Contacts of the helix formed by residues 56 - 69 (chain F) in PDB entry 4GOO
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 ASN 56 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54F ASP* 2.8 15.2 + - - +
55F ILE* 1.3 80.6 - - + +
57F SER* 1.3 62.4 + - - +
58F ASP* 2.6 24.2 + - - +
59F LEU* 3.1 19.8 + - + +
60F ILE* 3.2 22.3 + - - +
111F PHE* 4.9 1.2 - - - -
123F CYS* 4.0 16.0 - - - +
125F TYR* 3.6 25.9 + - - -
162F CYS* 3.9 1.6 - - - -
301F 0Y2 4.0 17.7 + - - +
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Residues in contact with SER 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ILE 3.4 4.6 + - - -
56F ASN* 1.3 73.8 + - - +
58F ASP* 1.3 68.9 + - - +
60F ILE* 4.1 0.6 - - - +
61F SER* 3.0 26.9 + - - -
162F CYS* 3.5 23.3 - - - -
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Residues in contact with ASP 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F ASN* 2.6 15.2 + - - +
57F SER* 1.3 81.0 + - - +
59F LEU* 1.3 56.4 + - - +
61F SER* 3.7 3.5 - - - -
62F LEU* 2.9 30.0 + - - +
98F PHE* 3.5 18.4 - - + -
107F ARG* 2.7 31.4 + - - -
108F ALA* 5.8 0.3 - - - +
111F PHE* 3.6 23.8 - - + -
125F TYR* 2.7 28.9 + - - -
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F LEU* 3.7 30.1 - - + -
36F VAL* 4.8 0.9 - - + -
37F GLY* 3.6 19.7 - - - +
54F ASP* 3.9 30.7 - - + +
56F ASN* 3.1 17.7 + - + +
58F ASP* 1.3 76.8 - - - +
60F ILE* 1.3 68.6 + - + +
62F LEU* 3.4 5.9 + - + +
63F TYR* 2.9 45.4 + - + +
111F PHE* 4.1 10.0 - - + -
301F 0Y2 3.9 28.5 - - + -
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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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36F VAL* 4.4 10.1 - - + -
52F LEU 4.2 10.5 - - - +
53F ALA 4.3 0.9 - - - -
54F ASP* 3.7 33.2 - - + +
56F ASN 3.2 6.4 + - - +
57F SER 4.4 1.3 - - - +
59F LEU* 1.3 80.7 - - + +
61F SER* 1.3 59.2 - - - +
63F TYR* 2.9 7.5 + - + +
64F ASN* 2.7 38.4 + - - +
160F PHE* 3.9 24.0 - - + +
161F TYR 3.2 28.0 - - - +
162F CYS* 3.7 26.9 - - + +
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Residues in contact with SER 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F SER 3.0 21.5 + - - -
58F ASP* 3.7 4.9 - - - -
60F ILE* 1.3 77.8 - - - +
62F LEU* 1.3 64.8 + - - +
64F ASN* 3.0 8.8 + - - +
65F ILE* 2.9 37.1 + - - +
104F PRO* 4.3 14.9 + - - +
108F ALA* 5.6 0.5 - - - +
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Residues in contact with LEU 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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7F PHE* 3.7 24.0 - - + -
8F LEU* 4.2 13.7 - - + -
58F ASP 2.9 21.3 + - - +
59F LEU* 3.7 4.7 - - + +
61F SER* 1.3 71.4 + - - +
63F TYR* 1.3 70.6 + - + +
65F ILE* 3.3 2.5 + - - +
66F VAL* 2.8 45.7 + - + +
73F TYR* 3.6 27.6 - - + +
108F ALA* 4.1 23.8 - - + +
111F PHE* 3.7 32.3 - - + -
112F LEU* 5.5 1.8 - - + -
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Residues in contact with TYR 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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7F PHE* 3.6 25.1 - + - -
8F LEU* 4.3 4.9 - - + +
36F VAL* 4.1 20.4 - - + -
37F GLY 2.5 29.7 + - - -
38F ALA* 3.2 18.4 + - - -
59F LEU* 2.9 40.7 + - + +
60F ILE* 2.9 9.8 + - + +
62F LEU* 1.3 77.6 - - + +
64F ASN* 1.4 58.7 + - - +
66F VAL* 3.0 5.4 + - - +
67F LYS* 2.9 28.9 + - - +
151F PHE* 3.5 35.2 - + + -
160F PHE* 3.5 40.4 - + + -
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Residues in contact with ASN 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 33.5 + - - +
61F SER* 3.7 8.4 - - - +
63F TYR* 1.4 71.4 - - - +
65F ILE* 1.3 64.9 + - + +
67F LYS* 3.1 17.7 + - - +
68F MET* 3.2 25.4 + - + +
160F PHE* 3.4 33.8 + - - +
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Residues in contact with ILE 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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61F SER* 2.9 24.1 + - - +
62F LEU* 3.6 7.0 - - - +
64F ASN* 1.3 75.6 - - + +
66F VAL* 1.3 65.0 + - - +
68F MET* 4.7 0.9 - - - +
69F ARG* 3.0 42.0 + - + +
73F TYR* 3.9 28.4 - - + +
104F PRO* 3.7 31.2 - - + +
105F PHE* 3.9 30.3 - - + +
108F ALA* 4.0 9.0 - - + -
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Residues in contact with VAL 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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7F PHE* 4.3 9.9 - - + -
62F LEU* 2.8 44.0 + - + +
63F TYR* 3.0 6.7 + - - +
65F ILE* 1.3 76.3 - - - +
67F LYS* 1.3 58.8 + - - +
68F MET 3.4 0.2 + - - -
70F THR* 2.9 30.7 + - + +
73F TYR* 4.0 27.8 - - + -
148F LEU* 4.2 24.7 - - + +
151F PHE* 4.1 22.9 - - + -
152F ALA* 3.9 8.1 - - + +
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Residues in contact with LYS 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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63F TYR 2.9 13.4 + - - +
64F ASN* 3.1 13.6 + - - +
66F VAL* 1.3 80.6 - - - +
68F MET* 1.3 78.7 + - + +
70F THR* 3.9 5.1 + - - -
151F PHE* 6.0 0.2 - - - -
152F ALA* 5.0 0.7 - - - +
155F ALA* 3.2 44.8 + - + +
156F GLN* 3.2 42.6 + - - +
158F ALA 2.7 25.6 + - - +
159F PHE* 4.0 18.4 - - - +
160F PHE* 4.4 11.9 - - + -
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Residues in contact with MET 68 (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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64F ASN* 3.2 21.8 + - + +
65F ILE* 5.2 0.2 - - - -
67F LYS* 1.3 107.2 - - + +
69F ARG* 1.3 71.8 + - + +
70F THR 3.6 2.7 + - - -
156F GLN* 5.5 2.2 - - - +
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Residues in contact with ARG 69 (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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65F ILE* 3.0 37.1 + - + +
68F MET* 1.3 90.2 - - + +
70F THR* 1.3 63.8 + - - +
71F ASP 3.7 1.3 - - - -
72F GLU* 2.5 53.5 + - - +
73F TYR* 2.8 20.8 + - - +
105F PHE* 3.7 34.1 - - + +
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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