Contacts of the strand formed by residues 78 - 83 (chain H) in PDB entry 1GC1
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 78 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21H SER* 3.8 10.8 - - - -
22H CYS 3.7 6.7 - - - +
23H LYS* 2.6 37.5 + - - +
29H PHE* 3.7 1.8 - - - -
72H ALA* 3.1 1.2 - - - -
73H ASP 2.7 35.6 + - - -
76H THR* 2.7 31.1 + - - -
77H SER* 1.3 77.4 - - - +
79H VAL* 1.3 76.3 + - - +
80H TYR* 3.6 24.4 - - + -
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Residues in contact with VAL 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H SER* 3.4 0.9 - - - -
22H CYS* 3.1 44.2 + - + +
24H ALA* 5.3 0.4 - - + -
29H PHE* 3.9 13.0 - - + -
34H PHE* 3.5 49.6 - - + -
36H TRP* 3.4 25.4 - - + +
51H ILE* 4.5 4.5 - - + -
70H ILE* 3.9 10.3 - - + -
71H THR 3.3 9.6 - - - +
72H ALA* 4.1 3.1 - - + +
78H THR* 1.3 82.5 - - - +
80H TYR* 1.3 65.9 + - - +
96H CYS* 5.4 0.7 - - + -
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Residues in contact with TYR 80 (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 LYS* 3.6 39.0 - - + -
20H VAL 3.5 8.7 - - - -
21H SER* 3.8 15.8 - - - -
23H LYS* 4.5 5.9 + - - -
36H TRP* 3.4 3.5 + - - -
69H THR 4.2 1.3 - - - +
70H ILE* 2.9 31.7 - - - +
71H THR* 2.6 35.3 + - - +
73H ASP* 4.4 14.6 + - + -
76H THR* 4.8 2.6 + - - -
78H THR* 3.6 34.7 - - + +
79H VAL* 1.3 80.0 - - - +
81H LEU* 1.3 60.1 + - - +
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Residues in contact with LEU 81 (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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18H VAL* 3.4 3.1 - - + +
19H LYS* 3.1 4.7 - - - -
20H VAL* 3.0 43.1 + - + +
36H TRP* 3.5 32.8 - - + -
48H MET* 4.2 9.2 - - + -
68H VAL* 3.3 33.4 - - + -
69H THR 3.3 5.8 - - - +
70H ILE* 4.1 7.6 - - + -
80H TYR* 1.3 77.8 - - - +
82H GLU* 1.3 66.8 + - - +
83H LEU* 4.9 6.3 - - + -
94H TYR* 3.3 39.0 - - + -
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Residues in contact with GLU 82 (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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17H SER* 4.4 13.6 + - - -
18H VAL 2.9 19.1 - - - +
19H LYS* 3.0 35.1 + - + +
67H ARG 3.9 0.3 - - - +
68H VAL* 3.4 3.6 - - - -
69H THR* 2.8 39.1 + - + +
80H TYR 4.3 0.2 - - - -
81H LEU* 1.3 76.8 - - - +
83H LEU* 1.3 64.3 + - - +
84H ARG* 2.9 40.4 + - - +
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Residues in contact with LEU 83 (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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16H SER 3.8 2.3 - - - +
17H SER* 3.5 2.1 - - - -
18H VAL* 2.8 46.4 + - + +
38H ARG* 4.7 2.5 - - - +
48H MET* 4.3 17.7 - - + -
64H LEU* 4.6 4.5 - - + -
67H ARG* 3.1 49.8 - - + +
68H VAL* 3.7 24.2 - - + -
81H LEU* 4.9 7.4 - - + -
82H GLU* 1.3 74.5 - - - +
84H ARG* 1.3 62.2 + - - +
86H LEU* 3.6 16.3 - - + +
90H ASP* 3.5 17.0 - - + +
94H TYR* 4.8 6.1 - - + +
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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