Contacts of the helix formed by residues 68 - 78 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H ARG* 3.7 26.3 - - + +
18H SER* 5.0 4.0 - - - +
19H VAL* 4.6 7.4 - - + -
56H PRO* 3.4 14.9 - - + +
67H GLN* 1.3 72.3 + - - +
69H ARG* 1.3 70.8 + - + +
71H ILE* 3.2 13.5 + - - +
72H LEU* 3.0 41.5 + - + +
100H LEU* 5.6 6.1 - - + -
301H IBG 2.9 30.3 + - - -
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Residues in contact with ARG 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ARG* 3.5 22.8 - - - +
97G GLU* 3.5 29.8 + - + -
15H ARG* 6.0 1.4 - - - +
67H GLN* 3.2 1.8 - - + +
68H THR* 1.3 79.9 - - - +
70H SER* 1.3 58.1 + - - +
72H LEU* 3.7 7.9 - - - +
73H HIS* 2.9 50.4 + - + +
97H GLU* 2.7 31.5 + - - +
100H LEU* 3.8 39.4 - - + +
101H ASP* 4.6 10.1 + - - -
301H IBG 4.6 17.4 + - - -
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Residues in contact with SER 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G THR* 5.6 4.0 - - - +
93G ASP* 3.1 37.4 + - - +
94G MET* 3.9 15.4 - - - -
97G GLU* 3.2 18.7 - - - +
65H LEU* 5.1 2.0 - - - +
66H VAL 3.7 10.3 - - - -
67H GLN* 2.9 12.6 + - - +
69H ARG* 1.3 75.4 - - - +
71H ILE* 1.3 65.6 + - - +
73H HIS* 3.4 2.8 + - - +
74H TYR* 3.0 23.6 + - - +
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Residues in contact with ILE 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H VAL* 4.4 17.7 - - + -
56H PRO* 3.9 37.7 - - + +
58H VAL* 4.1 20.4 - - + -
60H ILE* 6.3 0.2 - - + -
65H LEU* 3.8 34.8 - - + +
66H VAL 3.9 3.6 - - - +
67H GLN 2.9 20.5 + - - +
68H THR* 3.4 8.3 - - - +
70H SER* 1.3 78.6 - - - +
72H LEU* 1.3 61.8 + - - +
74H TYR* 3.0 14.7 + - - +
75H ILE* 3.1 33.3 + - + +
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Residues in contact with LEU 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H SER* 4.0 17.3 - - - -
19H VAL* 3.9 29.8 - - + +
22H VAL* 3.8 28.6 - - + +
68H THR* 3.0 30.4 + - + +
69H ARG* 3.7 10.1 - - - +
71H ILE* 1.3 76.3 - - - +
73H HIS* 1.3 66.6 + - + +
75H ILE* 3.3 5.9 + - + +
76H ALA* 3.0 23.6 + - - +
96H VAL* 5.4 3.1 - - + -
100H LEU* 4.8 13.5 - - + -
155H LEU* 4.2 19.1 - - + +
159H ILE* 4.3 13.2 - - + -
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Residues in contact with HIS 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G HIS* 4.1 24.0 - + - -
93G ASP* 2.9 30.0 + - - +
97G GLU* 5.0 1.8 - - - -
69H ARG* 2.9 29.3 + - + +
70H SER 3.6 5.2 - - - +
72H LEU* 1.3 79.0 - - + +
74H TYR* 1.3 64.9 + - - +
76H ALA* 3.7 1.1 - - - +
77H ASP* 2.9 30.1 + - - +
82H PHE* 3.6 36.1 - + + -
89H ARG* 5.3 2.2 - - - +
93H ASP* 4.6 5.1 + - - -
96H VAL* 5.8 3.8 - - + +
97H GLU* 4.2 12.1 + - - -
155H LEU* 4.5 9.2 - - + -
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Residues in contact with TYR 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G LEU* 4.1 12.6 - - + -
87G LYS* 3.5 26.2 + - - -
90G THR* 4.0 22.7 - - + +
60H ILE* 3.8 28.7 - - + -
61H ASP* 2.5 40.1 + - + +
63H MET* 4.5 9.6 - - - -
65H LEU* 3.7 26.0 - - + -
70H SER 3.0 14.9 + - - +
71H ILE 3.0 7.6 + - - +
73H HIS* 1.3 78.2 - - - +
75H ILE* 1.3 68.3 + - + +
77H ASP* 3.1 4.8 + - - +
78H LYS* 2.8 52.8 + - + +
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Residues in contact with ILE 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H VAL* 4.1 11.2 - - + +
22H VAL* 3.8 25.6 - - + +
23H LEU* 4.0 36.3 - - + +
26H ALA* 5.0 2.2 - - + -
58H VAL* 5.6 2.5 - - + -
60H ILE* 4.4 20.6 - - + -
71H ILE* 3.1 32.6 + - + +
72H LEU* 3.8 7.4 - - + +
74H TYR* 1.3 80.5 - - + +
76H ALA* 1.3 65.0 + - - +
78H LYS* 3.0 4.3 + - - +
79H HIS* 2.9 44.1 + - + +
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Residues in contact with ALA 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H VAL* 5.0 0.8 - - - +
72H LEU 3.0 17.5 + - - +
73H HIS 3.7 3.6 - - - +
75H ILE* 1.3 77.2 - - - +
77H ASP* 1.3 59.7 + - - +
79H HIS 2.9 14.4 + - - -
80H ASN* 3.2 1.7 + - - -
81H LEU* 3.0 48.4 + - + -
82H PHE* 3.7 21.1 + - + -
155H LEU* 4.0 15.5 - - + -
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Residues in contact with ASP 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G LEU* 4.2 26.7 - - + +
89G ARG* 4.8 3.1 + - - -
73H HIS* 2.9 19.2 + - - +
74H TYR* 3.6 5.1 - - - +
76H ALA* 1.3 79.9 - - - +
78H LYS* 1.3 63.5 + - - +
79H HIS 3.4 0.3 + - - -
80H ASN 4.3 3.5 + - - +
82H PHE* 3.4 11.3 - - - +
89H ARG* 2.7 46.0 + - - -
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Residues in contact with LYS 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G LEU* 4.0 18.5 - - + +
87G LYS* 5.0 5.2 - - - +
60H ILE* 5.9 0.9 - - + -
61H ASP* 4.1 7.9 - - - +
74H TYR* 2.8 61.5 + - + +
75H ILE* 3.0 3.3 + - - +
77H ASP* 1.3 79.1 - - - +
79H HIS* 1.3 85.1 + - + +
80H ASN 3.8 0.4 - - - -
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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