Contacts of the helix formed by residues 55 - 67 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLU* 2.8 19.3 + - + +
52A ASN 4.4 0.8 - - - -
54A TRP* 1.3 97.8 - - + +
56A PRO* 1.3 68.9 - - - +
57A GLU* 3.0 26.3 + - - +
58A VAL* 3.1 30.8 + - + +
59A ARG* 3.2 12.7 + - - +
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Residues in contact with PRO 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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9A ILE* 5.2 2.2 - - + -
54A TRP 3.4 10.5 - - - +
55A ASP* 1.3 87.6 - - - +
57A GLU* 1.3 51.1 + - - +
59A ARG* 3.1 13.8 + - + +
60A ILE* 2.8 40.2 + - - +
103A THR* 4.0 33.7 - - + +
106A SER* 6.2 0.9 - - - -
107A TYR* 4.0 20.2 - - + +
111A PHE* 4.1 6.7 - - + -
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Residues in contact with GLU 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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55A ASP* 3.0 13.3 + - - +
56A PRO* 1.3 78.5 - - - +
58A VAL* 1.3 63.4 + - - +
60A ILE* 3.4 7.8 + - - +
61A ARG* 3.1 47.5 + - - +
107A TYR* 4.0 19.2 + - - +
20B ARG* 3.6 37.2 + - - -
91B ASN* 5.4 2.6 + - - -
95B LEU* 5.1 5.9 - - - +
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Residues in contact with VAL 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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51A GLU* 4.1 29.4 - - + +
52A ASN* 4.1 16.6 - - + -
55A ASP* 3.1 31.1 + - + +
57A GLU* 1.3 72.9 - - + +
59A ARG* 1.3 68.2 + - - +
61A ARG* 2.9 40.3 + - + +
62A GLU* 3.2 30.5 + - + +
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Residues in contact with ARG 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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7A SER* 3.2 25.1 + - - -
8A HIS 2.8 31.8 + - - -
9A ILE* 3.6 30.3 - - - +
52A ASN 2.7 43.0 + - - +
53A CYS* 3.8 2.8 - - - +
55A ASP 3.2 8.0 + - - +
56A PRO* 3.1 12.7 + - - +
58A VAL* 1.3 75.1 - - - +
60A ILE* 1.3 65.3 + - - +
61A ARG 3.1 0.5 + - - -
62A GLU* 3.1 2.8 + - - +
63A MET* 2.9 40.8 + - + +
71A GLN* 2.9 19.4 + - - -
73A LEU* 3.7 11.0 - - - +
111A PHE* 4.4 5.6 - - + -
292A TYR* 3.4 36.2 + - + +
293A PRO* 4.4 0.8 - - - +
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Residues in contact with ILE 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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56A PRO 2.8 29.1 + - - +
57A GLU* 3.7 6.7 - - - +
59A ARG* 1.3 73.3 - - - +
61A ARG* 1.3 58.5 + - + +
63A MET* 3.6 6.2 - - + +
64A ASP* 2.7 45.0 + - - +
107A TYR* 3.6 49.1 - - + -
110A ARG* 4.1 27.6 - - + +
111A PHE* 3.6 20.9 - - + -
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Residues in contact with ARG 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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51A GLU* 6.0 0.2 - - - -
57A GLU* 3.1 40.8 + - - +
58A VAL* 2.9 38.9 + - + +
60A ILE* 1.3 80.5 - - + +
62A GLU* 1.3 58.0 + - + +
64A ASP* 3.4 12.2 + - + +
65A GLN* 3.1 29.3 + - - +
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Residues in contact with GLU 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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52A ASN* 3.3 29.1 + - - +
58A VAL* 3.2 18.2 + - + +
59A ARG 3.1 2.5 + - - +
61A ARG* 1.3 72.5 - - + +
63A MET* 1.3 63.1 + - - +
65A GLN* 3.2 14.6 + - - +
66A LYS* 2.9 53.9 + - + +
292A TYR* 3.5 34.4 + - + +
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Residues in contact with MET 63 (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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59A ARG* 2.9 43.9 + - + +
60A ILE* 3.6 8.5 - - - +
62A GLU* 1.3 72.1 - - - +
64A ASP* 1.3 63.4 + - - +
66A LYS* 4.5 0.4 - - - +
67A GLY* 3.0 21.3 + - - -
68A VAL* 3.2 37.3 + - + +
69A THR 5.0 0.9 - - - +
71A GLN* 3.2 49.6 - - + +
110A ARG* 3.6 26.2 - - - +
111A PHE* 3.3 24.2 - - + -
292A TYR* 5.5 1.7 - - + -
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Residues in contact with ASP 64 (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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60A ILE* 2.7 31.3 + - - +
61A ARG* 3.5 14.4 - - + +
62A GLU 3.3 0.2 - - - -
63A MET* 1.3 73.0 - - - +
65A GLN* 1.3 60.7 + - - +
67A GLY* 3.5 8.1 + - - -
110A ARG* 3.0 30.6 + - - +
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Residues in contact with GLN 65 (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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61A ARG* 3.1 15.8 + - - +
62A GLU* 3.2 16.5 + - - +
64A ASP* 1.3 77.1 - - - +
66A LYS* 1.3 81.4 + - - +
67A GLY 3.2 1.3 + - - -
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Residues in contact with LYS 66 (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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1A MET* 3.6 19.5 - - - +
62A GLU* 2.9 44.3 + - + +
63A MET* 4.3 0.4 - - - +
65A GLN* 1.3 95.7 - - - +
67A GLY* 1.3 60.8 + - - +
68A VAL* 3.4 9.9 + - + +
292A TYR* 5.5 4.9 - - + -
299A LEU 4.1 14.4 + - - +
300A GLU* 4.0 22.7 - - - +
301A PRO* 3.7 29.4 - - + +
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Residues in contact with GLY 67 (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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1A MET* 3.5 39.5 - - - +
2A LYS* 5.2 1.6 + - - -
63A MET 3.0 6.2 + - - -
64A ASP 3.5 6.1 + - - -
65A GLN 3.2 4.9 + - - -
66A LYS* 1.3 78.2 - - - +
68A VAL* 1.3 62.9 + - - +
69A THR* 3.6 5.9 + - - -
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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