Contacts of the strand formed by residues 104 - 111 (chain J) 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 104 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J PHE* 3.4 32.1 - + - -
44J PHE* 3.1 8.8 - - - +
45J ALA 2.8 35.2 + - - +
47J ALA* 3.8 23.2 - - + +
50J ALA* 3.5 25.8 - - + -
51J TYR* 3.6 18.3 + + - -
73J TRP* 3.5 20.6 - - + -
103J ALA* 1.3 73.1 - - - +
105J VAL* 1.3 58.2 + - - +
122J LEU* 3.9 5.8 - - + -
124J GLN 3.3 4.9 - - - -
125J ARG* 3.5 29.5 + - + -
126J PRO* 3.6 20.9 - - + -
129J ALA* 3.6 19.6 - - - +
131J ASP* 3.8 7.8 + - - -
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Residues in contact with VAL 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J LEU* 4.0 13.2 - - + -
43J GLU 3.4 10.3 - - - +
44J PHE* 3.9 10.8 - - + -
73J TRP* 4.2 0.2 - - - -
93J ILE* 5.7 0.4 - - + +
96J CYS* 3.8 25.8 - - + +
97J THR* 4.2 11.0 - - + -
100J PHE* 4.6 3.1 - - + +
103J ALA* 4.0 4.7 - - + +
104J TYR* 1.3 82.0 - - - +
106J ARG* 1.3 64.1 + - - +
122J LEU* 3.3 6.5 - - - +
123J VAL* 2.8 38.0 + - + -
124J GLN* 3.0 43.4 + - + +
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Residues in contact with ARG 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163H ASN* 3.9 20.9 + - - +
12J PHE* 5.3 5.5 - - + -
42J LEU* 3.6 8.8 - - - +
43J GLU* 2.9 60.8 + - + +
70J ASN 5.3 0.2 + - - -
71J ARG 3.0 24.0 + - - -
72J TYR* 4.7 0.2 - - - +
73J TRP* 3.3 62.2 - - + +
105J VAL* 1.3 75.0 - - - +
107J LEU* 1.3 60.8 + - - +
108J VAL* 4.0 15.0 + - + +
117J GLN* 5.8 1.7 + - - +
120J GLY* 6.3 0.2 - - - -
121J PHE 3.4 20.4 - - - +
122J LEU* 4.1 5.2 - - + +
123J VAL* 4.1 1.1 - - - +
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Residues in contact with LEU 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J VAL* 3.8 28.0 - - + -
33J ILE* 3.9 18.2 - - + -
40J PRO* 4.6 0.7 - - + -
41J CYS 3.6 21.1 - - - +
42J LEU* 3.9 16.6 - - + +
89J VAL* 3.9 21.1 - - + -
93J ILE* 4.4 8.5 - - + -
106J ARG* 1.3 72.8 - - - +
108J VAL* 1.3 69.2 + - - +
119J MET* 4.3 1.8 - - - +
120J GLY* 3.1 3.3 - - - -
121J PHE* 3.0 54.4 + - + +
123J VAL* 4.0 17.4 - - + +
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Residues in contact with VAL 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J ILE* 4.7 0.3 - - - +
40J PRO* 3.5 3.1 - - - +
41J CYS* 2.9 52.3 + - + +
43J GLU* 3.8 25.4 - - - +
106J ARG* 4.1 17.5 - - + +
107J LEU* 1.3 85.0 - - - +
109J ALA* 1.3 62.7 + - - +
110J PHE* 3.9 20.9 - - + -
117J GLN* 3.3 32.1 - - - +
119J MET* 3.4 9.2 - - - -
120J GLY* 4.1 2.7 - - - -
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Residues in contact with ALA 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J ILE* 3.8 25.1 - - + -
38J TRP* 3.9 10.3 - - + -
39J ILE 3.0 11.2 - - - +
108J VAL* 1.3 77.8 - - - +
110J PHE* 1.3 59.8 + - - +
117J GLN* 3.4 5.5 - - - +
118J ILE* 2.8 33.1 + - + -
119J MET* 3.2 28.1 + - + -
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Residues in contact with PHE 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E ASN* 5.0 4.3 - - - -
187E ARG* 3.8 45.1 - - - -
38J TRP* 3.5 6.6 - - - +
39J ILE* 2.8 57.1 + - + +
41J CYS* 3.7 30.3 - - + -
43J GLU* 4.7 1.8 - - - -
75J MET* 5.7 0.4 - - + -
79J PRO* 4.4 13.0 - - + -
108J VAL* 3.9 12.8 - - + -
109J ALA* 1.3 73.9 - - - +
111J ASP* 1.3 63.3 + - - +
112J ASN* 4.0 0.4 - - - -
116J VAL* 3.7 4.3 - - - +
117J GLN* 3.7 35.2 - - + -
118J ILE* 4.3 3.6 - - - -
74K LEU* 4.0 23.1 - - + +
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Residues in contact with ASP 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J TRP* 3.3 30.2 + - + -
110J PHE* 1.3 74.2 - - - +
112J ASN* 1.3 58.2 + - - +
113J GLN* 2.8 37.2 + - - +
114J LYS* 3.0 25.6 + - + +
115J GLN* 2.9 26.2 + - - -
116J VAL 2.9 15.9 + - - +
118J ILE* 4.0 21.0 - - + +
74K LEU 4.5 0.6 - - - +
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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