Contacts of the helix formed by residues 68 - 78 (chain A) in PDB entry 1GUL
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ARG* 3.7 26.1 - - + +
18A SER* 5.0 4.0 - - - +
19A VAL* 4.6 7.2 - - + -
56A PRO* 3.4 15.2 - - + +
67A GLN* 1.3 71.7 - - - +
69A ARG* 1.3 70.8 + - + +
71A ILE* 3.2 12.7 + - - +
72A LEU* 3.0 41.9 + - + +
100A LEU* 5.6 6.5 - - + -
301A IBG 2.9 31.2 + - - -
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Residues in contact with ARG 69 (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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15A ARG* 6.0 1.8 - - - +
67A GLN* 3.2 1.8 + - - +
68A THR* 1.3 80.7 - - - +
70A SER* 1.3 57.7 + - - +
72A LEU* 3.4 8.5 + - - +
73A HIS* 2.9 50.1 + - + +
97A GLU* 2.7 30.7 + - - +
100A LEU* 3.8 38.7 - - + +
101A ASP* 4.6 10.3 + - - -
301A IBG 4.6 17.4 + - - -
69B ARG* 3.5 21.9 - - - +
97B GLU* 3.5 28.4 + - + -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 5.5 2.0 - - - -
66A VAL 3.7 10.8 - - - -
67A GLN* 2.9 13.0 + - - +
69A ARG* 1.3 74.3 - - - +
71A ILE* 1.3 67.1 + - - +
73A HIS* 3.4 2.9 + - - +
74A TYR* 3.0 23.0 + - - +
90B THR* 5.3 3.9 - - - +
93B ASP* 3.1 27.8 + - - +
94B MET* 3.8 15.4 - - - -
97B GLU* 3.0 29.5 - - - +
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Residues in contact with ILE 71 (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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19A VAL* 4.4 17.0 - - + -
56A PRO* 3.9 37.0 - - + +
58A VAL* 4.1 20.2 - - + -
60A ILE* 6.3 0.2 - - + -
65A LEU* 3.8 35.9 - - + +
66A VAL 3.9 3.4 - - - +
67A GLN 2.9 21.6 + - - +
68A THR* 3.4 7.9 - - - +
70A SER* 1.3 77.8 - - - +
72A LEU* 1.3 63.1 + - - +
74A TYR* 3.0 15.2 + - - +
75A ILE* 3.1 33.2 + - + +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 4.0 16.8 - - - -
19A VAL* 3.9 30.3 - - + +
22A VAL* 3.8 29.0 - - + +
68A THR* 3.0 29.7 + - + +
69A ARG* 3.7 10.1 - - - +
70A SER 3.3 0.2 - - - -
71A ILE* 1.3 76.8 - - - +
73A HIS* 1.3 66.9 + - + +
75A ILE* 3.3 5.0 + - + +
76A ALA* 3.0 24.1 + - - +
96A VAL* 5.4 2.7 - - + -
100A LEU* 4.8 14.1 - - + -
155A LEU* 4.2 17.9 - - + +
159A ILE* 4.3 12.6 - - + -
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Residues in contact with HIS 73 (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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69A ARG* 2.9 30.6 + - + +
70A SER 3.6 4.9 - - - +
72A LEU* 1.3 79.7 - - + +
74A TYR* 1.3 64.2 + - - +
76A ALA* 3.7 1.8 - - - +
77A ASP* 2.9 30.5 + - - +
82A PHE* 3.6 35.4 - + + -
89A ARG* 5.3 2.2 - - - +
93A ASP* 4.6 5.3 + - - -
96A VAL* 5.8 3.8 - - + +
97A GLU* 4.2 13.2 + - - -
155A LEU* 4.5 8.7 - - + -
73B HIS* 4.0 25.1 - + - -
93B ASP* 2.9 29.0 + - - +
97B GLU* 4.9 1.6 - - - -
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Residues in contact with TYR 74 (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* 3.8 29.4 - - + -
61A ASP* 2.5 40.7 + - + +
63A MET* 4.5 9.8 - - - -
65A LEU* 3.7 24.0 - - + -
70A SER 3.0 14.1 + - - +
71A ILE 3.0 7.2 + - - +
73A HIS* 1.3 78.4 - - - +
75A ILE* 1.3 66.6 + - + +
77A ASP* 3.1 4.8 + - - +
78A LYS* 2.8 51.2 + - + +
86B LEU* 4.1 12.3 - - + -
87B LYS* 3.3 27.0 + - - -
90B THR* 3.8 26.2 - - + +
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Residues in contact with ILE 75 (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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19A VAL* 4.1 11.4 - - + +
22A VAL* 3.8 25.1 - - + +
23A LEU* 4.0 38.1 - - + +
26A ALA* 5.0 2.0 - - + -
58A VAL* 5.6 2.5 - - + -
60A ILE* 4.4 20.0 - - + -
71A ILE* 3.1 31.9 + - + +
72A LEU* 3.8 7.6 - - + +
74A TYR* 1.3 80.8 - - + +
76A ALA* 1.3 65.2 + - - +
78A LYS* 3.0 4.0 + - - -
79A HIS* 2.9 43.9 + - + +
81A LEU* 5.2 0.4 - - + -
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Residues in contact with ALA 76 (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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22A VAL* 5.0 0.8 - - - +
72A LEU 3.0 16.4 + - - +
73A HIS 3.7 3.6 - - - +
75A ILE* 1.3 76.5 - - - +
77A ASP* 1.3 58.7 + - - +
79A HIS 2.9 14.9 + - - -
80A ASN* 3.2 1.7 + - - -
81A LEU* 3.0 48.8 + - + -
82A PHE* 3.7 21.1 + - + -
155A LEU* 4.0 15.7 - - + -
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Residues in contact with ASP 77 (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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73A HIS* 2.9 19.5 + - - +
74A TYR* 3.6 4.2 - - - +
76A ALA* 1.3 80.5 - - - +
78A LYS* 1.3 61.9 + - - +
79A HIS 3.4 0.2 + - - -
80A ASN 4.3 3.8 + - - -
82A PHE* 3.4 10.8 - - - +
89A ARG* 2.7 45.8 + - - -
86B LEU* 4.2 28.4 - - + +
89B ARG* 4.6 3.5 + - - -
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Residues in contact with LYS 78 (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* 5.9 0.7 - - + -
61A ASP* 4.1 7.9 - - - +
74A TYR* 2.8 57.7 + - + +
75A ILE* 3.0 2.9 + - - +
77A ASP* 1.3 77.6 - - - +
79A HIS* 1.3 85.7 + - + +
80A ASN 3.8 0.4 - - - -
86B LEU* 3.8 24.5 - - + +
87B LYS* 4.8 5.8 - - - +
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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