Contacts of the helix formed by residues 55 - 67 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51F GLU* 3.0 23.9 + - + +
52F ASN 4.1 0.8 + - - -
54F TRP* 1.3 99.5 - - + +
56F PRO* 1.3 65.7 - - - +
57F GLU* 2.7 36.8 + - - +
58F VAL* 3.1 26.4 + - + +
59F ARG* 3.0 22.6 + - - +
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Residues in contact with PRO 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 5.1 2.5 - - + -
54F TRP 3.5 10.0 - - - +
55F ASP* 1.3 90.1 - - - +
57F GLU* 1.3 63.9 + - - +
59F ARG* 3.0 15.6 + - + +
60F ILE* 2.9 33.7 + - - +
103F THR* 4.0 35.7 - - + +
106F SER* 6.1 0.9 - - - +
107F TYR* 4.0 17.5 - - + -
111F PHE* 4.2 4.9 - - + -
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Residues in contact with GLU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ASP* 2.7 27.0 - - - +
56F PRO* 1.3 81.2 - - - +
58F VAL* 1.3 65.3 + - + +
60F ILE* 3.5 4.9 + - - +
61F ARG* 3.3 28.3 + - - +
107F TYR* 3.1 27.4 + - - +
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Residues in contact with VAL 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F GLU* 3.5 33.7 - - + +
52F ASN* 3.7 31.9 - - + +
55F ASP* 3.1 21.9 + - + +
57F GLU* 1.3 75.3 - - + +
59F ARG* 1.3 67.5 + - - +
61F ARG* 3.5 17.1 + - - +
62F GLU* 3.3 29.4 + - + +
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Residues in contact with ARG 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F SER* 3.2 20.8 + - - -
8F HIS 2.8 28.6 + - - +
9F ILE* 3.6 27.6 - - - +
52F ASN 3.0 33.7 + - - +
53F CYS* 4.2 3.6 - - - +
55F ASP 3.0 12.9 + - - +
56F PRO* 3.0 13.3 + - + +
58F VAL* 1.3 78.3 - - - +
60F ILE* 1.3 57.4 + - - +
62F GLU* 3.3 3.1 + - - +
63F MET* 2.9 42.9 + - + +
71F GLN* 3.0 27.6 + - - +
73F LEU* 3.4 14.6 - - - +
111F PHE* 4.1 3.3 - - + -
292F TYR* 3.4 34.4 + - + +
293F PRO* 4.4 0.4 - - - +
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Residues in contact with ILE 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F PRO 2.9 16.0 + - - +
57F GLU* 4.0 6.5 - - - +
58F VAL 3.4 0.2 - - - -
59F ARG* 1.3 71.3 - - - +
61F ARG* 1.3 56.6 + - + +
63F MET* 3.2 13.4 + - + +
64F ASP* 2.7 53.7 + - - +
107F TYR* 3.4 36.8 - - + -
110F ARG* 3.8 30.1 - - + +
111F PHE* 3.3 37.7 - - + -
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Residues in contact with ARG 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F GLU 3.3 14.9 + - - +
58F VAL* 3.7 18.1 + - - +
59F ARG 3.3 0.2 - - - -
60F ILE* 1.3 76.3 - - + +
62F GLU* 1.3 66.8 + - - +
64F ASP* 2.9 13.5 + - - +
65F GLN* 2.8 55.0 + - - +
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ASN* 3.5 20.8 + - - +
58F VAL* 3.3 17.2 + - + +
59F ARG 3.3 8.2 + - - +
61F ARG* 1.3 83.3 - - - +
63F MET* 1.3 56.7 + - - +
65F GLN* 3.2 24.6 + - - +
66F LYS* 2.9 36.4 + - + +
292F TYR* 3.4 35.0 + - + +
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Residues in contact with MET 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ARG* 2.9 33.6 + - + +
60F ILE* 3.3 16.4 - - + +
62F GLU* 1.3 77.8 - - + +
64F ASP* 1.3 57.2 + - - +
66F LYS* 3.4 2.0 + - - +
67F GLY 3.0 7.1 + - - -
68F VAL* 2.8 59.0 + - + +
69F THR 5.0 0.9 - - - +
71F GLN* 3.4 43.5 - - - +
110F ARG* 4.1 13.0 - - - +
111F PHE* 3.1 42.0 - - + -
292F TYR* 5.9 0.7 - - + -
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Residues in contact with ASP 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F ILE* 2.7 38.3 + - - +
61F ARG* 2.9 11.5 + - - +
63F MET* 1.3 69.4 - - - +
65F GLN* 1.3 67.8 + - - +
66F LYS 3.4 0.2 + - - -
67F GLY* 3.5 7.9 + - - +
110F ARG* 3.5 22.9 + - - +
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Residues in contact with GLN 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 5.3 2.3 - - - +
61F ARG* 2.8 48.3 + - - +
62F GLU* 3.4 24.6 - - - +
64F ASP* 1.3 75.6 - - - +
66F LYS* 1.3 78.3 + - + +
67F GLY* 3.2 4.3 + - - -
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Residues in contact with LYS 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 3.3 21.0 - - - +
62F GLU* 2.9 24.3 + - + +
63F MET* 3.4 3.3 + - - +
65F GLN* 1.3 96.8 - - - +
67F GLY* 1.3 60.0 + - - +
68F VAL* 3.3 8.5 + - + +
292F TYR* 6.6 0.2 - - + -
299F LEU* 3.0 26.4 + - - +
300F GLU* 3.5 19.4 + - + +
301F PRO* 3.8 30.7 - - + +
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Residues in contact with GLY 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 3.2 40.9 - - - +
2F LYS* 5.8 0.3 + - - -
63F MET 3.0 5.1 + - - -
64F ASP* 3.5 5.8 + - - -
65F GLN 3.2 5.8 + - - -
66F LYS* 1.3 76.2 - - - +
68F VAL* 1.3 61.2 + - - +
69F THR* 3.5 5.5 + - - -
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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