Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 1UW9
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 ARG 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TYR 3.8 4.5 - - - -
26A THR* 3.3 30.0 - - + +
29A TYR* 3.6 57.8 + - + +
58A ALA* 4.1 2.9 - - - -
78A ASP* 2.9 37.4 + - - +
81A LYS* 3.6 38.7 + - + +
82A GLY* 1.3 77.6 - - - +
84A CYS* 1.3 60.2 + - - +
85A TYR* 3.2 6.2 + - - -
101A VAL* 3.2 4.7 - - - +
102A ALA* 2.8 36.5 + - + +
104A HYP 4.7 5.2 + - - -
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Residues in contact with CYS 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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24A TYR 2.9 16.6 + - - +
25A TYR* 3.4 13.7 - - + -
26A THR 2.9 25.0 + - - -
54A GLY* 3.7 35.4 - - - +
55A ALA 4.1 1.1 - - - +
58A ALA* 3.6 6.6 - - + +
83A ARG* 1.3 70.0 - - - +
85A TYR* 1.3 55.8 + - - +
86A ASP 3.9 2.5 - - - -
87A ILE* 3.7 36.3 - - - -
99A ALA* 4.2 7.0 - - - -
100A TYR 3.2 14.4 - - - +
101A VAL* 4.3 2.0 - - + +
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Residues in contact with TYR 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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25A TYR* 5.2 0.9 - - - -
26A THR* 3.4 17.7 - - - +
27A PRO* 3.4 26.4 - - - +
29A TYR* 4.1 24.4 - - + +
31A VAL* 3.6 27.9 - - + +
37A LEU* 3.7 22.1 - - + +
83A ARG 3.2 11.5 + - - +
84A CYS* 1.3 73.0 - - - +
86A ASP* 1.3 69.2 + - + +
100A TYR* 2.9 37.5 + + + +
101A VAL 3.6 8.7 - - - -
102A ALA* 3.6 24.7 - - + -
364A PHE* 3.9 11.6 - - - -
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Residues in contact with ASP 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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25A TYR* 5.1 2.9 - - - -
27A PRO* 5.5 0.9 - - - -
84A CYS* 3.6 1.9 - - - -
85A TYR* 1.3 96.5 - - + +
87A ILE* 1.3 82.1 + - - +
88A GLU* 4.8 7.1 - - - +
100A TYR* 2.8 50.3 + - + +
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Residues in contact with ILE 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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25A TYR* 3.7 23.3 + - + +
42A MET* 4.6 3.1 - - + -
50A PRO* 3.5 30.5 - - + +
51A GLU* 3.6 22.7 - - + +
54A GLY* 4.9 0.7 - - - -
84A CYS* 3.7 17.0 - - - -
86A ASP* 1.3 89.4 + - - +
88A GLU* 1.3 63.8 + - - +
89A PRO* 4.1 4.9 - - - +
97A TYR* 3.8 34.1 - - + -
98A ILE 3.4 5.8 - - - +
99A ALA* 4.5 3.6 - - - -
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Residues in contact with GLU 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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86A ASP* 4.3 8.9 - - - +
87A ILE* 1.3 76.2 - - - +
89A PRO* 1.3 72.9 - - + +
97A TYR* 3.2 5.6 - - - +
98A ILE* 2.7 48.6 + - + +
100A TYR* 3.0 29.8 + - + -
356A LYS* 5.3 5.7 + - - -
358A ARG* 2.9 32.4 + - - -
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Residues in contact with PRO 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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87A ILE 4.1 5.2 - - - +
88A GLU* 1.3 96.7 - - + +
90A VAL* 1.3 64.9 + - - +
91A PRO* 3.6 8.3 - - - +
93A GLU 5.9 1.3 - - - +
96A GLN 4.1 5.2 - - - +
97A TYR* 4.1 14.3 - - + -
98A ILE* 5.3 0.7 - - - +
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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