Contacts of the strand formed by residues 97 - 103 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40O PHE 3.2 1.2 - - - +
41O ARG* 3.4 2.9 - - - +
42O MET* 2.7 46.5 + - + +
44O PRO* 3.9 32.1 - - + -
50O PRO* 3.8 38.7 - - + +
87O ILE* 3.8 20.0 - - + -
88O GLU 3.2 7.9 - - - +
89O PRO* 4.0 21.1 - - + -
90O VAL* 3.9 3.6 - - - -
94O ASP 4.0 14.4 + - - -
95O ASN* 4.0 16.9 + - - -
96O GLN* 1.3 79.0 - - - +
98O ILE* 1.3 62.6 + - - +
99O ALA 3.8 0.2 - - - -
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Residues in contact with ILE 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O ALA* 4.0 18.8 - - + -
40O PHE 3.2 6.1 - - - +
41O ARG* 3.9 31.2 - - + +
87O ILE* 3.3 4.8 - - - -
88O GLU* 2.7 59.3 + - + +
89O PRO 5.4 0.7 - - - +
90O VAL* 3.8 21.8 - - + -
97O TYR* 1.3 71.1 - - - +
99O ALA* 1.3 60.3 + - - +
100O TYR* 3.6 31.7 - - + +
136O GLU* 5.0 1.1 - - + -
358O ARG* 4.3 5.6 - - - +
363O TYR* 4.1 24.0 - - + +
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Residues in contact with ALA 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O ALA 3.6 2.6 - - - +
40O PHE* 2.7 45.2 + - + +
42O MET* 3.9 33.9 - - + -
54O GLY* 4.3 3.6 - - - -
57O VAL* 6.1 1.6 - - + -
84O CYS* 4.3 15.9 - - - -
86O ASP 3.6 3.8 - - - -
87O ILE* 4.5 3.1 - - + -
97O TYR 3.7 1.0 + - - -
98O ILE* 1.3 73.8 - - - +
100O TYR* 1.3 62.1 + - - +
101O VAL* 3.9 4.8 + - + -
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Residues in contact with TYR 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O ALA 3.3 3.8 - - - -
39O ALA* 3.8 19.1 - - + -
84O CYS* 3.2 6.8 - - - -
85O TYR* 2.9 51.7 + + + -
86O ASP* 2.8 37.3 + - + +
88O GLU* 3.0 41.9 + - + -
98O ILE* 3.6 26.0 - - + +
99O ALA* 1.3 72.1 - - - +
101O VAL* 1.3 59.8 + - - +
356O LYS* 5.6 3.0 + - - -
358O ARG* 3.4 12.0 + - - -
363O TYR* 3.8 11.8 + + + +
364O PHE* 3.8 31.6 - + - -
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Residues in contact with VAL 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O ILE 3.8 1.2 - - - +
37O LEU* 3.3 4.3 - - - -
38O ALA 2.8 37.4 + - - +
40O PHE* 3.9 24.7 - - + -
54O GLY 4.7 1.6 - - - +
57O VAL* 4.5 4.5 - - + -
58O ALA* 3.8 31.2 - - + +
82O GLY 4.5 0.2 - - - -
83O ARG 3.2 14.8 - - - +
84O CYS* 4.4 6.7 - - + -
85O TYR* 3.6 4.2 - - - -
99O ALA* 4.4 4.7 - - + +
100O TYR* 1.3 79.2 - - - +
102O ALA* 1.3 62.3 + - - +
103O TYR* 3.4 35.6 - - + +
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Residues in contact with ALA 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O TYR* 3.7 26.7 - - + -
31O VAL* 4.2 0.7 - - + -
35O ASP* 4.0 6.3 - - - +
36O ILE 3.5 3.6 - - - -
37O LEU* 3.7 18.8 - - + -
81O LYS 4.2 0.5 - - - +
82O GLY* 3.4 4.7 - - - -
83O ARG* 2.9 32.7 + - + +
85O TYR* 3.6 15.0 - - + -
101O VAL* 1.3 73.4 - - - +
103O TYR* 1.3 62.0 + - - +
104O HYP 3.9 3.9 - - - -
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Residues in contact with TYR 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ASP* 3.4 4.7 - - - -
36O ILE* 2.8 48.7 + - + +
38O ALA* 3.8 21.1 - - + -
40O PHE* 3.6 21.5 - - - -
58O ALA 4.6 0.4 - - - -
61O SER* 2.6 50.8 + - - -
62O SER* 4.3 6.3 - - - -
82O GLY* 4.4 3.8 - - - -
101O VAL* 3.4 25.2 - - + +
102O ALA* 1.3 75.0 - - - +
104O HYP 1.3 68.8 + - + +
107O LEU* 4.2 13.5 - - + -
108O PHE* 3.5 26.2 - + + -
119O SER* 5.6 0.7 - - - -
120O ILE* 3.9 24.8 - - + +
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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