Contacts of the strand formed by residues 76 - 81 (chain C) in PDB entry 3BX7
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 GLN 76 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C VAL* 3.6 20.0 - - + +
23C CYS 3.3 12.8 - - - +
24C GLU* 3.9 16.5 - - + +
25C TYR* 3.8 6.6 + - - -
72C SER* 3.5 5.9 + - - -
73C SER* 3.1 46.7 + - - +
74C GLY 3.3 1.6 + - - -
75C ASN* 1.3 88.4 - - - +
77C VAL* 1.3 64.6 + - - +
78C ASN* 2.9 25.7 + - - +
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Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 3.5 4.0 - - - +
23C CYS* 3.0 51.0 + - + +
25C TYR* 3.8 5.8 - - + +
36C VAL* 4.3 15.3 - - + -
54C TYR* 2.8 44.2 - - + +
60C LEU* 4.3 9.6 - - + -
71C THR 3.4 6.5 - - - +
72C SER* 4.6 1.1 - - - -
76C GLN* 1.3 79.6 - - - +
78C ASN* 1.3 64.2 + - - +
79C LEU* 3.7 19.8 + - + +
96C VAL* 5.4 0.4 - - + -
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Residues in contact with ASN 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE 4.0 4.0 - - - -
22C VAL* 3.5 14.8 - - + +
70C GLY* 3.0 26.0 - - - -
71C THR* 2.8 34.5 + - - +
73C SER* 3.2 26.1 + - - +
76C GLN* 2.9 27.8 + - - +
77C VAL* 1.3 70.5 - - - +
79C LEU* 1.3 62.1 + - - +
80C THR* 5.4 0.2 + - - -
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ALA 4.0 0.4 - - - +
20C SER* 3.2 5.0 - - - -
21C PHE* 2.9 57.2 + - + +
23C CYS* 4.4 1.1 - - - -
36C VAL* 4.7 5.8 - - + -
38C VAL* 4.0 18.8 - - + -
60C LEU* 3.9 27.8 - - + -
62C PHE* 3.9 17.0 - - + -
68C CYS* 5.6 2.5 - - + -
69C THR 3.6 5.8 - - - +
77C VAL* 4.3 19.3 - - + +
78C ASN* 1.3 77.9 - - - +
80C THR* 1.3 65.0 + - - +
81C ILE* 4.3 3.8 - - + -
94C CYS* 3.8 29.2 - - - -
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Residues in contact with THR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 3.5 28.3 - - + -
19C ALA 3.2 4.7 - - - -
20C SER* 2.8 19.4 + - - +
67C ILE 3.5 1.6 - - - +
68C CYS* 3.4 5.4 - - - +
69C THR* 3.0 45.6 + - - +
70C GLY* 5.9 0.2 - - - -
79C LEU* 1.3 74.7 + - - +
81C ILE* 1.3 65.8 + - - +
82C GLN* 4.8 8.0 - - + +
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Residues in contact with ILE 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLY 3.8 1.1 - - - +
18C ILE* 3.3 3.7 - - - +
19C ALA* 2.8 37.2 + - + +
21C PHE* 3.9 30.3 - - + -
38C VAL* 4.1 15.3 - - + -
49C VAL* 5.1 0.4 - - + -
67C ILE* 3.4 31.4 - - + -
68C CYS* 4.2 13.2 - - - -
79C LEU* 5.2 3.6 - - + -
80C THR* 1.3 79.7 - - - +
82C GLN* 1.3 62.7 - - - +
84C LEU* 3.9 25.8 - - + +
92C TYR* 3.7 28.0 - - + -
114C ILE* 4.4 2.2 - - + -
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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