Contacts of the strand formed by residues 73 - 82 (chain A) in PDB entry 1OWK
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 MET 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.6 7.8 - - - +
60A LEU 3.0 25.2 + - - +
71A GLY 4.4 4.0 - - - +
72A GLU* 1.3 83.1 - - - +
74A LYS* 1.3 60.3 + - - +
75A PHE* 3.3 33.7 - - + -
109A CYS 5.3 0.9 - - - +
110A ALA* 4.5 0.4 - - - -
111A GLN* 3.0 57.7 - - + +
113A SER* 5.1 4.7 - - - +
116A ILE* 3.5 24.0 - - + -
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Residues in contact with LYS 74 (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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21A ARG* 5.3 7.1 - - - +
57A ILE* 3.9 29.8 - - + +
58A VAL 4.1 2.0 - - - -
59A TYR* 3.5 39.0 + - + +
73A MET* 1.3 73.1 - - - +
75A PHE* 1.3 68.8 + - - +
76A GLU* 6.2 2.5 - - + -
104A SER* 4.3 12.5 - - - -
105A LYS* 5.2 12.3 + - - +
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Residues in contact with PHE 75 (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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57A ILE* 3.7 11.3 - - - +
58A VAL* 2.9 41.6 + - + +
60A LEU* 3.9 20.9 - - + -
73A MET* 3.3 45.8 - - + -
74A LYS* 1.3 76.8 - - - +
76A GLU* 1.3 69.5 + - - +
102A ILE* 3.9 26.7 - - + -
103A ARG 4.1 5.2 - - - -
104A SER* 3.9 22.7 - - - +
108A ARG 4.1 3.6 - - - -
109A CYS 3.7 8.1 - - - -
110A ALA* 3.6 40.6 - - + -
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Residues in contact with GLU 76 (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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21A ARG* 3.7 23.5 + - - +
56A TYR 4.5 6.7 - - - +
58A VAL* 5.2 0.9 - - - +
74A LYS* 6.2 2.5 - - + -
75A PHE* 1.3 80.5 - - - +
77A VAL* 1.3 63.6 + - - +
78A GLU 3.4 1.4 + - - -
102A ILE* 3.3 6.0 - - - -
103A ARG* 2.8 47.5 + - + +
104A SER 4.6 0.5 - - - -
105A LYS* 4.0 38.6 - - + +
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Residues in contact with VAL 77 (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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53A LYS* 3.4 35.4 + - + +
54A GLU* 5.4 1.9 - - - +
56A TYR* 3.7 31.9 + - + +
58A VAL* 4.3 11.2 - - + -
76A GLU* 1.3 72.9 - - - +
78A GLU* 1.3 61.1 + - - +
79A ASN 3.6 27.6 - - - +
80A LEU* 3.9 16.8 - - + +
100A LEU* 4.2 28.3 - - + -
101A LYS 3.9 3.4 - - - +
102A ILE* 4.6 2.0 - - + +
103A ARG* 5.0 2.6 + - - -
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Residues in contact with GLU 78 (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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53A LYS* 3.3 20.0 - - - +
76A GLU 3.4 3.8 + - - -
77A VAL* 1.3 73.8 - - - +
79A ASN* 1.3 59.6 + - + +
101A LYS* 2.7 55.7 + - + +
102A ILE 4.3 1.4 - - - +
103A ARG* 3.8 57.5 + - + +
109A CYS* 6.0 0.9 - - - -
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Residues in contact with ASN 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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39A TRP* 5.0 3.0 - - + -
53A LYS* 4.4 3.1 - - - -
77A VAL* 3.3 4.2 - - - +
78A GLU* 1.3 84.8 + - + +
80A LEU* 1.3 62.3 + - - +
81A ILE* 2.8 39.9 - - - +
99A LEU 3.5 1.9 - - - +
100A LEU* 3.4 3.6 - - - -
101A LYS* 2.8 51.7 + - + +
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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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47A PHE* 4.0 27.8 - - + -
51A PRO* 4.5 21.1 - - + +
53A LYS* 4.1 18.0 - - + +
56A TYR* 4.3 16.6 - - + -
77A VAL* 3.9 10.7 - - + +
79A ASN* 1.3 76.9 + - - +
81A ILE* 1.3 60.4 + - - +
82A LEU* 4.0 24.3 + - + +
99A LEU 3.6 1.6 - - - +
100A LEU* 3.3 40.8 - - + -
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Residues in contact with ILE 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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39A TRP* 4.2 12.3 - - + -
79A ASN* 2.8 31.6 - - - +
80A LEU* 1.3 71.9 - - - +
82A LEU* 1.3 72.3 - - - +
83A HIS 4.3 0.2 + - - -
84A LYS* 5.6 0.4 - - - -
98A ALA* 3.7 1.0 - - - -
99A LEU* 2.8 45.6 + - + +
239A TRP* 4.4 10.5 - - + -
243A HIS* 3.7 48.7 - - + +
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Residues in contact with LEU 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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44A THR* 4.0 29.4 - - + +
47A PHE* 4.6 8.5 - - + +
48A ILE* 4.4 26.5 - - + +
51A PRO* 4.9 12.6 - - + -
80A LEU* 4.0 28.4 + - + +
81A ILE* 1.3 86.5 - - - +
83A HIS* 1.3 68.9 + - - +
84A LYS* 3.2 12.3 + - - +
98A ALA* 3.9 17.9 - - + -
239A TRP* 4.4 2.5 - - - -
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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