Contacts of the strand formed by residues 73 - 80 (chain A) in PDB entry 2Z4U
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 VAL 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LEU* 4.5 22.7 - - + -
65A MET 3.5 5.6 - - - +
66A LEU* 4.0 15.0 - - + +
71A LEU 3.5 0.2 + - - -
72A TYR* 1.3 73.3 - - - +
74A MET* 1.3 60.1 + - - +
75A GLY 3.7 23.1 - - - +
89A PHE* 3.3 30.0 - - + +
91A ASP* 5.5 0.5 - - - +
120A SER* 4.4 8.1 + - - -
166A LEU* 5.0 5.2 - - + -
170A ILE* 3.8 33.7 - - + +
174A SER* 3.9 18.4 - - - +
501A EDO 5.8 1.8 + - - -
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Residues in contact with MET 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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49A TYR* 3.6 34.3 - - + -
65A MET* 2.9 15.7 + - + +
66A LEU 4.3 1.6 - - - -
67A ARG* 3.9 29.6 - - - +
72A TYR 4.0 9.2 - - - +
73A VAL* 1.3 75.7 - - - +
75A GLY* 1.3 56.4 + - - +
88A ILE* 3.8 9.5 - - - +
89A PHE* 3.1 28.2 + - - +
92A ILE* 4.1 12.9 - - + +
96A GLU* 3.7 41.3 - - + +
100A VAL* 3.6 31.2 - - + -
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Residues in contact with GLY 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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64A LEU* 3.7 2.1 - - - -
65A MET* 3.0 23.8 + - - +
73A VAL* 3.6 11.6 - - - +
74A MET* 1.3 79.7 - - - +
76A TYR* 1.3 64.7 + - - +
87A HIS 3.0 15.7 - - - -
88A ILE* 4.2 2.5 - - - -
89A PHE 4.4 1.6 - - - -
100A VAL* 4.9 1.6 - - - -
104A LEU* 4.3 9.0 - - - -
116A ILE* 4.4 6.1 - - - -
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Residues in contact with TYR 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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62A ILE* 3.6 27.6 - - + -
63A THR 3.0 13.7 - - - +
64A LEU* 4.0 9.6 - - + -
75A GLY* 1.3 75.4 - - - +
77A SER* 1.3 65.0 + - - +
78A ASP* 4.8 0.9 - - - -
87A HIS* 2.8 73.7 + + + +
104A LEU* 3.6 9.0 - - - +
116A ILE* 3.8 16.8 - - + -
151A ILE* 3.7 21.2 - - + +
157A PHE* 3.4 12.3 - - - -
162A GLU* 2.7 36.2 + - + +
165A PHE* 4.6 6.7 - + - -
166A LEU* 4.1 21.5 - - + -
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Residues in contact with SER 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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62A ILE* 3.4 9.2 - - - +
63A THR* 2.8 48.2 + - - -
76A TYR* 1.3 78.5 - - - +
78A ASP* 1.3 62.5 + - - +
84A CYS* 4.3 15.0 - - - -
85A ARG 3.1 13.0 - - - -
87A HIS* 4.2 0.2 - - - -
104A LEU* 3.8 29.1 + - - +
105A CYS* 4.4 0.2 - - - -
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Residues in contact with ASP 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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61A THR 4.0 6.5 - - - +
62A ILE* 4.5 5.2 - - + -
76A TYR* 5.2 1.1 - - + -
77A SER* 1.3 76.7 - - - +
79A LEU* 1.3 60.9 + - - +
80A TYR* 4.0 0.5 - - - +
84A CYS* 3.9 2.4 - - - -
85A ARG* 2.8 59.8 + - - +
87A HIS* 2.7 33.3 - - + -
151A ILE* 3.5 2.6 - - - +
152A SER* 4.0 21.5 - - - +
153A GLY* 2.8 27.3 + - - -
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Residues in contact with LEU 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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61A THR* 4.7 6.1 + - - +
78A ASP* 1.3 71.3 - - - +
80A TYR* 1.3 59.0 + - - +
81A ASN 4.2 0.4 - - - +
82A GLY* 3.7 30.3 - - - +
83A LYS 3.4 16.4 - - - +
84A CYS* 4.7 2.7 - - + +
152A SER* 4.6 2.4 + - - +
153A GLY* 3.3 21.8 + - - -
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Residues in contact with TYR 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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78A ASP* 4.0 1.8 - - - +
79A LEU* 1.3 76.2 - - - +
81A ASN* 1.3 100.0 + - - +
82A GLY 3.0 0.2 - - - -
83A LYS* 2.9 40.0 + - - +
85A ARG* 3.6 42.2 - - + +
112A GLU* 3.7 23.6 - - - -
153A GLY* 3.5 24.2 - - - -
155A SER* 3.2 45.6 + - - -
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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