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Residues in contact with THR 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 ALA 2.7 23.7 + - - -
52A SER* 3.5 7.9 - - - -
53A PHE 3.2 0.4 - - - -
54A LEU* 1.3 72.3 - - - +
56A ARG* 1.3 67.5 + - + +
58A LYS* 3.2 10.2 + - + +
59A GLU* 3.1 39.5 + - - +
389A LEU* 3.3 24.2 - - + +
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Residues in contact with ARG 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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45A ASP* 4.5 13.7 + - - +
48A LYS* 6.2 2.2 - - - +
52A SER* 3.3 34.3 + - - +
53A PHE* 3.0 35.3 + - - +
55A THR* 1.3 76.8 - - + +
57A MET* 1.3 63.9 - - + +
59A GLU* 3.2 18.6 + - - +
60A LYS* 3.0 32.1 + - + +
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Residues in contact with MET 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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33A ASP* 3.9 18.4 - - - +
42A TYR* 3.8 23.1 - - + +
53A PHE* 3.1 51.3 + - + +
54A LEU* 3.8 4.5 - - - +
56A ARG* 1.3 79.5 - - + +
58A LYS* 1.3 59.0 + - - +
60A LYS* 4.2 16.6 - - + +
61A HIS* 2.9 44.7 + - - +
65A PHE* 3.4 29.1 - - + -
67A ILE* 4.2 11.0 - - - -
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Residues in contact with LYS 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 LEU 3.0 14.4 + - - +
55A THR* 3.2 13.4 + - + +
57A MET* 1.3 74.4 - - - +
59A GLU* 1.3 60.0 + - + +
62A GLY* 2.9 41.8 + - - +
63A ASP* 3.4 21.2 + - - +
65A PHE* 3.9 2.8 - - - -
78A LEU* 3.8 23.0 + - + -
389A LEU* 5.4 7.7 + - + -
390A SER* 4.4 11.6 + - - -
394A ASP* 3.6 27.9 + - - +
395A PRO* 5.9 1.2 - - - +
422A LYS* 4.1 8.4 - - - +
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Residues in contact with GLU 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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55A THR* 3.1 32.7 + - - +
56A ARG* 3.2 20.9 + - - +
58A LYS* 1.3 76.9 - - + +
60A LYS* 1.3 62.5 + - + +
62A GLY 4.7 0.7 + - - -
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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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33A ASP* 3.0 22.2 + - - -
42A TYR* 4.6 5.5 + - - -
56A ARG* 3.0 17.2 + - + +
57A MET* 3.7 15.6 - - + +
58A LYS 3.3 0.2 - - - -
59A GLU* 1.3 78.6 - - + +
61A HIS* 1.3 86.4 + - + +
62A GLY 3.8 0.4 - - - -
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Residues in contact with HIS 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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31A PRO* 4.2 25.5 - - + +
32A LEU 5.3 2.0 - - - -
33A ASP* 2.7 41.8 + - + -
57A MET* 2.9 39.4 + - - +
60A LYS* 1.3 105.1 + - + +
62A GLY* 1.3 61.1 + - - +
64A ILE 3.9 8.0 - - - +
65A PHE* 3.7 30.5 - + + -
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Residues in contact with GLY 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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58A LYS* 2.9 32.7 + - - +
59A GLU 4.7 0.8 + - - -
60A LYS 3.8 0.4 - - - -
61A HIS* 1.3 79.8 - - - +
63A ASP* 1.3 61.6 + - - -
64A ILE 3.3 8.2 + - - -
65A PHE* 3.6 8.8 - - - -
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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