Contacts of the strand formed by residues 97 - 103 (chain R) 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 TYR 97 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40R PHE 3.3 1.0 - - - +
41R ARG* 3.4 3.3 - - - +
42R MET* 2.7 47.4 + - + +
44R PRO* 3.9 28.7 - - + -
50R PRO* 3.9 33.9 - - + +
87R ILE* 3.8 24.9 - - + -
88R GLU 3.2 8.1 - - - +
89R PRO* 4.0 21.1 - - + -
90R VAL* 3.9 3.1 - - - -
94R ASP 4.0 14.4 + - - -
95R ASN* 4.0 20.9 + - - -
96R GLN* 1.3 78.9 - - - +
98R ILE* 1.3 61.7 + - - +
99R ALA 3.8 0.2 - - - -
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Residues in contact with ILE 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39R ALA* 4.1 11.7 - - + -
40R PHE 3.2 6.5 - - - +
41R ARG* 3.9 31.9 - - + +
87R ILE* 3.3 4.3 - - - -
88R GLU* 2.7 59.2 + - + +
89R PRO 5.4 0.7 - - - +
90R VAL* 3.8 22.0 - - + +
97R TYR* 1.3 71.0 - - - +
99R ALA* 1.3 61.6 + - - +
100R TYR* 3.6 30.3 - - + +
136R GLU* 4.9 0.9 - - + -
358R ARG* 4.4 11.0 - - - +
363R TYR* 4.1 25.8 - - + +
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Residues in contact with ALA 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ALA 3.5 2.3 - - - +
40R PHE* 2.7 46.1 + - + +
42R MET* 4.0 33.0 - - + -
54R GLY* 4.3 3.6 - - - -
57R VAL* 6.1 1.6 - - + -
84R CYS* 4.2 15.7 - - - -
86R ASP 3.6 4.7 - - - -
87R ILE* 4.5 3.1 - - + -
97R TYR 3.8 0.6 + - - -
98R ILE* 1.3 73.2 - - - +
100R TYR* 1.3 62.1 + - - +
101R VAL* 3.9 4.6 + - + -
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Residues in contact with TYR 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ALA 3.3 3.4 - - - -
39R ALA* 3.8 19.1 - - + -
84R CYS* 3.2 5.4 - - - -
85R TYR* 2.9 53.3 + + + -
86R ASP* 2.8 36.7 + - + +
88R GLU* 3.0 41.9 + - + -
98R ILE* 3.6 27.2 - - + +
99R ALA* 1.3 72.7 - - - +
101R VAL* 1.3 60.3 + - - +
356R LYS* 5.6 3.2 + - - -
358R ARG* 3.4 12.1 + - - -
363R TYR* 3.7 11.6 + + + +
364R PHE* 3.8 30.7 - + - -
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Residues in contact with VAL 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R ILE 3.7 0.9 - - - +
37R LEU* 3.3 4.0 - - - -
38R ALA 2.8 37.4 + - - +
40R PHE* 3.9 24.7 - - + -
54R GLY 4.7 2.0 - - - +
57R VAL* 4.6 2.5 - - + -
58R ALA* 3.8 33.4 - - + +
82R GLY 4.5 0.2 - - - -
83R ARG 3.2 14.1 - - - +
84R CYS* 4.3 7.0 - - + -
85R TYR* 3.6 4.0 - - - -
99R ALA* 4.5 4.5 - - + +
100R TYR* 1.3 78.8 - - - +
102R ALA* 1.3 62.7 + - - +
103R TYR* 3.4 37.3 - - + +
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Residues in contact with ALA 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R TYR* 3.7 29.6 - - + -
31R VAL* 4.2 0.7 - - + -
35R ASP* 4.0 6.1 - - - +
36R ILE 3.5 4.0 - - - -
37R LEU* 3.8 16.6 - - + -
81R LYS 4.2 0.2 - - - +
82R GLY* 3.3 5.7 - - - -
83R ARG* 2.8 36.0 + - + +
85R TYR* 3.6 14.1 - - + -
101R VAL* 1.3 72.8 - - - +
103R TYR* 1.3 61.9 + - - +
104R HYP 3.9 3.6 - - - -
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Residues in contact with TYR 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R ASP* 3.4 5.3 - - - -
36R ILE* 2.8 49.4 + - - +
38R ALA* 3.7 21.3 - - + -
40R PHE* 3.5 23.0 - - - -
58R ALA 4.6 0.2 - - - -
61R SER* 2.7 49.3 + - - -
62R SER* 4.3 6.5 - - - -
82R GLY* 4.4 0.9 - - - -
101R VAL* 3.4 25.6 - - + +
102R ALA* 1.3 74.3 - - - +
104R HYP 1.3 68.7 + - + +
107R LEU* 4.2 14.6 - - + -
108R PHE* 3.5 26.9 - + + -
119R SER* 5.6 0.2 - - - -
120R ILE* 3.9 25.1 - - + +
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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