Contacts of the strand formed by residues 82 - 89 (chain A) in PDB entry 5GZE
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 CYS 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A PRO* 3.5 2.9 - - - +
76A ARG* 2.8 53.8 + - - +
81A GLY* 1.3 76.8 - - - +
83A ILE* 1.3 61.5 + - - +
84A VAL* 4.1 20.2 - - - -
98A ILE* 4.1 9.4 - - + -
99A THR 3.4 13.9 - - - +
100A TYR* 4.1 18.8 - - + -
102A THR* 3.9 10.3 + - - +
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Residues in contact with ILE 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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73A PHE* 3.8 25.6 - - + -
74A ASN 3.6 21.1 - - - +
75A PRO* 4.0 8.5 - - + -
82A CYS* 1.3 77.6 - - - +
84A VAL* 1.3 67.6 + - - +
85A CYS* 4.1 1.9 + - - -
97A GLU 3.7 0.9 - - - +
98A ILE* 3.5 3.1 - - - +
99A THR* 2.8 44.2 + - + +
102A THR* 3.7 23.8 - - - +
103A PRO* 4.0 3.4 - - + -
104A PHE* 3.9 17.0 - - + -
130A THR* 3.9 28.7 - - + -
131A LEU* 4.1 9.9 - - + -
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Residues in contact with VAL 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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72A HIS* 3.5 1.7 - - - +
73A PHE 3.8 0.2 - - - -
74A ASN* 2.9 39.5 + - - +
76A ARG* 3.5 40.4 - - - +
82A CYS* 4.1 11.0 - - - -
83A ILE* 1.3 75.4 - - - +
85A CYS* 1.3 64.5 + - - +
96A GLU* 3.7 35.9 - - + +
97A GLU 3.7 3.6 - - - +
98A ILE* 4.4 14.8 - - + +
1B BGC 4.5 0.9 - - - +
2B GAL 4.0 17.0 - - - +
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Residues in contact with CYS 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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71A PHE* 3.7 19.5 - - + -
72A HIS 3.0 7.4 - - - +
73A PHE* 3.9 12.1 - - - -
83A ILE* 4.1 1.8 - - - -
84A VAL* 1.3 78.6 - - - +
86A ASN* 1.3 63.4 + - - +
96A GLU* 3.6 1.7 - - - -
97A GLU* 2.9 39.6 + - + +
131A LEU* 3.8 32.8 - - - -
133A TYR* 3.3 26.9 - - + -
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Residues in contact with ASN 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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71A PHE* 3.7 2.8 - - - -
72A HIS* 2.9 35.9 + - + +
85A CYS* 1.3 75.1 - - - +
87A THR* 1.3 69.7 + - - +
93A TRP* 3.7 23.0 - - + +
94A GLY 2.8 45.0 + - - -
95A ARG 3.2 11.4 - - - +
96A GLU* 3.3 10.7 - - - +
133A TYR* 2.7 15.7 + - - -
136A ARG* 3.3 3.8 + - - -
2B GAL 3.0 28.6 + - - +
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Residues in contact with THR 87 (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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69A VAL 3.2 15.5 - - - +
70A ALA 2.8 19.7 + - - +
86A ASN* 1.3 76.7 + - - +
88A LEU* 1.4 58.9 + - - +
89A ILE* 3.9 28.4 + - + +
92A LYS 3.9 0.5 - - - +
93A TRP* 3.6 5.1 - - - -
94A GLY* 3.1 25.3 + - - -
133A TYR* 2.8 21.1 + - - -
136A ARG* 3.5 23.5 - - + +
137A ILE* 4.1 14.8 - - + -
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Residues in contact with LEU 88 (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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66A ARG* 3.4 46.0 - - + +
67A ALA 3.6 16.8 - - - +
68A ASP* 3.3 8.7 - - - +
69A VAL* 2.8 37.4 + - + +
87A THR* 1.4 70.2 - - - +
89A ILE* 1.3 62.5 + - - +
91A GLU* 3.5 16.8 - - - +
92A LYS 3.5 32.1 - - - +
93A TRP* 3.5 35.9 - - + +
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Residues in contact with ILE 89 (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* 3.3 11.9 - - - +
87A THR* 3.9 23.3 + - + +
88A LEU* 1.3 78.8 - - - +
90A ASN* 1.3 70.7 + - + +
91A GLU 3.1 1.3 - - - -
92A LYS* 2.7 41.1 + - - +
136A ARG* 5.9 2.7 - - + +
137A ILE* 4.3 18.4 - - + -
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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