Contacts of the helix formed by residues 68 - 79 (chain F) in PDB entry 1GUM
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 THR 68 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15F ARG* 3.7 38.8 - - + +
18F SER* 5.0 4.5 - - - +
19F VAL* 4.3 15.9 - - + -
56F PRO* 3.6 21.2 - - + +
67F GLN* 1.3 73.1 + - - +
69F ARG* 1.3 72.6 + - - +
71F ILE* 3.1 11.4 + - - +
72F LEU* 2.8 37.3 + - + +
100F LEU* 6.1 1.6 - - + -
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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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69E ARG* 3.2 39.9 - - - +
97E GLU* 4.0 13.0 - - + +
15F ARG* 5.2 10.5 - - - +
67F GLN* 3.3 1.4 - - - +
68F THR* 1.3 81.9 - - - +
70F SER* 1.3 58.0 + - - +
72F LEU* 3.3 8.4 + - - +
73F HIS* 2.9 51.7 + - + +
97F GLU* 3.0 32.3 + - - +
100F LEU* 3.9 33.7 - - + +
101F ASP* 4.8 9.5 + - - -
104F GLU* 5.7 3.4 + - - -
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Residues in contact with SER 70 (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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90E THR* 5.3 4.2 - - - +
93E ASP* 3.0 29.3 + - - +
94E MET* 3.5 17.8 + - - -
97E GLU* 3.0 25.5 - - - +
65F LEU* 5.4 1.9 - - - +
66F VAL 3.5 7.0 - - - -
67F GLN* 2.7 23.1 + - - +
69F ARG* 1.3 79.4 - - - +
71F ILE* 1.3 60.5 + - - +
73F HIS 3.4 0.3 + - - -
74F TYR* 3.1 20.1 + - - +
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Residues in contact with ILE 71 (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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19F VAL* 4.2 18.8 - - + -
56F PRO* 4.0 19.5 - - + -
58F VAL* 4.7 16.4 - - + -
60F ILE* 6.4 0.4 - - + -
65F LEU* 3.8 39.5 - - + +
66F VAL 3.9 9.0 - - - -
67F GLN 2.7 27.2 + - - +
68F THR* 3.4 11.4 - - - +
70F SER* 1.3 75.7 - - - +
72F LEU* 1.3 68.8 + - - +
74F TYR* 2.8 16.5 + - - +
75F ILE* 3.0 32.0 + - + +
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F SER* 3.6 40.2 - - - +
19F VAL* 4.1 14.4 - - + -
22F VAL* 3.9 17.7 - - + +
68F THR* 2.8 35.2 + - + +
69F ARG* 3.8 7.9 - - - +
71F ILE* 1.3 76.6 - - - +
73F HIS* 1.3 66.7 + - + +
75F ILE* 3.5 5.7 + - + +
76F ALA* 2.9 25.6 + - - +
96F VAL* 5.4 2.0 - - + -
100F LEU* 4.6 15.7 - - + -
155F LEU* 4.2 19.3 - - + +
159F ILE* 4.5 10.8 - - + -
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Residues in contact with HIS 73 (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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73E HIS* 3.5 30.4 - + - -
93E ASP* 3.3 26.1 + - - +
97E GLU* 4.8 0.9 - - - -
69F ARG* 2.9 36.9 + - + +
70F SER 3.7 4.0 - - - +
72F LEU* 1.3 79.5 - - + +
74F TYR* 1.3 62.7 + - - +
76F ALA* 3.4 1.8 + - - +
77F ASP* 2.9 27.9 + - - +
82F PHE* 3.7 34.0 - + + -
89F ARG* 5.1 5.2 + - - +
93F ASP* 4.3 6.1 + - - -
96F VAL* 5.8 3.9 - - + +
97F GLU* 3.8 15.7 + - - -
155F LEU* 4.4 9.9 - - + -
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Residues in contact with TYR 74 (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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86E LEU* 3.6 24.7 - - + -
87E LYS* 3.1 31.1 + - - -
90E THR* 3.8 23.3 - - + +
60F ILE* 3.0 40.4 - - + -
61F ASP* 2.5 26.5 + - + +
63F MET* 4.5 5.4 - - - -
65F LEU* 3.8 22.9 - - + -
70F SER 3.1 12.5 + - - +
71F ILE 2.8 10.0 + - - +
73F HIS* 1.3 77.1 - - - +
75F ILE* 1.3 55.0 + - + +
77F ASP* 2.8 8.4 + - - +
78F LYS* 2.7 51.4 + - + +
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Residues in contact with ILE 75 (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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19F VAL* 4.1 11.4 - - + +
22F VAL* 3.8 26.2 - - + +
23F LEU* 3.8 39.0 - - + -
26F ALA* 5.0 2.7 - - + -
58F VAL* 5.9 2.9 - - + -
60F ILE* 4.6 9.4 - - + -
71F ILE* 3.4 32.1 - - + +
72F LEU* 3.8 6.3 - - + +
74F TYR* 1.3 87.9 - - + +
76F ALA* 1.3 64.1 + - - +
78F LYS* 3.0 5.2 + - - +
79F HIS* 2.9 42.6 + - + +
81F LEU* 5.2 0.4 - - + -
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Residues in contact with ALA 76 (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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22F VAL* 5.1 0.4 - - - +
72F LEU 2.9 19.1 + - - +
75F ILE* 1.3 77.0 - - - +
77F ASP* 1.3 59.6 + - - +
79F HIS 2.9 15.1 + - - -
80F ASN* 3.0 13.3 + - - -
81F LEU* 3.1 33.4 + - + -
82F PHE* 3.6 28.7 + - + -
155F LEU* 4.2 13.7 - - + -
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Residues in contact with ASP 77 (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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86E LEU* 4.2 28.5 - - + +
89E ARG* 4.4 4.2 + - - -
73F HIS* 2.9 13.8 + - - +
74F TYR 2.8 8.2 + - - +
76F ALA* 1.3 79.8 - - - +
78F LYS* 1.3 62.2 + - - +
79F HIS 3.3 0.5 + - - -
80F ASN* 4.1 4.0 + - - +
82F PHE* 3.4 11.8 - - - +
89F ARG* 3.0 42.8 + - - -
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Residues in contact with LYS 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E LEU* 3.9 23.3 - - + +
87E LYS* 5.6 3.2 - - - +
61F ASP* 4.2 8.1 - - - +
74F TYR* 2.7 53.6 + - + +
75F ILE* 3.5 4.5 - - - +
77F ASP* 1.3 75.7 - - - +
79F HIS* 1.3 83.9 + - + +
80F ASN 3.8 0.4 - - - -
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Residues in contact with HIS 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 5.6 1.1 - - + -
26F ALA* 3.9 29.2 - - + -
28F VAL* 3.3 26.3 - - + +
75F ILE* 2.9 29.7 + - + +
76F ALA 2.9 0.6 + - - -
78F LYS* 1.3 98.4 + - + +
80F ASN* 1.3 74.9 + - - +
81F LEU* 3.1 14.8 + - + +
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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