Contacts of the strand formed by residues 104 - 111 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.4 33.4 - + - -
44C PHE* 3.1 8.8 - - - +
45C ALA 2.8 34.7 + - - +
47C ALA* 3.8 22.7 - - + +
50C ALA* 3.5 27.1 - - + -
51C TYR* 4.0 5.2 + + - -
73C TRP* 3.5 20.6 - - + -
103C ALA* 1.3 72.3 - - - +
105C VAL* 1.3 58.5 + - - +
122C LEU* 3.9 6.3 - - + -
124C GLN 3.3 5.2 - - - -
125C ARG* 3.5 31.3 + - + -
126C PRO* 3.6 21.3 - - + -
129C ALA* 3.7 18.9 - - - +
131C ASP* 3.8 17.8 + - - -
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 4.0 13.2 - - + -
43C GLU 3.4 10.3 - - - +
44C PHE* 4.0 10.5 - - + -
73C TRP* 4.1 0.4 - - - -
96C CYS* 3.8 26.7 - - + +
97C THR* 4.1 11.7 - - + -
100C PHE* 4.6 5.8 - - + +
103C ALA* 4.1 2.5 - - + +
104C TYR* 1.3 81.1 - - - +
106C ARG* 1.3 63.1 + - - +
122C LEU* 3.3 6.8 - - - +
123C VAL* 2.8 38.1 + - + -
124C GLN* 2.9 42.3 + - + +
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Residues in contact with ARG 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASN* 4.0 20.4 + - - +
12C PHE* 5.3 5.3 - - + -
42C LEU* 3.5 9.0 - - - +
43C GLU* 2.8 60.1 + - + +
71C ARG 3.0 23.6 + - - -
73C TRP* 3.3 61.8 - - + +
105C VAL* 1.3 75.9 - - - +
107C LEU* 1.3 60.2 + - - +
108C VAL* 3.9 15.2 + - + +
117C GLN* 5.7 2.6 - - - +
120C GLY 6.3 0.2 - - - -
121C PHE 3.4 20.9 - - - +
122C LEU* 4.1 5.2 - - + -
123C VAL* 4.4 0.2 - - - -
183V LYS* 5.9 0.4 - - - +
187V ARG* 5.8 0.6 - - - +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 5.4 0.2 - - + -
30C VAL* 3.8 28.3 - - + -
33C ILE* 3.9 18.6 - - + -
40C PRO* 4.7 0.4 - - + -
41C CYS 3.7 19.3 - - - +
42C LEU* 3.9 17.4 - - + +
89C VAL* 3.8 22.2 - - + -
93C ILE* 4.5 8.1 - - + -
106C ARG* 1.3 72.5 - - - +
108C VAL* 1.3 69.0 + - - +
119C MET* 4.3 1.8 - - + +
120C GLY* 3.1 3.8 - - - -
121C PHE* 3.0 53.1 + - + +
123C VAL* 4.0 17.2 - - + +
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 4.6 0.2 - - - +
40C PRO* 3.5 3.1 - - - +
41C CYS* 2.9 52.0 + - + +
43C GLU* 3.9 24.5 - - - +
106C ARG* 4.1 18.6 - - + +
107C LEU* 1.3 83.6 - - - +
109C ALA* 1.3 64.1 + - - +
110C PHE* 3.8 21.1 - - + -
117C GLN* 3.3 32.5 - - - +
119C MET* 3.4 9.6 - - - +
120C GLY* 4.0 2.2 - - - -
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 3.9 26.2 - - + -
38C TRP* 4.0 9.6 - - + -
39C ILE 3.1 11.2 - - - +
108C VAL* 1.3 78.1 - - - +
110C PHE* 1.3 64.7 + - - +
117C GLN* 3.4 5.5 - - - +
118C ILE* 2.8 27.5 + - + +
119C MET* 3.2 28.1 + - + -
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Residues in contact with PHE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C TRP* 3.4 6.1 - - - +
39C ILE* 2.8 55.9 + - + +
41C CYS* 3.6 29.4 - - + -
43C GLU* 4.7 1.8 - - - -
75C MET* 5.7 0.4 - - + -
79C PRO* 4.4 12.3 - - + -
108C VAL* 3.8 14.6 - - + -
109C ALA* 1.3 74.1 - - - +
111C ASP* 1.3 63.3 + - - +
112C ASN* 4.0 0.4 - - - -
116C VAL* 3.7 4.3 - - - +
117C GLN* 3.7 34.3 - - + -
118C ILE* 4.2 3.6 - - - -
74O LEU* 4.0 24.7 - - + +
184V ASN* 5.0 5.4 - - - -
187V ARG* 3.8 43.1 - - - -
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Residues in contact with ASP 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C TRP* 3.3 30.0 + - + +
110C PHE* 1.3 74.2 - - - +
112C ASN* 1.3 57.9 + - - +
113C GLN* 2.8 37.2 + - - +
114C LYS* 2.9 26.2 + - + +
115C GLN* 3.0 25.8 + - - -
116C VAL 2.9 15.7 + - - +
118C ILE* 4.0 20.2 - - + +
74O LEU 4.6 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