Contacts of the strand formed by residues 60 - 64 (chain A) in PDB entry 1ZN8
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 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 3.6 7.2 - - - +
59A ASP* 1.3 95.0 - - + +
61A ILE* 1.3 69.4 - - - +
81A LEU* 4.3 2.2 - - - -
82A GLY* 3.6 23.6 - - - +
84A VAL* 4.2 10.8 - - + -
117A LEU* 3.4 27.4 - - + -
121A GLN* 3.8 33.4 + - + -
122A ARG 3.2 2.9 + - - -
123A VAL* 3.2 10.3 - - + +
124A VAL 3.1 22.9 + - - -
34B LYS* 3.4 45.6 + - + +
36B PRO* 6.0 0.2 - - + -
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Residues in contact with ILE 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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50A LEU* 4.5 0.7 - - + -
58A ILE* 4.4 1.8 - - + -
60A TYR* 1.3 78.0 - - - +
62A ALA* 1.3 64.2 + - - +
63A GLY 4.1 0.2 - - - -
72A GLY* 4.0 14.6 - - - +
75A LEU* 4.3 13.2 - - + -
76A ALA* 3.8 35.2 - - + +
79A LEU* 3.8 22.7 - - + -
81A LEU* 4.2 9.2 - - + +
82A GLY 3.2 5.3 + - - +
83A CYS* 3.2 4.7 - - - -
84A VAL* 2.8 27.4 + - - +
124A VAL* 3.3 28.3 - - + +
126A VAL* 3.6 30.3 - - + -
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Residues in contact with ALA 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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61A ILE* 1.3 76.2 - - - +
63A GLY* 1.3 61.0 + - - +
84A VAL* 3.3 18.6 - - + +
86A ILE* 4.2 22.4 - - + -
123A VAL* 3.6 20.8 - - + +
124A VAL 2.9 9.3 + - - +
125A VAL* 3.3 12.7 - - + +
126A VAL* 2.9 25.1 + - - +
143A LEU* 4.5 1.3 - - + -
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Residues in contact with GLY 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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62A ALA* 1.3 73.2 - - - +
64A LEU* 1.3 62.9 + - - +
68A GLY 4.1 13.5 - - - -
69A PHE* 3.4 15.8 - - - -
72A GLY* 4.6 0.7 - - - -
83A CYS* 3.9 12.7 - - - -
84A VAL 3.0 11.0 + - - +
85A LEU* 5.5 0.2 - - - -
86A ILE 3.2 23.6 + - - -
126A VAL* 3.9 10.1 - - - -
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Residues in contact with LEU 64 (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 ALA 4.5 0.7 - - - +
63A GLY* 1.3 73.1 - - - -
65A ASP* 1.3 63.5 + - - +
68A GLY* 2.8 31.8 + - - -
69A PHE* 3.3 5.3 + - - -
86A ILE* 3.8 23.8 - - + -
110A LEU* 5.0 2.7 - - + -
125A VAL* 3.5 27.1 - - + -
126A VAL 3.2 18.1 + - - +
127A ASP* 3.6 31.5 - - + +
135A THR* 3.8 29.4 - - + +
136A MET* 4.3 8.5 - - + -
139A ALA* 3.7 17.0 - - + -
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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