Contacts of the strand formed by residues 97 - 103 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B PHE 3.3 1.0 - - - +
41B ARG* 3.4 2.9 - - - -
42B MET* 2.7 46.9 + - + +
44B PRO* 3.9 27.4 - - + -
50B PRO* 3.8 39.8 - - + +
87B ILE* 3.8 20.9 - - + -
88B GLU 3.3 7.4 - - - +
89B PRO* 4.1 19.3 - - + -
90B VAL* 3.9 3.6 - - - -
94B ASP 4.0 14.4 + - - -
95B ASN* 4.0 21.2 + - - -
96B GLN* 1.3 79.8 - - - +
98B ILE* 1.3 62.9 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ALA* 4.0 18.8 - - + -
40B PHE 3.2 5.6 - - - +
41B ARG* 3.9 33.2 - - + +
87B ILE* 3.3 4.3 - - - -
88B GLU* 2.7 58.8 + - + +
89B PRO 5.4 0.9 - - - +
90B VAL* 3.9 20.2 - - + -
97B TYR* 1.3 72.1 - - - +
99B ALA* 1.3 60.8 + - - +
100B TYR* 3.6 30.2 - - + +
136B GLU* 4.9 0.9 - - + -
358B ARG* 4.3 10.3 - - - +
363B TYR* 4.1 21.3 - - + +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ALA 3.6 2.3 - - - +
39B ALA* 3.8 0.3 - - - -
40B PHE* 2.7 46.0 + - + +
42B MET* 4.0 32.5 - - + -
54B GLY* 4.3 4.3 - - - -
57B VAL* 6.1 1.3 - - + -
84B CYS* 4.3 16.4 - - - -
86B ASP 3.6 4.0 - - - -
87B ILE* 4.5 3.1 - - + -
97B TYR 3.8 1.2 + - - -
98B ILE* 1.3 72.4 - - - +
100B TYR* 1.3 61.0 - - - +
101B VAL* 3.9 4.7 + - + -
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ALA 3.3 3.1 - - - -
39B ALA* 3.9 17.7 - - + -
84B CYS* 3.3 5.7 - - - -
85B TYR* 2.9 52.3 + + + -
86B ASP* 2.9 34.4 + - + +
88B GLU* 3.0 41.1 + - + -
98B ILE* 3.6 27.2 - - + +
99B ALA* 1.3 72.1 - - - +
101B VAL* 1.3 60.8 + - - +
356B LYS* 5.6 2.8 + - - -
358B ARG* 3.4 11.8 + - - -
363B TYR* 3.8 11.1 + + + +
364B PHE* 3.7 32.1 - + - -
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE 3.7 0.9 - - - +
37B LEU* 3.3 4.9 - - - -
38B ALA 2.8 37.0 + - - +
40B PHE* 3.9 25.4 - - + -
54B GLY 4.7 1.8 - - - +
57B VAL* 4.5 4.5 - - + -
58B ALA* 3.9 32.3 - - + +
83B ARG 3.2 13.7 - - - +
84B CYS* 4.4 6.1 - - + -
85B TYR* 3.6 4.3 - - - -
99B ALA* 4.5 4.7 - - + +
100B TYR* 1.3 78.5 - - - +
102B ALA* 1.3 62.8 + - - +
103B TYR* 3.4 37.2 - - + +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 3.7 29.8 - - + -
31B VAL* 4.2 0.2 - - + -
35B ASP* 4.0 6.1 - - - +
36B ILE 3.5 4.3 - - - -
37B LEU* 3.8 17.0 - - + -
81B LYS 4.2 0.3 - - - +
82B GLY* 3.4 4.5 - - - -
83B ARG* 2.9 34.5 + - + +
85B TYR* 3.6 14.1 - - + -
101B VAL* 1.3 73.4 - - - +
103B TYR* 1.3 61.1 + - - +
104B HYP 3.9 3.4 - - - -
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASP* 3.3 6.1 - - - +
36B ILE* 2.8 49.4 + - + +
38B ALA* 3.8 20.9 - - + -
40B PHE* 3.6 22.3 - - - -
58B ALA 4.6 0.4 - - - -
61B SER* 2.7 50.5 + - - -
62B SER* 4.3 6.5 - - - -
82B GLY* 4.4 3.1 - - - -
101B VAL* 3.4 23.6 - - + +
102B ALA* 1.3 73.7 - - - +
104B HYP 1.3 68.1 + - + +
107B LEU* 4.2 14.1 - - + -
108B PHE* 3.5 26.0 - + + -
119B SER* 5.6 0.4 - - - -
120B ILE* 3.9 25.2 - - + +
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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