Contacts of the helix formed by residues 55 - 66 (chain E) in PDB entry 4IGM
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 55 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E GLU* 2.9 21.0 + - + +
52E ASN 4.2 1.2 + - - -
54E TRP* 1.3 93.2 - - + +
56E PRO* 1.3 68.9 - - - +
57E GLU* 3.2 34.0 + - - +
58E VAL* 3.1 33.2 + - + +
59E ARG* 3.1 15.2 + - - +
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Residues in contact with PRO 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 5.3 1.3 - - + -
54E TRP 3.2 11.6 - - - +
55E ASP* 1.3 89.5 - - - +
57E GLU* 1.3 59.5 + - + +
59E ARG* 3.1 13.1 + - + +
60E ILE* 2.8 36.2 + - - +
103E THR* 3.7 33.2 - - + +
106E SER* 5.9 1.1 - - - +
107E TYR* 3.6 24.2 - - + +
111E PHE* 4.0 5.8 - - + -
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Residues in contact with GLU 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E ASP* 3.1 20.5 + - - +
56E PRO* 1.3 76.7 - - + +
58E VAL* 1.3 65.2 + - + +
60E ILE* 3.1 17.1 + - - +
61E ARG* 3.1 20.8 + - - +
107E TYR* 3.5 22.3 + - - +
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Residues in contact with VAL 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E GLU* 4.0 26.0 - - + +
52E ASN* 4.1 24.9 - - + +
55E ASP* 3.4 35.4 - - + +
57E GLU* 1.3 75.8 - - + +
59E ARG* 1.3 63.1 + - - +
61E ARG* 3.5 22.8 + - + +
62E GLU* 3.4 30.3 + - + +
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Residues in contact with ARG 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E SER* 3.5 18.8 - - - -
8E HIS 2.7 31.2 + - - +
9E ILE* 3.7 26.5 - - - +
52E ASN* 3.1 34.9 + - - +
53E CYS* 4.1 3.6 + - - +
55E ASP 3.1 14.9 + - - +
56E PRO* 3.1 11.2 + - - +
58E VAL* 1.3 75.9 - - - +
60E ILE* 1.3 52.3 + - - +
61E ARG 3.2 0.2 + - - -
62E GLU* 3.3 3.6 + - - +
63E MET* 2.7 51.7 + - + +
71E GLN* 2.8 27.7 + - - +
73E LEU* 3.3 22.2 - - - +
111E PHE* 4.2 4.0 - - + -
292E TYR* 3.6 29.4 + - + -
293E PRO* 4.3 1.4 - - - +
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Residues in contact with ILE 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E PRO 2.8 20.0 + - - +
57E GLU* 3.1 10.0 + - - +
59E ARG* 1.3 77.0 - - - +
61E ARG* 1.3 56.9 + - + +
63E MET* 3.6 15.6 - - + +
64E ASP* 2.9 39.3 + - - +
107E TYR* 3.6 38.4 - - + -
110E ARG* 3.6 47.3 - - + +
111E PHE* 4.0 5.4 - - + -
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Residues in contact with ARG 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E GLU* 5.8 1.4 + - - -
57E GLU* 3.1 17.6 + - - +
58E VAL* 3.8 25.3 - - + +
59E ARG 3.2 0.2 - - - -
60E ILE* 1.3 76.0 - - + +
62E GLU* 1.3 64.8 - - + +
64E ASP* 3.2 9.7 + - - +
65E GLN* 3.1 28.3 + - - +
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Residues in contact with GLU 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ASN* 3.1 26.4 + - - +
58E VAL* 3.4 17.1 + - + +
59E ARG 3.3 3.9 + - - +
61E ARG* 1.3 73.0 - - + +
63E MET* 1.3 64.8 - - - +
65E GLN* 3.4 6.5 + - - +
66E LYS* 3.0 41.2 + - + +
292E TYR* 2.7 43.1 + - + +
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Residues in contact with MET 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ARG* 2.7 52.3 + - + +
60E ILE* 3.4 14.6 - - + +
61E ARG 3.2 0.2 - - - -
62E GLU* 1.3 73.2 - - - +
64E ASP* 1.3 56.9 + - - +
66E LYS* 3.4 2.0 + - - -
67E GLY* 3.0 23.4 + - - -
68E VAL* 3.0 43.4 + - + +
69E THR 4.9 1.3 - - - +
71E GLN* 3.5 35.4 - - - +
110E ARG* 4.0 19.5 - - - +
111E PHE* 3.3 33.4 - - + -
292E TYR* 5.9 0.2 - - - -
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Residues in contact with ASP 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E ILE* 2.9 30.7 + - - +
61E ARG* 3.2 10.9 + - - +
63E MET* 1.3 76.8 - - - +
65E GLN* 1.3 64.7 + - + +
66E LYS 3.3 0.5 + - - -
67E GLY* 3.3 11.4 + - - -
110E ARG* 3.4 23.9 + - - +
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Residues in contact with GLN 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ARG* 3.1 17.1 + - + +
62E GLU* 3.4 3.3 + - - +
64E ASP* 1.3 75.7 - - + +
66E LYS* 1.3 79.9 + - - +
67E GLY 3.5 0.2 - - - -
300E GLU* 5.4 0.9 - - - +
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Residues in contact with LYS 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 4.5 5.9 - - - +
62E GLU* 3.0 29.9 + - + +
63E MET* 4.3 1.6 - - - +
65E GLN* 1.3 97.7 - - - +
67E GLY* 1.3 63.6 + - - +
68E VAL* 3.2 9.2 + - + +
292E TYR* 6.4 1.6 - - + -
299E LEU 4.7 6.7 + - - +
300E GLU* 3.1 32.6 + - - +
301E PRO* 4.0 38.5 - - + +
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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