Contacts of the helix formed by residues 45 - 54 (chain A) in PDB entry 1IG4
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TYR* 3.5 9.2 - - - -
43A ILE* 3.0 21.4 - - - +
44A ARG* 1.3 83.5 - - - +
46A LYS* 1.3 75.1 + - - +
47A VAL 3.0 6.6 + - - -
48A GLU 4.1 0.9 - - - -
49A LEU* 3.3 4.0 + - - +
62A PHE* 5.2 0.9 - - - -
64A PHE* 3.5 17.5 - - - -
117C C 2.5 43.1 + - - -
118C 5CM 3.1 15.9 + - - -
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Residues in contact with LYS 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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45A SER* 1.3 80.5 + - - +
47A VAL* 1.3 53.5 + - + +
49A LEU* 2.9 7.9 + - - +
50A THR* 2.6 44.3 + - - -
58A ASP* 4.7 6.8 + - - -
59A LEU* 3.0 45.9 + - + +
60A THR* 4.1 12.5 - - - +
62A PHE* 3.8 31.4 - - + +
64A PHE* 4.1 8.0 - - + -
117C C 2.8 20.3 + - - +
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Residues in contact with VAL 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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45A SER* 3.0 1.6 + - - -
46A LYS* 1.3 78.2 - - + +
48A GLU* 1.3 66.3 + - - +
50A THR* 2.7 21.3 + - - -
51A ARG* 2.8 44.8 + - - +
117C C 3.1 44.4 - - - +
118C 5CM 3.6 4.0 - - - +
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Residues in contact with GLU 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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41A ASP* 4.7 1.7 - - - +
42A ARG 2.6 24.4 - - - +
43A ILE* 2.9 48.6 - - + +
44A ARG* 3.7 10.7 + - + +
45A SER* 3.8 2.6 + - - +
47A VAL* 1.3 79.8 - - - +
49A LEU* 1.3 62.0 + - - +
51A ARG* 3.1 28.2 + - + +
52A TYR 3.4 4.5 + - - -
118C 5CM 2.9 34.9 + - + +
119C G 5.5 3.8 + - - +
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Residues in contact with LEU 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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11A LEU* 3.1 32.3 - - + -
15A TRP* 3.0 39.9 - - + -
35A TYR* 4.4 8.5 - - + -
43A ILE* 3.1 21.6 - - + +
45A SER 3.3 7.8 + - - +
46A LYS* 2.9 13.2 + - - +
48A GLU* 1.3 82.3 - - - +
50A THR* 1.3 58.8 + - - +
51A ARG 3.0 1.0 + - - -
52A TYR* 3.6 1.2 + - - +
53A LEU* 2.8 31.4 + - - +
59A LEU* 3.2 17.7 - - + -
62A PHE* 3.5 32.3 - - + -
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Residues in contact with THR 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 LYS* 2.6 25.3 + - - -
47A VAL* 2.7 15.7 + - + -
49A LEU* 1.3 72.5 - - - +
51A ARG* 1.3 57.1 + - + +
53A LEU* 4.4 2.2 - - - -
54A GLY 2.5 45.6 + - - +
55A PRO* 4.2 14.7 - - + +
57A CYS 4.2 7.0 - - - +
58A ASP* 4.5 10.7 + - - +
59A LEU* 3.8 24.5 + - - +
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Residues in contact with ARG 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* 2.8 40.0 + - + +
48A GLU* 3.1 19.1 - - + +
49A LEU 3.0 0.4 - - - -
50A THR* 1.3 76.3 - - + +
52A TYR* 1.3 65.7 + - - +
53A LEU 2.9 3.8 - - - -
54A GLY* 2.8 15.0 + - - -
55A PRO* 5.3 1.0 - - - +
118C 5CM 4.4 6.5 + - - +
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Residues in contact with TYR 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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15A TRP* 4.8 3.4 - + + -
37A SER* 2.6 33.2 - - - +
38A PRO* 4.4 9.4 - - + -
39A THR* 4.5 12.8 - - + +
40A GLY* 2.8 16.6 + - - -
41A ASP* 2.7 39.9 + - + +
43A ILE* 4.6 3.1 - - + -
48A GLU 3.4 6.0 + - - +
49A LEU 3.6 5.1 + - - +
51A ARG* 1.3 79.7 - - - +
53A LEU* 1.3 67.7 + - + +
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Residues in contact with LEU 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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11A LEU* 3.4 28.7 - - + -
15A TRP* 4.5 11.9 - - + +
38A PRO* 6.1 0.9 - - + -
49A LEU* 2.8 21.5 - - + +
50A THR* 4.2 3.1 - - - +
51A ARG 2.9 1.0 - - - -
52A TYR* 1.3 86.7 - - + +
54A GLY* 1.3 59.1 + - - +
57A CYS* 3.2 34.4 - - + +
59A LEU* 3.2 32.3 - - + -
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Residues in contact with GLY 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 THR* 2.5 25.4 + - - +
51A ARG 2.8 12.5 + - - -
52A TYR 3.4 0.2 - - - -
53A LEU* 1.3 81.1 - - - +
55A PRO* 1.3 75.3 - - - +
56A ALA* 3.2 3.4 - - - -
57A CYS* 3.2 11.3 + - - +
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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