Contacts of the strand formed by residues 83 - 89 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24V TYR 3.8 3.6 - - - -
26V THR* 3.3 30.3 + - + +
29V TYR* 3.6 55.8 + - + +
78V ASP* 3.0 36.6 + - - +
81V LYS* 3.6 41.6 + - + +
82V GLY* 1.3 80.2 - - - +
84V CYS* 1.3 59.8 - - - +
85V TYR* 3.2 6.9 + - - -
101V VAL* 3.2 6.2 - - - +
102V ALA 2.8 37.5 + - - +
104V HYP 4.8 4.5 + - - -
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Residues in contact with CYS 84 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24V TYR 2.9 17.2 + - - +
25V TYR* 3.4 14.8 - - + -
26V THR 2.9 25.1 + - - -
54V GLY* 3.6 35.0 - - - +
55V ALA 4.1 1.1 - - - +
58V ALA* 3.6 6.1 - - + +
83V ARG* 1.3 68.7 - - - +
85V TYR* 1.3 56.0 + - - +
86V ASP 4.0 3.4 - - - -
87V ILE* 3.7 35.4 - - - -
99V ALA* 4.2 6.3 - - - -
100V TYR 3.2 13.9 - - - -
101V VAL* 4.3 2.5 - - + +
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Residues in contact with TYR 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V TYR* 5.2 0.9 - - - -
26V THR* 3.4 18.6 - - - +
27V PRO* 3.5 25.9 - - - +
29V TYR* 4.1 23.9 - - + +
31V VAL* 3.6 27.6 - - + -
37V LEU* 3.7 22.2 - - + +
83V ARG 3.2 11.8 + - - +
84V CYS* 1.3 72.4 - - - +
86V ASP* 1.3 71.1 + - + +
100V TYR* 2.9 35.5 + + + +
101V VAL 3.6 8.3 - - - -
102V ALA* 3.6 25.8 - - + -
364V PHE* 3.9 11.8 - - - -
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Residues in contact with ASP 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V TYR* 5.1 3.1 - - - -
27V PRO* 5.5 1.1 - - - -
84V CYS* 3.6 1.9 - - - -
85V TYR* 1.3 95.6 - - + +
87V ILE* 1.3 81.1 + - - +
88V GLU* 4.7 7.5 - - - +
100V TYR* 2.8 51.1 + - + +
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Residues in contact with ILE 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V TYR* 3.8 22.1 + - + +
42V MET* 4.7 2.5 - - + -
50V PRO* 3.5 30.7 - - + +
51V GLU* 3.6 22.2 - - + +
54V GLY* 4.9 0.9 - - - -
84V CYS* 3.7 17.5 - - - -
86V ASP* 1.3 89.3 + - - +
88V GLU* 1.3 63.8 + - - +
89V PRO* 4.1 4.7 - - - +
97V TYR* 3.9 35.2 - - + -
98V ILE 3.3 5.6 - - - +
99V ALA* 4.5 4.0 - - - -
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Residues in contact with GLU 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86V ASP* 4.3 8.5 - - - +
87V ILE* 1.3 77.3 - - - +
89V PRO* 1.3 72.7 - - + +
97V TYR* 3.2 4.9 - - - +
98V ILE* 2.7 47.9 + - + +
100V TYR* 3.0 29.6 + - + -
356V LYS* 5.3 5.5 + - - -
358V ARG* 2.9 31.7 + - - -
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Residues in contact with PRO 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87V ILE 4.1 5.2 - - - +
88V GLU* 1.3 95.5 - - + +
90V VAL* 1.3 63.6 + - - +
91V PRO* 3.5 8.1 - - - +
93V GLU 5.9 1.3 - - - +
96V GLN 4.1 0.4 - - - +
97V TYR* 4.1 20.4 - - + -
98V ILE* 5.4 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