Contacts of the strand formed by residues 78 - 86 (chain A) in PDB entry 5ZF6
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 THR 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLN* 3.4 3.0 - - - +
75A SER 3.0 35.7 + - - -
77A ASP* 1.3 78.9 - - - +
79A ALA* 1.3 62.1 + - - +
158A ALA 3.3 12.3 - - - +
159A VAL* 3.6 2.0 - - - -
160A ASP* 2.8 36.4 + - - -
163A ASN 3.0 20.7 + - - +
165A PRO* 3.6 28.7 - - + -
168A LEU* 3.6 13.1 - - + +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 4.4 11.2 - - + -
73A VAL 3.5 4.9 - - - +
74A GLN* 3.9 25.8 - - + +
77A ASP 4.1 1.4 + - - +
78A THR* 1.3 75.6 - - - +
80A VAL* 1.3 64.6 + - - +
156A LEU* 4.1 0.2 - - - -
157A LEU* 3.0 36.6 + - + +
158A ALA* 3.2 17.4 + - + +
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Residues in contact with VAL 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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71A ALA 3.8 0.3 - - - +
72A VAL* 3.2 5.8 - - - -
73A VAL* 2.9 34.7 + - - +
78A THR* 4.7 0.2 - - + -
79A ALA* 1.3 78.3 - - - +
81A MET* 1.3 69.0 + - - +
82A VAL* 4.1 10.2 + - + +
154A CYS* 4.4 0.9 - - + -
155A ASN 3.6 15.0 - - - +
156A LEU* 3.8 18.2 - - + -
157A LEU* 4.8 0.4 - - - -
165A PRO* 3.5 40.2 - - + +
168A LEU* 4.0 10.8 - - + +
169A ALA* 4.0 24.7 - - + +
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Residues in contact with MET 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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61A GLY* 4.7 10.5 - - - -
70A SER* 3.9 25.4 - - - +
71A ALA 3.2 12.3 - - - +
72A VAL* 3.8 17.3 - - + -
80A VAL* 1.3 73.0 - - - +
82A VAL* 1.3 64.4 + - - +
83A THR* 4.0 13.9 - - + -
153A LEU 3.7 1.4 - - - +
154A CYS* 3.5 0.7 - - - -
155A ASN* 2.6 52.2 + - + +
157A LEU* 4.1 18.7 - - + +
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Residues in contact with VAL 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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70A SER* 3.3 2.4 - - - -
71A ALA 2.9 31.0 + - - +
80A VAL* 4.1 15.0 - - + +
81A MET* 1.3 79.9 - - - +
83A THR* 1.3 64.0 + - - +
152A VAL* 3.6 28.3 - - + -
153A LEU 3.1 6.5 - - - +
154A CYS* 3.8 14.8 - - - -
169A ALA* 3.7 10.3 - - - +
172A GLY* 3.6 29.6 - - - +
173A ALA* 3.6 17.7 - - - +
176A ALA* 3.5 6.8 - - + +
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Residues in contact with THR 83 (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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67A ALA* 3.8 20.2 - - + -
69A GLY 3.5 2.0 - - - -
70A SER* 3.7 23.1 - - - -
81A MET* 4.0 16.8 - - + -
82A VAL* 1.3 75.5 - - - +
84A ALA* 1.3 61.6 + - - +
85A VAL* 6.1 0.2 - - - -
151A GLN 3.6 0.9 - - - +
152A VAL* 3.2 5.0 - - - +
153A LEU* 2.7 64.4 + - - +
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Residues in contact with ALA 84 (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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67A ALA* 4.8 0.9 - - - -
68A ASP* 2.9 24.0 + - - +
69A GLY 2.8 21.7 + - - +
83A THR* 1.3 74.7 - - - +
85A VAL* 1.3 60.2 + - - +
150A THR* 5.7 0.2 - - + -
151A GLN 3.2 5.8 - - - +
152A VAL* 4.3 7.2 - - + -
176A ALA* 4.1 15.3 - - + +
177A LEU* 3.8 33.4 - - + +
180A SER* 4.9 0.2 - - - -
182A ILE* 4.0 5.4 - - + -
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Residues in contact with VAL 85 (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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67A ALA* 4.4 11.9 - - - +
68A ASP* 3.5 24.0 - - - +
83A THR* 6.1 0.4 - - - -
84A ALA* 1.3 74.9 - - - +
86A SER* 1.3 66.4 + - - +
87A LYS* 5.1 3.6 - - + +
149A ASP 4.5 0.4 - - - +
150A THR* 3.2 5.4 - - - +
151A GLN* 2.8 66.0 + - + +
182A ILE* 3.9 1.8 - - - -
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Residues in contact with SER 86 (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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68A ASP* 2.8 12.4 + - - +
85A VAL* 1.3 79.0 - - - +
87A LYS* 1.3 62.6 + - - +
88A THR* 3.7 2.6 + - - +
146A TYR* 2.6 31.8 + - - -
148A TYR* 4.0 1.2 - - - +
149A ASP 3.3 5.8 + - - -
150A THR* 3.1 18.8 + - - -
182A ILE* 3.6 22.4 - - - -
271A ARG* 2.9 25.7 + - - -
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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