Contacts of the strand formed by residues 116 - 124 (chain T) 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 VAL 116 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ASN* 6.0 0.7 - - - +
156O GLN* 4.2 23.8 - - + +
159O ARG* 4.4 11.0 - - + -
160O ASP* 3.9 19.5 - - - +
165O TYR* 4.0 8.3 - - + -
110T PHE* 4.3 6.8 - - - +
111T ASP* 2.9 27.7 + - - +
114T LYS* 3.8 36.3 - - + +
115T GLN* 1.3 77.0 - - - +
117T GLN* 1.3 78.1 + - - +
118T ILE* 3.5 6.4 + - + -
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Residues in contact with GLN 117 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LYS* 5.1 0.5 + - - -
187A ARG* 4.3 9.9 + - - -
159O ARG* 4.9 2.9 - - - -
160O ASP* 5.0 1.0 + - - -
163O ASN* 5.4 0.3 + - - -
165O TYR* 3.1 64.5 - - + +
166O GLY 5.2 0.3 + - - -
43T GLU* 4.6 2.9 - - - +
106T ARG* 5.7 2.3 + - - +
108T VAL* 3.3 30.8 - - + +
109T ALA 3.4 11.7 - - - +
110T PHE* 3.7 23.0 - - + -
116T VAL* 1.3 84.1 - - - +
118T ILE* 1.3 57.8 + - - +
119T MET 3.1 27.1 + - - +
120T GLY* 3.9 4.0 - - - -
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Residues in contact with ILE 118 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166O GLY* 3.4 17.7 + - - +
396O ASP* 4.3 8.0 - - - +
32T TYR* 5.2 2.2 + - - +
38T TRP* 3.4 63.4 - - + -
109T ALA* 2.8 21.4 + - + +
111T ASP* 4.0 26.0 - - + +
114T LYS* 4.0 31.2 - - + +
116T VAL* 4.3 4.0 - - + +
117T GLN* 1.3 73.1 - - - +
119T MET* 1.3 64.1 + - - +
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Residues in contact with MET 119 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165O TYR* 4.5 2.9 - - - +
166O GLY* 3.8 13.0 - - - +
432O ASN* 5.5 1.3 - - - +
15T PHE* 5.6 0.9 - - + -
29T GLN* 4.1 20.4 - - - +
32T TYR* 4.5 14.6 - - + -
33T ILE* 3.5 37.7 - - + -
38T TRP* 4.7 4.5 - - + -
107T LEU 4.4 2.7 - - - +
108T VAL* 4.0 4.7 - - - -
109T ALA* 3.2 39.4 + - + -
117T GLN* 3.1 19.9 + - - +
118T ILE* 1.3 85.5 - - + +
120T GLY* 1.3 61.9 + - - +
121T PHE* 3.5 30.5 - - + -
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Residues in contact with GLY 120 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165O TYR* 4.4 4.9 + - - +
166O GLY* 4.7 0.8 - - - -
14T THR* 3.4 25.8 + - - +
15T PHE* 5.2 0.5 - - - -
106T ARG* 6.4 0.4 - - - -
107T LEU 3.1 14.8 - - - -
108T VAL* 4.3 1.3 - - - -
117T GLN* 3.9 11.2 - - - -
119T MET* 1.3 82.4 - - - +
121T PHE* 1.3 69.4 + - - +
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Residues in contact with PHE 121 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T PHE 5.3 3.1 - - - -
14T THR 3.4 20.0 - - - +
15T PHE* 3.8 20.4 - + + -
21T LEU* 3.8 21.3 - - + -
26T ILE* 4.2 15.0 - - + -
29T GLN* 3.6 26.7 - - + -
106T ARG* 3.4 7.9 - - - +
107T LEU* 3.0 48.2 + - + -
108T VAL* 5.3 0.2 - - - +
119T MET* 3.5 29.8 - - + -
120T GLY* 1.3 79.2 - - - +
122T LEU* 1.3 72.3 + - - +
123T VAL* 3.6 19.5 - - + -
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Residues in contact with LEU 122 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T PHE* 3.8 59.6 + - + +
14T THR 4.8 1.2 + - - -
21T LEU* 5.5 1.6 - - - +
26T ILE* 5.8 0.7 - - - +
73T TRP* 4.1 6.5 - - + -
104T TYR* 4.0 7.4 - - + -
105T VAL 3.4 21.1 - - - +
106T ARG* 4.1 2.9 - - + +
121T PHE* 1.3 85.6 - - - +
123T VAL* 1.3 59.2 + - - +
124T GLN 3.5 15.5 - - - +
125T ARG* 4.1 38.1 - - + +
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Residues in contact with VAL 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T ILE* 4.9 18.4 - - + +
42T LEU* 4.4 3.8 - - + -
93T ILE* 4.2 31.0 - - + +
97T THR* 5.1 1.3 - - + +
105T VAL* 2.8 39.7 + - + +
106T ARG 4.3 0.2 - - - -
107T LEU* 4.0 20.4 - - + +
121T PHE* 3.6 31.4 + - + +
122T LEU* 1.3 72.8 - - - +
124T GLN* 1.3 63.4 + - + +
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Residues in contact with GLN 124 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97T THR* 3.2 38.7 - - + +
100T PHE 2.9 28.1 + - - -
101T PRO* 3.5 16.1 + - - +
103T ALA 3.0 16.8 + - - +
104T TYR* 3.3 4.0 - - - -
105T VAL* 2.9 38.4 + - + +
122T LEU* 3.5 11.8 - - - +
123T VAL* 1.3 81.0 - - - +
125T ARG* 1.3 71.1 + - - +
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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