Contacts of the strand formed by residues 74 - 81 (chain A) in PDB entry 5V8V
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 SER 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A THR* 3.9 16.3 - - - +
73A THR* 1.3 75.5 - - - +
75A SER* 1.3 58.3 + - - +
165A VAL 4.2 0.2 + - - -
166A GLY* 4.0 5.8 - - - -
167A GLY* 3.7 29.5 + - - -
168A ILE* 4.2 8.5 - - - +
243A VAL* 3.5 2.9 - - - -
244A LEU* 2.7 52.5 + - - +
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Residues in contact with SER 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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73A THR 4.2 1.3 + - - -
74A SER* 1.3 76.7 - - - +
76A VAL* 1.3 70.0 + - - +
77A ILE* 4.4 5.0 + - - +
166A GLY* 4.1 10.2 - - - -
241A GLN* 3.2 27.4 + - - +
242A ILE 3.3 11.2 - - - -
243A VAL* 4.4 7.2 - - - -
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Residues in contact with VAL 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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75A SER* 1.3 80.5 - - - +
77A ILE* 1.3 77.2 + - - +
78A LEU* 3.5 4.6 + - + +
88A GLY* 4.3 4.9 - - - -
89A GLU* 4.1 25.8 - - + +
103A PHE* 4.4 6.5 - - + -
165A VAL* 3.7 28.5 - - + -
166A GLY* 3.8 13.7 - - - +
241A GLN* 3.4 4.3 - - - -
242A ILE* 2.9 45.8 + - + +
244A LEU* 5.1 6.5 - - + -
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Residues in contact with ILE 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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75A SER* 4.3 4.7 - - - +
76A VAL* 1.3 84.1 - - - +
78A LEU* 1.3 67.7 - - - +
79A THR* 5.5 0.4 + - - +
87A TYR 4.2 0.2 - - - +
88A GLY* 3.6 9.4 - - - -
89A GLU 4.6 0.9 + - - -
238A LEU* 3.6 33.7 - - + -
240A GLY 3.8 2.2 - - - +
241A GLN* 4.1 18.2 - - - +
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Residues in contact with LEU 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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76A VAL* 3.9 10.1 - - + +
77A ILE* 1.3 83.5 - - - +
79A THR* 1.3 65.8 + - - +
86A TYR* 4.5 7.0 - - + +
87A TYR* 3.2 7.2 - - - +
88A GLY* 3.6 27.1 - - - +
103A PHE* 4.0 12.3 - - + -
226A PHE* 4.8 4.7 - - + -
228A TYR* 3.6 32.8 - - + +
239A GLY* 3.5 7.3 + - - -
240A GLY* 2.8 39.8 + - - +
241A GLN* 3.8 19.7 - - - +
242A ILE* 4.0 18.6 - - + +
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Residues in contact with THR 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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77A ILE* 5.5 0.7 + - - +
78A LEU* 1.3 74.9 - - - +
80A ASN* 1.3 68.7 + - - +
81A TYR* 3.9 1.8 - - + +
85A GLN 3.4 1.6 - - - +
86A TYR* 3.2 9.7 - - - +
87A TYR* 2.7 70.7 + - + +
88A GLY* 5.7 0.2 - - - -
239A GLY* 4.6 1.3 - - - -
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Residues in contact with ASN 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 LEU 4.1 1.0 + - - -
79A THR* 1.3 80.8 - - - +
81A TYR* 1.3 59.5 + - - +
82A MET 3.4 3.6 + - - -
83A ASP* 2.8 39.1 + - - -
85A GLN 3.7 2.7 - - - -
86A TYR* 3.0 23.1 + - + -
229A ASN 2.8 30.5 + - - -
230A ARG 3.8 0.4 - - - -
231A ASP* 3.4 23.1 - - - +
239A GLY* 3.8 21.2 + - - -
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Residues in contact with TYR 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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79A THR* 3.9 2.5 - - + +
80A ASN* 1.3 68.3 - - - +
82A MET* 1.3 106.3 + - + +
83A ASP 3.2 2.5 + - - -
84A THR* 3.2 15.6 + - - -
85A GLN* 2.9 42.8 + - + +
87A TYR* 4.3 11.9 - - + +
187A LEU 5.6 0.7 - - - -
189A GLU* 3.7 43.0 + - + -
502A 90D 5.8 4.5 - - - -
182B ALA* 6.0 2.3 - - - +
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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