Contacts of the strand formed by residues 76 - 81 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H SER* 3.8 18.8 - - - +
20H CYS 3.5 14.1 - - - +
21H LYS* 3.4 17.7 - - + +
27H PHE* 3.6 5.5 - - - -
70H ALA* 3.6 1.2 - - - -
71H VAL 3.0 31.5 + - - +
74H ALA* 2.9 26.0 + - - +
75H SER* 1.3 76.0 - - - +
77H ALA* 1.3 63.3 + - - +
78H TYR* 3.6 34.3 + - + +
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Residues in contact with ALA 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H SER* 3.3 2.1 - - - -
20H CYS* 2.7 47.1 + - + +
27H PHE* 3.9 15.2 - - + -
32H MET* 4.1 24.9 - - + -
34H TRP* 3.6 14.4 - - + +
49H ILE* 4.8 5.6 - - + -
69H THR 3.9 6.3 - - - +
70H ALA* 4.4 3.6 - - + -
76H THR* 1.3 72.5 - - - +
78H TYR* 1.3 62.1 + - - +
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Residues in contact with TYR 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H LYS* 3.5 40.2 - - + -
18H MET 3.5 4.7 - - - +
19H SER* 3.6 23.8 - - - -
34H TRP* 4.0 6.4 + - - -
49H ILE* 5.6 0.3 - - - +
68H LEU* 3.5 7.3 - - - +
69H THR* 2.8 50.0 + - - +
70H ALA* 4.5 0.9 - - - -
71H VAL* 4.2 26.2 - - + +
74H ALA* 5.2 4.0 - - - +
76H THR* 3.6 38.3 + - + +
77H ALA* 1.3 75.4 - - - +
79H MET* 1.3 63.0 + - - +
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Residues in contact with MET 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H VAL 3.7 1.6 - - - +
17H LYS* 3.6 0.8 - - - -
18H MET* 3.0 38.7 + - + +
34H TRP* 3.2 42.6 - - + -
46H ILE* 3.9 16.6 - - + -
66H ALA* 4.1 10.5 - - - -
67H LYS 3.4 3.8 - - - +
68H LEU* 3.5 28.0 - - + -
78H TYR* 1.3 73.9 - - - +
80H GLU* 1.3 66.1 + - - +
81H LEU* 3.5 30.7 - - + +
92H TYR* 3.8 29.4 - - + -
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Residues in contact with GLU 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H SER* 5.7 6.7 - - - -
16H VAL 3.5 4.0 - - - +
17H LYS* 3.7 38.2 - - + +
65H LYS 3.5 0.7 - - - +
66H ALA* 3.2 6.9 - - - -
67H LYS* 2.8 54.0 + - + +
69H THR* 5.7 6.0 + - + +
79H MET* 1.3 73.1 - - - +
81H LEU* 1.3 64.0 + - - +
82H SER* 4.6 5.0 + - - +
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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
----------------------------------------------------------
15H SER* 3.2 8.1 - - - -
16H VAL* 2.8 40.4 + - + +
18H MET* 4.7 8.5 - - + -
46H ILE* 5.8 1.1 - - + -
62H PHE* 5.8 3.8 - - + -
65H LYS* 3.5 7.4 - - + +
66H ALA* 3.8 14.4 - - + -
79H MET* 3.5 31.8 + - + +
80H GLU* 1.3 77.2 - - - +
82H SER* 1.3 60.6 + - - +
84H LEU* 3.6 18.6 - - + +
88H ASP* 4.8 6.5 - - - +
92H TYR* 3.4 39.5 - - + +
111H LEU* 3.9 18.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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