Contacts of the strand formed by residues 104 - 111 (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 TYR 104 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12T PHE* 3.4 33.4 - + - -
44T PHE* 3.1 7.4 - - - +
45T ALA 2.8 35.5 + - - +
47T ALA* 3.8 21.5 - - + +
50T ALA* 3.5 25.4 - - + -
51T TYR* 3.9 5.3 + + - -
73T TRP* 3.6 20.6 - - + -
103T ALA* 1.3 73.3 - - - +
105T VAL* 1.3 58.5 + - - +
122T LEU* 4.0 6.5 - - + -
124T GLN 3.3 5.4 - - - +
125T ARG* 3.5 29.3 + - + -
126T PRO* 3.6 21.9 - - + +
129T ALA* 3.7 18.9 - - - +
131T ASP* 3.8 17.8 + - - -
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Residues in contact with VAL 105 (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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42T LEU* 4.0 12.6 - - + -
43T GLU 3.4 10.8 - - - +
44T PHE* 4.0 11.2 - - + -
73T TRP* 4.2 0.4 - - - -
93T ILE* 5.8 0.2 - - + -
96T CYS* 3.8 26.0 - - + -
97T THR* 4.1 11.7 - - + -
100T PHE* 4.6 5.4 - - + +
103T ALA* 4.1 2.5 - - + +
104T TYR* 1.3 79.5 - - - +
106T ARG* 1.3 62.4 + - - +
122T LEU* 3.4 5.6 - - - +
123T VAL* 2.8 38.9 + - + -
124T GLN* 2.9 40.7 + - + +
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Residues in contact with ARG 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS* 5.9 0.2 - - - +
187A ARG* 5.8 0.6 - - - +
163O ASN* 4.0 21.9 + - - +
12T PHE* 5.3 5.3 - - + -
42T LEU* 3.6 9.0 - - - +
43T GLU* 2.8 59.5 + - + +
70T ASN 5.3 0.4 + - - -
71T ARG 3.0 23.6 + - - -
72T TYR* 4.7 0.2 - - - +
73T TRP* 3.3 60.8 - - + +
105T VAL* 1.3 75.3 - - - +
107T LEU* 1.3 61.5 + - - +
108T VAL* 4.0 15.2 + - + +
117T GLN* 5.7 1.7 + - - +
121T PHE 3.4 20.2 - - - +
122T LEU* 4.1 4.7 - - + -
123T VAL* 4.3 0.2 - - - -
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Residues in contact with LEU 107 (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* 5.4 0.2 - - + -
30T VAL* 3.8 28.9 - - + -
33T ILE* 3.9 17.7 - - + -
40T PRO* 4.7 0.9 - - + -
41T CYS 3.7 19.1 - - - +
42T LEU* 3.9 18.1 - - + +
89T VAL* 3.8 22.0 - - + -
93T ILE* 4.4 8.7 - - + -
106T ARG* 1.3 72.1 - - - +
108T VAL* 1.3 69.9 + - - +
119T MET* 4.4 1.5 - - - +
120T GLY* 3.1 3.3 - - - -
121T PHE* 3.0 54.0 + - + +
123T VAL* 4.0 17.6 - - + +
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Residues in contact with VAL 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40T PRO* 3.5 2.6 - - - +
41T CYS* 2.9 50.6 + - + +
43T GLU* 3.8 23.8 - - - +
106T ARG* 4.0 19.1 - - + +
107T LEU* 1.3 83.7 - - - +
109T ALA* 1.3 63.5 + - - +
110T PHE* 3.8 21.5 - - + -
117T GLN* 3.3 32.3 - - - +
119T MET* 3.4 9.6 - - - +
120T GLY* 4.0 2.2 - - - -
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Residues in contact with ALA 109 (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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33T ILE* 3.8 26.7 - - + -
38T TRP* 3.9 9.9 - - + -
39T ILE 3.0 11.0 - - - +
108T VAL* 1.3 76.4 - - - +
110T PHE* 1.3 64.9 + - - +
117T GLN* 3.4 5.2 - - - +
118T ILE* 2.8 27.3 + - + +
119T MET* 3.2 27.8 + - + -
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Residues in contact with PHE 110 (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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184A ASN* 4.9 5.2 - - - -
187A ARG* 3.9 41.5 - - - -
74B LEU* 4.0 27.1 - - + +
38T TRP* 3.5 5.7 - - - +
39T ILE* 2.8 56.0 + - + +
41T CYS* 3.7 28.9 - - + -
43T GLU* 4.7 1.8 - - - -
75T MET* 5.7 0.2 - - + -
79T PRO* 4.4 9.0 - - + -
108T VAL* 3.8 14.4 - - + -
109T ALA* 1.3 72.9 - - - +
111T ASP* 1.3 63.3 + - - +
112T ASN 4.0 0.2 - - - -
116T VAL 3.6 3.8 - - - +
117T GLN* 3.7 35.9 - - + -
118T ILE* 4.3 3.1 - - - -
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Residues in contact with ASP 111 (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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74B LEU 4.6 0.3 - - - +
38T TRP* 3.2 29.2 + - + -
110T PHE* 1.3 74.5 - - - +
112T ASN* 1.3 59.2 + - - +
113T GLN* 2.8 37.2 + - - +
114T LYS* 2.9 26.2 + - + +
115T GLN* 2.9 26.5 + - - -
116T VAL 2.9 15.6 + - - +
118T ILE* 4.0 18.9 - - + +
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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