Contacts of the helix formed by residues 68 - 78 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG* 3.7 26.7 - - + +
18B SER* 5.0 3.8 - - - +
19B VAL* 4.6 7.9 - - + -
56B PRO* 3.4 14.6 - - - +
67B GLN* 1.3 71.5 - - - +
69B ARG* 1.3 71.2 + - + +
71B ILE* 3.2 13.3 + - - +
72B LEU* 3.0 42.3 + - + +
100B LEU* 5.6 6.3 - - + -
301B IBG 2.9 30.6 + - - -
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Residues in contact with ARG 69 (chain B).
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* 3.5 23.5 - - - +
97A GLU* 3.5 29.5 + - + -
15B ARG* 6.0 1.6 - - - +
67B GLN* 3.2 1.6 + - - +
68B THR* 1.3 80.5 - - - +
70B SER* 1.3 58.0 + - - +
72B LEU* 3.7 7.7 - - - +
73B HIS* 2.9 49.1 + - + +
97B GLU* 2.7 32.5 + - - +
100B LEU* 3.8 38.6 + - + +
101B ASP* 4.6 11.1 + - - -
301B IBG 4.6 17.6 + - - -
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 5.2 4.8 - - - +
93A ASP* 2.9 39.1 + - - +
94A MET* 3.8 14.3 + - - -
97A GLU* 3.2 18.2 - - - +
65B LEU* 5.5 1.6 - - - -
66B VAL 3.7 10.8 - - - -
67B GLN* 2.9 12.4 + - - +
69B ARG* 1.3 74.7 - - - +
71B ILE* 1.3 67.2 + - - +
73B HIS* 3.4 2.6 + - - +
74B TYR* 3.0 23.2 + - - +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.4 17.3 - - + -
56B PRO* 3.9 37.5 - - + +
58B VAL* 4.1 20.0 - - + -
60B ILE* 6.3 0.2 - - + -
65B LEU* 3.8 34.3 - - + +
66B VAL 3.9 3.8 - - - +
67B GLN 2.9 21.2 + - - +
68B THR* 3.4 8.3 - - - +
70B SER* 1.3 79.0 - - - +
72B LEU* 1.3 63.2 + - - +
74B TYR* 3.0 15.0 + - - +
75B ILE* 3.1 33.0 + - + +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER* 4.0 17.0 - - - -
19B VAL* 3.9 29.8 - - + +
22B VAL* 3.8 27.9 - - + +
68B THR* 3.0 30.3 + - + +
69B ARG* 3.7 10.3 - - - +
71B ILE* 1.3 75.8 - - - +
73B HIS* 1.3 66.7 + - + +
75B ILE* 3.3 5.1 + - + +
76B ALA* 3.0 23.7 + - - +
96B VAL* 5.4 2.9 - - + -
100B LEU* 4.8 13.9 - - + -
155B LEU* 4.2 18.3 - - + +
159B ILE* 4.3 13.2 - - + -
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Residues in contact with HIS 73 (chain B).
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* 4.0 25.4 - + - -
93A ASP* 2.8 29.1 + - - +
97A GLU* 5.1 0.7 - - - -
69B ARG* 2.9 29.6 + - + +
70B SER 3.6 4.5 - - - +
72B LEU* 1.3 79.7 - - + +
74B TYR* 1.3 64.8 + - - +
76B ALA* 3.7 1.6 - - - +
77B ASP* 2.9 29.9 + - - +
82B PHE* 3.6 36.5 - + + -
89B ARG* 5.3 2.2 - - - +
93B ASP* 4.6 5.3 + - - -
96B VAL* 5.8 3.8 - - + +
97B GLU* 4.2 12.5 + - - -
155B LEU* 4.5 8.7 - - + -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.9 13.2 - - + -
87A LYS* 3.3 28.0 + - - -
90A THR* 3.9 21.8 - - + +
60B ILE* 3.8 28.9 - - + -
61B ASP* 2.5 40.8 + - + +
63B MET* 4.5 7.9 - - - -
65B LEU* 3.7 25.8 - - + -
70B SER 3.0 13.5 + - - +
71B ILE 3.0 7.8 + - - +
73B HIS* 1.3 79.8 - - - +
75B ILE* 1.3 66.7 - - + +
77B ASP* 3.1 4.3 + - - +
78B LYS* 2.8 52.0 + - + +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.1 10.5 - - + +
22B VAL* 3.8 25.4 - - + +
23B LEU* 4.0 38.1 - - + +
26B ALA* 5.0 2.0 - - + -
58B VAL* 5.6 2.2 - - + -
60B ILE* 4.4 20.6 - - + -
71B ILE* 3.1 32.4 + - + +
72B LEU* 3.8 7.9 - - + +
74B TYR* 1.3 80.5 - - + +
76B ALA* 1.3 66.4 + - - +
78B LYS* 3.0 3.3 + - - -
79B HIS* 2.9 45.2 + - + +
81B LEU* 5.2 0.2 - - + -
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B VAL* 5.0 0.6 - - - +
72B LEU 3.0 17.5 + - - +
73B HIS 3.7 3.4 - - - +
75B ILE* 1.3 76.9 - - - +
77B ASP* 1.3 59.2 + - - +
79B HIS 2.9 14.9 + - - -
80B ASN* 3.2 1.2 + - - -
81B LEU* 3.0 48.9 + - + -
82B PHE* 3.7 20.9 + - + -
155B LEU* 4.0 15.5 - - + -
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 4.1 28.6 - - + +
89A ARG* 4.7 3.6 + - - -
73B HIS* 2.9 18.9 + - - +
74B TYR 3.6 3.4 - - - +
76B ALA* 1.3 80.3 - - - +
78B LYS* 1.3 62.4 + - - +
79B HIS 3.4 0.2 + - - -
80B ASN 4.3 3.5 + - - -
82B PHE* 3.4 10.9 - - - +
89B ARG* 2.7 47.2 + - - -
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.8 22.6 - - + +
87A LYS* 5.0 5.7 - - - +
60B ILE* 5.9 0.9 - - + -
61B ASP* 4.1 8.3 - - - +
74B TYR* 2.8 57.4 + - + +
75B ILE* 3.0 3.8 + - - +
77B ASP* 1.3 78.8 - - - +
79B HIS* 1.3 85.0 + - + +
80B ASN 3.8 0.9 - - - -
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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