Contacts of the strand formed by residues 64 - 71 (chain A) in PDB entry 1OZ7
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A MET* 3.5 0.9 - - - +
63A TYR* 1.3 107.3 + - + +
65A ILE* 1.3 71.8 + - - +
102A VAL* 4.1 14.6 - - + -
103A LEU 3.0 11.0 - - - +
104A GLU* 4.4 10.7 + - - +
113A VAL* 3.7 25.3 - - + +
115A THR* 5.2 6.5 - - + -
121A PHE* 3.4 52.7 - - + +
122A PRO* 3.4 10.6 - - - +
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Residues in contact with ILE 65 (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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55A VAL* 3.8 31.2 - - + -
59A ILE* 4.2 13.0 - - + -
62A MET* 4.3 9.9 - - + +
64A LYS* 1.3 100.0 - - - +
66A TRP* 1.3 70.0 + - - +
67A THR 3.6 0.3 + - - -
102A VAL* 3.0 6.2 - - - +
103A LEU* 2.6 49.1 + - + +
109A PHE* 3.1 35.4 - - + -
122A PRO* 3.6 8.7 - - + -
123A PHE* 3.8 23.6 - - - +
124A MET* 4.2 5.2 - - + +
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Residues in contact with TRP 66 (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 LYS 3.0 28.8 + - - -
22A THR 4.2 2.9 - - - -
23A TRP* 3.7 20.9 - + - +
26A ALA* 4.6 3.6 - - + -
39A LEU* 4.1 14.3 - - + +
64A LYS 4.4 0.2 - - - -
65A ILE* 1.3 75.7 - - - +
67A THR* 1.3 66.2 + - - +
100A CYS* 3.4 22.4 - - + -
101A PHE 3.1 24.0 - - - -
102A VAL* 3.5 6.1 - - + -
115A THR* 3.3 36.6 - - + -
116A PRO 3.4 23.8 - - - -
117A CYS* 3.6 7.0 - - - -
119A ASN 3.2 14.2 + - - -
121A PHE* 3.5 32.1 - + + +
122A PRO 3.0 11.8 + - - +
123A PHE* 3.8 9.4 - - + +
124A MET* 3.5 22.9 + - - +
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Residues in contact with THR 67 (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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23A TRP* 4.3 6.4 - - - -
39A LEU* 3.7 13.9 - - - +
40A LEU* 3.5 18.8 - - + +
42A ILE* 4.4 14.1 - - + -
51A VAL* 5.6 1.3 - - + -
65A ILE* 3.6 1.3 + - + -
66A TRP* 1.3 78.0 - - - +
68A GLY* 1.3 59.5 + - - +
69A LEU* 3.1 11.3 + - - +
101A PHE* 3.4 24.7 + - - +
102A VAL* 3.8 8.7 - - - -
103A LEU* 3.6 38.4 - - + +
112A TRP* 5.3 4.1 - - - +
124A MET* 5.8 1.1 - - + -
79B TRP* 4.3 10.5 - - - -
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Residues in contact with GLY 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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23A TRP* 4.6 3.1 - - - -
39A LEU* 3.3 25.9 - - - +
40A LEU 2.8 18.3 + - - -
67A THR* 1.3 69.6 - - - +
69A LEU* 1.3 56.7 + - - +
70A SER 3.3 3.9 + - - -
79B TRP* 3.2 11.8 - - - -
80B SER* 2.8 37.4 + - - -
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Residues in contact with LEU 69 (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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23A TRP* 4.0 3.8 + - - -
67A THR* 3.1 8.0 + - - +
68A GLY* 1.3 74.3 - - - +
70A SER* 1.3 56.5 + - - +
100A CYS* 4.0 4.3 - - - -
101A PHE* 3.5 55.1 + - + +
112A TRP* 3.7 35.4 - - + -
77B TRP* 4.3 6.3 - - + -
78B GLU* 3.7 30.3 - - - +
79B TRP* 3.6 18.5 - - + -
85B LEU* 4.1 22.9 - - + -
90B TRP* 4.3 11.7 - - + -
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Residues in contact with SER 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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23A TRP* 3.1 40.9 + - - +
68A GLY 3.3 1.7 + - - -
69A LEU* 1.3 73.3 - - - +
71A GLU* 1.3 71.4 + - - +
99A GLU* 3.9 5.5 + - - +
100A CYS* 5.0 0.7 - - - -
77B TRP* 3.3 4.5 - - - -
78B GLU* 2.6 55.5 + - - +
80B SER* 5.5 1.6 - - - -
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Residues in contact with GLU 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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70A SER* 1.3 84.6 + - - +
72A ARG* 1.3 60.5 + - - +
73A SER* 2.4 51.2 + - - -
75A GLU* 2.8 17.2 - - - +
99A GLU* 3.0 47.8 + - + +
76B ASN* 2.5 37.7 + - - +
77B TRP* 3.5 26.8 - - + -
78B GLU* 4.3 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