Contacts of the helix formed by residues 55 - 67 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D GLU* 2.9 18.7 + - + +
52D ASN 4.5 1.0 - - - -
54D TRP* 1.3 94.5 - - + +
56D PRO* 1.3 77.3 - - - +
57D GLU* 3.0 23.7 + - - +
58D VAL* 3.2 28.0 + - + +
59D ARG* 3.2 20.3 + - - +
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Residues in contact with PRO 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 5.1 2.2 - - + -
54D TRP 3.5 8.3 - - - +
55D ASP* 1.3 91.4 - - - +
57D GLU* 1.3 64.6 + - - +
59D ARG* 3.0 16.1 + - + +
60D ILE* 2.9 33.4 + - - +
103D THR* 3.8 32.5 - - + +
106D SER* 6.3 0.2 - - - -
107D TYR* 3.9 18.2 - - + -
111D PHE* 4.1 8.9 - - + -
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ASP* 3.0 18.4 + - - +
56D PRO* 1.3 80.9 - - - +
58D VAL* 1.3 58.0 + - + +
60D ILE* 3.4 9.3 + - - +
61D ARG* 2.9 37.8 + - - +
107D TYR* 2.7 37.9 + - + +
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Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLU* 4.1 27.8 - - + +
52D ASN* 4.2 20.0 - - + +
55D ASP* 3.2 30.4 + - + +
57D GLU* 1.3 73.3 - - + +
59D ARG* 1.3 63.8 + - - +
61D ARG* 3.3 32.5 + - - +
62D GLU* 3.0 47.4 + - + +
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Residues in contact with ARG 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D SER* 3.6 16.8 + - - -
8D HIS 2.7 30.7 + - - -
9D ILE* 3.7 20.3 - - - +
52D ASN 2.7 41.4 + - - +
53D CYS* 3.7 11.3 + - - +
55D ASP 3.2 13.7 + - - +
56D PRO* 3.0 11.3 + - + +
58D VAL* 1.3 77.1 - - - +
60D ILE* 1.3 52.2 + - - +
62D GLU* 3.0 4.2 + - - +
63D MET* 2.6 53.4 + - + +
71D GLN* 3.0 26.2 + - - +
73D LEU* 3.8 11.1 - - - +
111D PHE* 4.8 2.9 - - - -
292D TYR* 3.2 34.4 + - + +
293D PRO* 4.4 1.0 - - - +
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Residues in contact with ILE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D PRO 2.9 28.7 + - - +
57D GLU* 3.7 8.1 - - - +
59D ARG* 1.3 70.9 - - - +
61D ARG* 1.3 63.8 + - - +
63D MET* 3.2 10.0 + - + +
64D ASP* 3.0 37.6 + - - +
107D TYR* 3.5 44.4 - - + -
110D ARG* 4.0 30.5 - - + +
111D PHE* 3.8 18.8 - - + -
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLU* 4.8 5.5 + - - -
57D GLU* 2.9 25.0 + - - +
58D VAL* 3.6 39.6 - - - +
59D ARG 3.2 0.2 - - - -
60D ILE* 1.3 80.3 - - - +
62D GLU* 1.3 62.7 + - + +
64D ASP* 3.6 6.1 + - - +
65D GLN* 3.5 44.3 + - - +
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ASN* 3.2 21.8 + - - +
58D VAL* 3.0 30.4 + - + +
59D ARG 3.0 2.0 + - - +
61D ARG* 1.3 79.3 - - + +
63D MET* 1.3 61.1 + - - +
65D GLN* 3.6 8.2 + - - +
66D LYS* 3.2 28.5 + - + +
292D TYR* 2.5 41.3 + - + +
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Residues in contact with MET 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ARG* 2.6 44.6 + - + +
60D ILE* 3.2 11.6 + - - +
62D GLU* 1.3 71.5 - - + +
64D ASP* 1.3 59.9 + - - +
66D LYS* 3.2 0.9 + - - -
67D GLY 2.9 7.8 + - - -
68D VAL* 2.8 56.3 + - + +
69D THR 5.0 0.7 - - - +
71D GLN* 3.1 43.3 - - - +
110D ARG* 3.7 19.1 - - - +
111D PHE* 3.0 38.8 - - + -
292D TYR* 5.8 1.1 - - + -
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Residues in contact with ASP 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ILE* 3.0 28.0 + - - +
61D ARG* 4.0 5.7 - - - +
63D MET* 1.3 73.7 - - - +
65D GLN* 1.3 62.2 + - + +
67D GLY* 3.0 18.8 + - - -
68D VAL 5.0 0.2 - - - -
110D ARG* 2.7 35.9 + - - +
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Residues in contact with GLN 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 5.2 2.8 - - - +
61D ARG* 3.5 37.8 + - - +
62D GLU* 3.8 8.5 - - - +
63D MET 3.3 0.4 - - - -
64D ASP* 1.3 81.3 - - + +
66D LYS* 1.3 66.7 + - + +
67D GLY 3.7 0.2 + - - -
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.0 32.0 - - - +
62D GLU* 3.2 18.0 + - + +
63D MET 3.2 4.5 + - - +
64D ASP 3.2 0.4 - - - -
65D GLN* 1.3 83.7 - - + +
67D GLY* 1.3 59.5 + - - +
68D VAL* 3.5 11.5 + - + +
299D LEU* 3.3 19.6 + - - +
300D GLU* 2.7 40.1 + - - +
301D PRO* 3.7 27.2 - - + +
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Residues in contact with GLY 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 2.1 41.7 - - - +
2D LYS* 5.4 0.9 - - - -
63D MET 2.9 5.4 + - - -
64D ASP* 3.0 13.8 + - - -
65D GLN 3.3 0.6 - - - -
66D LYS* 1.3 78.2 - - - +
68D VAL* 1.3 56.5 + - - +
69D THR* 3.5 3.8 + - - -
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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