Contacts of the strand formed by residues 59 - 66 (chain U) in PDB entry 5OA3
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 LYS 59 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15482 G 5.7 4.9 - - - +
15792 A 5.8 3.3 - - - +
15802 A 3.5 42.6 + - - -
8D LYS* 5.2 17.7 - - + -
56U MET* 5.8 0.9 - - - -
57U PRO* 3.4 24.9 + - + +
58U THR* 1.3 75.0 - - - +
60U THR* 1.3 61.5 + - - +
61U LEU* 4.2 1.1 + - + -
82U MET 4.0 0.3 - - - +
83U ARG* 3.6 1.6 - - - -
84U ILE* 2.8 56.8 + - + +
86U LYS* 5.9 7.0 - - + +
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Residues in contact with THR 60 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15482 G 4.6 27.0 + - - +
15492 U 4.2 11.6 + - - -
8D LYS* 5.4 1.0 + - - -
58U THR* 3.8 11.4 + - - +
59U LYS* 1.3 76.6 + - - +
61U LEU* 1.3 73.5 + - - +
62U ARG* 3.9 17.8 + - + +
81U GLN* 3.9 22.9 - - - +
82U MET 3.5 11.2 - - - +
83U ARG* 3.6 26.4 + - + +
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Residues in contact with LEU 61 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LYS* 3.8 37.5 - - + +
11D PHE* 5.8 0.4 - - + -
12D VAL* 4.5 20.0 - - + -
59U LYS* 5.1 1.8 - - + +
60U THR* 1.3 77.6 - - - +
62U ARG* 1.3 62.2 + - - +
63U ILE 4.2 0.2 + - - -
80U PHE 3.7 0.2 - - - +
81U GLN* 3.2 6.8 - - - +
82U MET* 2.8 62.9 + - + +
84U ILE* 4.2 23.1 - - + -
34d TYR* 3.6 30.3 - - + +
52d PHE* 4.2 14.3 - - + -
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Residues in contact with ARG 62 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13922 U 6.3 1.4 - - - -
15472 C 3.9 23.2 + - - -
15482 G 4.0 23.9 + - - -
15492 U 4.5 2.0 + - - +
16692 G 4.7 12.5 + - - -
16702 C 5.5 3.6 + - - -
60U THR* 3.9 17.1 + - + +
61U LEU* 1.3 75.5 - - - +
63U ILE* 1.3 67.2 + - - +
64U THR* 4.2 6.9 - - + +
80U PHE 3.4 4.7 - - - +
81U GLN* 3.7 33.9 - - + +
83U ARG* 5.8 2.0 - - - +
33d LYS* 4.0 18.5 + - - +
34d TYR* 4.0 5.9 + - - -
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Residues in contact with ILE 63 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12562 G 5.1 1.1 - - - +
62U ARG* 1.3 79.2 - - - +
64U THR* 1.3 64.1 + - - +
65U THR* 3.7 22.3 + - + -
78U ASP 3.7 1.6 - - - +
79U ARG* 3.8 0.2 - - - -
80U PHE* 2.9 40.6 + - + +
31d ILE* 4.5 17.3 - - + -
33d LYS* 5.7 2.5 - - + -
34d TYR* 4.4 20.9 - - + -
36d LEU* 4.7 8.3 - - + -
43d PHE* 3.6 27.6 - - + -
52d PHE* 3.5 36.3 - - + -
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Residues in contact with THR 64 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12562 G 3.0 13.0 - - - +
16572 G 5.4 3.6 + - - -
16682 U 3.4 30.7 + - - +
16692 G 5.4 0.7 - - - +
62U ARG* 4.4 6.5 + - + -
63U ILE* 1.3 79.3 - - - +
65U THR* 1.3 61.5 + - - +
77U TRP* 3.2 27.6 - - - -
78U ASP 3.3 6.1 - - - -
79U ARG* 4.1 19.7 - - + -
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Residues in contact with THR 65 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12562 G 3.2 20.0 - - - +
63U ILE* 3.7 12.1 + - + +
64U THR* 1.3 76.0 - - - +
66U ARG* 1.3 66.7 + - - +
77U TRP* 3.5 10.2 - - - -
78U ASP* 2.9 46.4 + - - +
80U PHE* 4.2 7.0 - - + -
31d ILE* 4.4 4.5 - - + -
40d ARG* 4.6 10.1 - - + -
43d PHE* 3.6 33.2 - - + -
44d ARG* 4.4 8.1 - - - +
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Residues in contact with ARG 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12542 C 3.4 29.3 + - - +
12552 G 4.6 5.7 + - - +
12562 G 3.8 26.7 + - + +
65U THR* 1.3 79.0 + - - +
67U LYS* 1.3 69.4 + - - +
68U THR* 3.3 36.2 - - - +
71U GLY* 3.5 17.5 + - - -
73U GLY 4.4 1.0 - - - +
75U LYS* 3.5 35.0 - - - +
76U THR 3.3 18.3 + - - +
77U TRP* 3.5 33.4 - - + +
40d ARG* 4.6 18.4 + - - +
44d ARG* 4.5 3.3 - - - -
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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