Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 2UXG
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 HIS 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASN* 4.8 1.3 - - - -
16A MET* 3.5 33.0 - - + +
38A LYS 5.4 0.9 - - - -
39A GLY* 3.5 20.4 - - - -
40A HIS* 3.3 23.5 + + - -
77A LYS* 5.7 0.2 - - - +
78A CYS* 3.0 21.5 + - - +
79A THR 3.1 1.1 - - - -
80A PRO* 1.3 91.6 - - + +
82A PRO* 1.3 66.1 - - + +
83A PHE 3.4 1.6 - - - -
84A MET* 3.0 28.9 + - + +
1123A CU 2.6 26.2 - - - -
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Residues in contact with PRO 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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16A MET* 6.2 0.2 - - + -
77A LYS* 5.9 0.7 - - - +
78A CYS 5.0 0.7 - - - +
79A THR 4.9 2.0 - - - +
80A PRO 3.6 9.2 - - - +
81A HIS* 1.3 84.9 - - + +
83A PHE* 1.3 79.5 + - + +
84A MET 3.2 0.9 + - - -
85A VAL* 4.3 5.7 - - - +
106A PRO* 5.1 9.1 - - + +
109A ALA* 3.8 14.6 - - - +
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Residues in contact with PHE 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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15A ALA 5.0 3.8 - - - +
16A MET* 5.3 2.6 - - + +
81A HIS* 3.4 0.8 - - - +
82A PRO* 1.3 94.1 - - + +
84A MET* 1.3 58.2 + - - +
85A VAL* 3.3 8.4 + - - +
106A PRO* 4.1 20.0 - - + -
108A LYS* 3.3 45.3 - - + -
109A ALA* 4.1 9.3 - - - -
112A ARG* 2.8 42.1 + - - +
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Residues in contact with MET 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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7A MET* 3.5 35.7 - - + -
16A MET* 3.3 34.9 - - + +
17A VAL* 3.4 24.7 - - - +
18A PHE* 3.9 12.6 - - + +
40A HIS* 3.4 9.0 - - + +
77A LYS* 3.2 4.3 - - - +
78A CYS* 3.0 32.8 + - + -
81A HIS* 3.0 21.2 + - + +
82A PRO 3.2 1.2 - - - -
83A PHE* 1.3 76.2 - - - +
85A VAL* 1.3 59.7 + - - +
112A ARG* 4.0 0.2 - - - +
1123A CU 2.4 30.5 - - - -
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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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17A VAL* 5.8 0.2 - - - -
18A PHE* 3.5 15.9 + - - +
21A ALA* 4.0 13.3 - - - +
45A ILE* 4.3 9.2 - - + -
76A VAL 3.2 13.7 - - - +
77A LYS* 4.0 10.3 - - + -
82A PRO 4.3 4.3 - - - +
83A PHE 3.3 7.0 + - - +
84A MET* 1.3 83.2 - - - +
86A GLY* 1.3 59.5 + - - +
109A ALA* 3.5 29.8 - - + +
112A ARG* 3.5 35.7 - - + +
113A LEU* 3.8 17.5 - - + +
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Residues in contact with GLY 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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18A PHE* 4.4 2.5 - - - -
21A ALA* 3.1 18.2 - - - -
75A GLY* 3.5 1.6 - - - -
76A VAL* 2.9 42.6 + - - +
85A VAL* 1.3 78.0 - - - +
87A VAL* 1.3 69.0 + - - +
112A ARG 5.8 0.4 - - - -
113A LEU* 3.6 3.9 - - - +
116A ALA* 5.1 2.5 - - - -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA 2.8 9.3 + - - -
22A SER* 3.2 6.1 - - - -
23A LEU 3.1 23.0 + - - +
73A VAL* 3.9 20.6 - - + -
74A TYR 3.3 7.6 - - - +
75A GLY* 4.6 1.6 - - - -
76A VAL* 4.5 0.4 - - - +
86A GLY* 1.3 79.5 - - - +
88A VAL* 1.3 74.8 + - - +
100A VAL* 4.3 11.2 - - + -
113A LEU* 3.8 24.0 - - + +
116A ALA* 3.7 23.8 - - + -
117A LEU* 4.0 6.5 - - + -
120A LEU* 3.6 20.7 - - + +
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Residues in contact with VAL 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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5A VAL* 5.8 1.8 - - + -
23A LEU* 3.5 16.4 - - + +
25A VAL* 4.2 21.1 - - + -
31A VAL* 4.5 9.4 - - + -
33A PHE* 4.4 17.7 - - + -
68A PHE* 3.9 49.1 - - + -
73A VAL* 3.4 1.0 - - - -
74A TYR* 2.8 44.2 + - + +
76A VAL* 5.2 6.7 - - + -
86A GLY 4.3 0.2 - - - -
87A VAL* 1.3 77.0 - - - +
89A GLN* 1.3 64.0 + - - +
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Residues in contact with GLN 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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23A LEU 2.8 9.8 + - - +
24A LYS* 3.4 19.0 - - + +
25A VAL* 2.7 35.7 + - - +
72A GLY 3.4 8.7 - - - +
73A VAL* 3.6 9.5 - - + +
87A VAL 4.1 0.6 + - - -
88A VAL* 1.3 76.3 - - - +
90A VAL* 1.3 62.2 + - - +
91A GLY 2.8 24.8 + - - +
92A ASP* 4.0 4.2 - - - +
94A PRO* 3.5 26.0 - - + +
120A LEU* 3.4 26.7 + - + +
122A ASN* 2.6 32.5 + - - +
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Residues in contact with VAL 90 (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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25A VAL* 3.3 14.4 - - + -
27A PRO* 3.7 35.7 - - + -
68A PHE* 3.4 35.4 - - + +
69A THR 3.7 8.1 - - - +
70A ALA 3.4 26.2 - - - +
71A PRO* 3.6 9.6 - - + +
72A GLY* 2.8 28.4 + - - +
74A TYR* 3.8 7.6 - - + -
88A VAL* 4.9 0.2 - - + -
89A GLN* 1.3 71.4 - - - +
91A GLY* 1.3 69.1 + - - +
92A ASP 4.8 1.4 - - - +
94A PRO* 5.3 0.5 - - - +
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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