Contacts of the strand formed by residues 76 - 81 (chain C) in PDB entry 3IU3
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 76 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER* 3.7 23.3 - - - +
20C CYS 3.5 12.3 - - - +
21C LYS* 3.4 15.4 - - + +
27C PHE* 3.8 6.1 - - - -
70C ALA* 3.6 2.9 - - - -
71C VAL 3.1 28.9 + - - -
74C ALA* 3.0 26.1 + - - +
75C SER* 1.3 75.7 - - - +
77C ALA* 1.3 61.4 + - - +
78C TYR* 3.6 35.1 + - + +
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Residues in contact with ALA 77 (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 SER* 3.3 3.8 - - - -
20C CYS* 2.7 43.3 + - + +
27C PHE* 3.9 12.9 - - + -
32C MET* 3.9 27.4 - - + -
34C TRP* 3.6 17.2 - - + +
49C ILE* 4.8 7.2 - - + -
69C THR 3.8 7.0 - - - +
70C ALA* 4.5 0.7 - - + +
76C THR* 1.3 72.6 - - - +
78C TYR* 1.3 61.7 + - - +
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Residues in contact with TYR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LYS* 3.8 30.5 - - + -
18C MET 3.4 8.1 - - - +
19C SER* 3.9 22.0 - - - -
34C TRP* 4.3 4.7 + - - -
49C ILE* 5.9 0.3 - - - +
68C LEU* 3.5 6.9 - - - +
69C THR* 2.8 49.0 + - - +
70C ALA* 4.6 0.9 - - - -
71C VAL* 3.8 26.1 - - + +
74C ALA* 4.7 6.1 - - - +
76C THR* 3.6 38.5 + - + +
77C ALA* 1.3 76.7 - - - +
79C MET* 1.3 62.3 + - - +
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Residues in contact with MET 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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16C VAL 3.7 1.4 - - - +
17C LYS* 3.4 4.3 - - - +
18C MET* 3.0 46.4 + - + +
34C TRP* 3.5 36.6 - - + -
46C ILE* 4.1 22.0 - - + -
66C ALA* 4.2 3.6 - - + -
67C LYS 3.2 6.3 - - - +
68C LEU* 3.7 26.2 - - + -
78C TYR* 1.3 76.6 - - - +
80C GLU* 1.3 64.0 - - - +
81C LEU* 3.6 23.1 + - + +
92C TYR* 3.6 28.9 - - + -
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Residues in contact with GLU 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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15C SER* 5.0 10.8 + - - -
16C VAL 3.1 12.6 - - - +
17C LYS* 3.8 30.1 - - + +
65C LYS 3.6 0.5 - - - +
66C ALA* 3.3 4.2 - - - +
67C LYS* 2.9 74.9 + - + +
69C THR* 6.1 0.4 - - + +
79C MET* 1.3 73.7 - - - +
81C LEU* 1.3 65.7 + - - +
82C SER* 4.0 7.9 + - - +
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Residues in contact with LEU 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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14C ALA 4.1 0.5 - - - +
15C SER* 3.2 9.1 + - - -
16C VAL* 3.0 32.4 + - + +
18C MET* 4.6 12.6 - - + -
46C ILE* 5.8 1.3 - - + -
62C PHE* 5.2 7.2 - - + -
65C LYS* 3.3 27.8 - - + +
66C ALA* 3.8 15.7 - - + -
79C MET* 3.6 37.0 - - + +
80C GLU* 1.3 73.6 - - - +
82C SER* 1.3 60.4 + - - +
84C LEU* 3.6 23.9 - - + +
88C ASP* 4.9 2.2 - - - +
92C TYR* 4.4 26.7 - - + +
111C LEU* 4.8 2.0 - - + -
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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