Contacts of the strand formed by residues 57 - 63 (chain A) in PDB entry 2OB4
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU* 5.4 0.3 + - - -
44A ALA* 4.1 23.1 - - + +
45A ILE 3.5 5.2 - - - -
46A PHE* 4.1 29.8 - + + +
55A GLY 5.1 1.8 - - - +
56A GLY* 1.3 73.2 - - - +
58A PHE* 1.3 65.6 + - - +
59A LYS* 3.4 28.0 + - + +
79A THR* 4.6 1.4 + - - -
172A THR* 3.1 29.2 + - - +
175A ASP* 3.9 20.5 - - + +
176A ALA* 3.3 34.1 - - + -
179A ASP* 2.7 29.8 + - - -
180A GLY 5.0 6.3 - - - -
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Residues in contact with PHE 58 (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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44A ALA* 3.6 3.1 - - - -
45A ILE* 2.7 63.6 + - + +
47A GLY* 4.5 5.8 - - - -
53A TYR* 3.5 44.0 - + + -
56A GLY* 4.3 13.9 - - - -
57A TYR* 1.3 75.7 - - - +
59A LYS* 1.3 62.4 + - - +
77A PHE* 4.3 14.6 - + + -
79A THR* 3.6 15.5 - - + +
81A MET* 3.5 29.4 - - + -
131A LEU* 5.1 4.7 - - + -
165A ILE 5.6 0.2 - - - -
168A GLN* 4.6 6.1 - - + -
169A VAL* 3.8 21.8 - - + -
172A THR* 3.6 21.1 - - + -
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Residues in contact with LYS 59 (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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42A GLU* 3.7 32.7 + - + +
43A VAL 3.6 8.5 - - - +
44A ALA* 5.0 1.8 - - + -
57A TYR* 3.4 32.1 + - + +
58A PHE* 1.3 75.4 - - - +
60A ALA* 1.3 56.8 + - - +
61A ARG* 6.0 0.4 - - - +
77A PHE* 3.8 4.6 - - - -
78A LEU* 2.8 46.7 + - + -
79A THR* 2.9 18.6 + - - +
175A ASP* 5.8 2.0 - - + -
178A ARG* 3.2 30.3 - - - +
179A ASP* 4.3 5.1 + - - -
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Residues in contact with ALA 60 (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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42A GLU* 3.7 4.0 - - - +
43A VAL* 2.9 31.1 + - + +
45A ILE* 4.0 9.0 - - + -
58A PHE 4.3 0.4 + - - -
59A LYS* 1.3 74.5 - - - +
61A ARG* 1.3 70.3 + - - +
75A PHE* 3.5 34.3 - - + -
76A ARG 3.4 10.5 - - - +
77A PHE* 3.8 11.9 - - + -
78A LEU* 3.9 2.2 - - - +
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Residues in contact with ARG 61 (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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33A VAL* 3.7 34.2 - - - +
40A ASN* 6.1 2.8 - - - +
41A TRP 3.5 15.0 - - - +
42A GLU* 2.8 27.1 + - - +
43A VAL* 4.8 1.3 - - - +
59A LYS* 6.0 0.4 - - - +
60A ALA* 1.3 79.4 - - - +
62A LEU* 1.3 64.1 + - - +
74A ALA 3.5 4.0 - - - +
75A PHE* 3.7 6.8 - - - -
76A ARG* 2.8 52.5 + - + +
78A LEU* 3.8 32.1 - - + +
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Residues in contact with LEU 62 (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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39A TYR 4.3 0.4 - - - -
40A ASN* 3.4 5.6 + - - +
41A TRP* 2.8 43.8 + - + +
43A VAL* 3.7 24.4 - - + +
61A ARG* 1.3 78.5 - - - +
63A LYS* 1.3 59.4 + - - +
64A PHE* 3.9 20.2 - - + -
73A PRO* 3.8 31.2 - - + -
74A ALA 3.4 8.3 - - - +
75A PHE* 4.2 17.7 - - + -
94A ILE* 5.5 0.2 - - + -
120A VAL* 3.8 27.4 - - + -
123A ILE* 4.4 11.4 - - + -
124A LEU* 4.5 6.5 - - + -
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Residues in contact with LYS 63 (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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39A TYR* 3.3 5.6 - - + +
40A ASN* 3.5 28.3 - - - +
62A LEU* 1.3 74.4 - - - +
64A PHE* 1.3 69.3 + - - +
65A PRO* 4.3 0.5 - - - +
73A PRO* 3.0 2.8 - - - +
74A ALA* 2.7 50.8 + - + +
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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