Contacts of the strand formed by residues 67 - 71 (chain A) in PDB entry 1OWH
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 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.2 11.0 - - + -
19A TYR 3.3 14.1 - - - +
20A ARG* 4.0 22.6 - - + -
21A ARG* 3.8 11.4 + - - -
32A VAL* 4.5 9.6 - - + -
55A CYS 4.3 2.4 + - - -
56A PHE* 3.5 44.4 - + - -
59A TYR* 2.7 43.2 + - - +
61A LYS 3.4 20.2 - - - -
62A LYS* 3.4 12.3 + - - +
63A GLU 3.4 2.6 - - - +
65A ASP* 1.3 83.6 - - + +
68A ILE* 1.3 61.6 - - - +
69A VAL 4.3 0.2 - - - -
89A GLU* 4.2 17.0 - - - +
90A VAL* 3.9 23.4 + - + -
93A LEU* 4.6 8.5 - - + -
113A LEU* 5.4 1.6 - - + -
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Residues in contact with ILE 68 (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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17A ALA 3.7 1.7 - - - +
18A ILE* 3.5 2.6 - - - +
19A TYR* 2.8 43.4 + - + +
21A ARG* 3.6 39.5 - - + +
29A VAL* 3.8 35.2 - - + -
65A ASP 4.9 1.8 - - - +
67A TYR* 1.3 77.1 - - - +
69A VAL* 1.3 63.9 + - - +
70A TYR* 3.7 27.8 - - + +
87A LYS* 3.8 32.8 - - + +
88A PHE 3.6 6.3 - - - +
89A GLU* 6.2 0.9 - - + -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 4.2 23.8 - - + -
17A ALA 3.5 4.9 - - - +
18A ILE* 4.2 21.8 - - + -
49A VAL* 4.4 9.2 - - + -
68A ILE* 1.3 78.7 - - - +
70A TYR* 1.3 63.1 + - - +
71A LEU* 5.1 2.7 - - + -
87A LYS* 3.5 1.4 - - - -
88A PHE* 2.8 46.5 + - + +
90A VAL* 4.1 24.9 - - + -
113A LEU* 4.4 6.7 - - + -
115A ILE* 4.2 24.0 - - + -
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Residues in contact with TYR 70 (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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15A PHE 4.2 0.5 - - - +
16A ALA* 3.5 8.1 - - - +
17A ALA* 2.9 33.8 + - + +
19A TYR* 3.6 33.0 - + - -
29A VAL* 6.4 0.7 - - + -
68A ILE* 3.7 17.5 - - + +
69A VAL* 1.3 75.1 - - - +
71A LEU* 1.3 63.8 + - - +
73A ARG* 3.4 49.3 + - + -
81A ASN* 4.7 2.5 + - - -
85A GLU* 3.4 26.0 - - - -
86A MET 3.3 13.9 - - - +
87A LYS* 3.8 40.1 + - + +
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Residues in contact with LEU 71 (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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13A PRO 5.4 1.8 - - - +
14A TRP 4.8 1.8 - - - +
15A PHE 4.1 9.2 - - - +
16A ALA* 3.9 23.1 - - + -
39A LEU* 3.8 37.0 - - + -
49A VAL* 4.8 2.5 - - + -
69A VAL* 4.3 2.4 - - + -
70A TYR* 1.3 78.6 - - - +
72A GLY* 1.3 61.1 + - - +
73A ARG 3.3 3.0 + - - -
85A GLU* 3.3 2.4 - - - +
86A MET 2.9 29.8 + - - +
88A PHE* 3.7 19.7 - - + -
115A ILE* 3.9 5.2 - - + -
123A ALA* 3.5 32.1 - - + -
129A ILE* 3.8 23.1 - - + +
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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