Contacts of the strand formed by residues 116 - 124 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B ASN* 6.0 0.2 - - - +
156E GLN* 4.2 24.9 - - + +
159E ARG* 4.4 10.1 - - + -
160E ASP* 3.8 20.2 - - - +
165E TYR* 3.9 9.0 - - + -
110F PHE* 4.3 6.2 - - - +
111F ASP* 2.9 28.0 + - + +
114F LYS* 3.8 35.4 - - + +
115F GLN* 1.3 77.1 - - - +
117F GLN* 1.3 79.0 + - - +
118F ILE* 3.4 6.6 + - + -
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Residues in contact with GLN 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B LYS* 5.0 0.9 + - - -
187B ARG* 4.4 9.0 + - - -
159E ARG* 4.9 2.9 - - - -
160E ASP* 5.0 1.0 + - - -
163E ASN* 5.3 0.2 + - - -
165E TYR* 3.1 66.0 - - + +
43F GLU* 4.7 2.8 - - - +
106F ARG* 5.8 1.7 + - - +
108F VAL* 3.3 31.7 - - + +
109F ALA 3.4 11.2 - - - +
110F PHE* 3.7 24.2 - - + -
116F VAL* 1.3 84.1 - - - +
118F ILE* 1.3 58.1 + - - +
119F MET 3.1 27.5 + - - +
120F GLY* 4.0 3.8 - - - -
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Residues in contact with ILE 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E GLY* 3.4 18.6 + - - +
396E ASP* 4.4 6.9 - - - +
32F TYR* 5.8 0.5 - - - -
38F TRP* 3.4 62.1 - - + -
109F ALA* 2.8 22.3 + - + +
111F ASP* 4.0 30.7 - - + +
114F LYS* 4.0 28.0 - - + +
116F VAL* 4.9 2.9 - - + -
117F GLN* 1.3 75.1 - - - +
119F MET* 1.3 63.4 + - + +
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Residues in contact with MET 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E TYR* 4.5 2.7 - - - -
166E GLY* 3.8 13.4 - - - +
432E ASN* 5.6 1.8 - - - +
15F PHE* 5.6 1.1 - - + -
29F GLN* 4.1 21.1 - - - +
32F TYR* 4.9 13.5 - - + -
33F ILE* 3.6 37.0 - - + -
38F TRP* 4.7 4.9 - - + -
107F LEU 4.4 3.1 - - - +
108F VAL* 4.0 3.8 - - - -
109F ALA* 3.3 39.6 + - + -
117F GLN* 3.1 19.5 + - - +
118F ILE* 1.3 86.0 - - + +
120F GLY* 1.3 64.3 + - - +
121F PHE* 3.5 29.6 - - + -
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Residues in contact with GLY 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E TYR* 4.4 4.7 + - - +
166E GLY* 4.8 0.8 - - - -
14F THR* 3.3 26.6 + - - +
15F PHE* 4.9 0.3 - - - -
106F ARG* 6.4 0.2 - - - -
107F LEU 3.1 14.1 - - - -
108F VAL* 4.4 1.3 - - - -
117F GLN* 4.0 10.5 - - - -
119F MET* 1.3 83.2 - - - +
121F PHE* 1.3 68.6 + - - +
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Residues in contact with PHE 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE 5.3 2.9 - - - -
14F THR 3.4 19.7 - - - +
15F PHE* 3.8 20.9 - + + -
21F LEU* 3.8 20.0 - - + -
26F ILE* 4.3 15.5 - - + -
29F GLN* 3.6 26.2 - - + -
106F ARG* 3.4 7.4 - - - +
107F LEU* 3.0 50.2 + - + +
119F MET* 3.5 29.4 - - + -
120F GLY* 1.3 79.9 - - - +
122F LEU* 1.3 72.3 + - - +
123F VAL* 3.6 19.3 - - + -
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Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 3.9 58.9 + - + +
14F THR 4.8 1.0 + - - -
21F LEU* 5.5 1.4 - - - +
26F ILE* 5.9 0.5 - - - +
73F TRP* 4.1 4.9 - - + -
104F TYR* 4.0 6.5 - - + -
105F VAL 3.3 22.2 - - - +
106F ARG* 4.1 3.8 - - + +
121F PHE* 1.3 85.5 - - - +
123F VAL* 1.3 60.7 + - - +
124F GLN 3.5 20.2 - - - +
125F ARG* 4.0 34.5 - - + +
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Residues in contact with VAL 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ILE* 4.8 17.4 - - + +
42F LEU* 4.4 3.8 - - + -
93F ILE* 4.3 31.0 - - + +
97F THR* 5.1 1.9 - - + +
105F VAL* 2.8 39.5 + - + +
106F ARG 4.3 0.2 - - - -
107F LEU* 4.0 21.5 - - + +
121F PHE* 3.6 30.7 + - + +
122F LEU* 1.3 73.5 - - - +
124F GLN* 1.3 62.6 + - + +
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Residues in contact with GLN 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F THR* 3.2 37.8 - - + +
100F PHE 2.9 28.1 + - - -
101F PRO* 3.5 17.8 + - - +
103F ALA 2.9 16.9 + - - +
104F TYR* 3.3 4.2 - - - -
105F VAL* 2.9 38.9 + - + +
122F LEU* 3.5 12.2 - - - +
123F VAL* 1.3 81.9 - - - +
125F ARG* 1.3 70.9 + - - +
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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