Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 5O6I
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 TYR 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A THR* 3.2 4.0 - - - -
42A GLN 2.7 37.3 + - - +
43A LYS 3.4 19.5 - - - -
45A GLU* 3.3 54.3 + - + -
48A ILE* 3.5 14.3 - - + +
71A ILE* 4.3 13.2 - - + -
72A VAL 3.5 4.9 - - - -
73A LYS* 3.2 55.2 - - + +
77A ARG* 1.3 79.7 - - - +
79A GLU* 1.3 60.8 + - - +
203A CL 4.2 15.3 - - + -
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 4.6 0.9 + - - -
39A VAL* 3.6 32.7 - - + +
40A ILE 3.6 2.9 - - - -
41A THR* 4.3 2.9 - - + +
48A ILE* 4.5 2.2 - - - -
70A GLN 3.4 2.1 - - - +
71A ILE* 3.3 6.0 - - - -
72A VAL* 2.8 45.1 + - + +
77A ARG* 3.3 22.5 + - - +
78A TYR* 1.3 74.6 - - - +
80A LEU* 1.3 64.8 + - - +
81A ARG* 2.8 49.5 + - + +
16C T 5.0 2.6 - - - +
17C T 4.6 3.3 - - - +
9D A 3.1 18.4 + - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL 4.9 1.6 - - - +
39A VAL* 3.2 7.3 - - - +
40A ILE* 2.7 52.7 + - + +
48A ILE* 3.9 20.2 - - + +
52A PHE* 3.8 16.4 - - + -
53A ALA* 3.6 41.3 - - + +
56A MET* 4.2 31.2 - - + -
69A ILE* 4.0 16.4 - - + -
70A GLN 3.5 3.6 - - - -
71A ILE* 4.7 1.3 - - + +
79A GLU* 1.3 70.5 - - - +
81A ARG* 1.3 62.9 + - - +
82A VAL* 4.3 8.3 - - + -
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 4.6 1.6 - - - -
37A ARG* 3.2 39.2 - - + +
38A VAL 3.4 3.6 - - - -
39A VAL* 4.4 3.8 - - + +
68A LYS 3.7 1.2 - - - +
69A ILE 3.7 0.9 - - - -
70A GLN* 2.8 66.0 + - + +
72A VAL* 3.9 14.3 - - + +
79A GLU* 2.8 45.3 + - + +
80A LEU* 1.3 75.7 - - - +
82A VAL* 1.3 72.7 + - - +
83A SER* 4.5 0.9 - - - +
7D G 3.2 24.5 + - - -
8D G 3.1 29.5 + - - -
9D A 3.2 18.4 + - - +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.4 3.3 - - - -
38A VAL* 2.9 38.4 + - - +
56A MET* 3.8 29.8 - - + -
60A ILE* 4.4 11.9 - - + -
67A SER* 4.0 12.3 - - - -
68A LYS 4.0 7.9 - - - +
69A ILE* 4.2 12.8 - - + -
80A LEU* 4.3 6.5 - - + -
81A ARG* 1.3 79.7 - - - +
83A SER* 1.3 60.7 + - - +
84A SER* 3.4 17.5 + - - -
87A LEU* 3.6 27.8 - - + -
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.0 39.0 + - - +
36A TYR 3.2 6.3 + - - -
37A ARG* 4.6 2.2 - - - +
67A SER* 2.6 26.1 + - - -
68A LYS 4.5 4.4 + - - -
70A GLN* 4.0 16.0 - - - +
81A ARG* 4.1 2.5 + - - +
82A VAL* 1.3 69.7 - - - +
84A SER* 1.3 53.6 + - - +
5D C 3.4 37.9 + - - +
6D C 4.5 1.6 - - - -
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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