Contacts of the strand formed by residues 104 - 111 (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 TYR 104 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F PHE* 3.4 34.5 - + - -
44F PHE* 3.1 8.3 - - - +
45F ALA 2.8 35.2 + - - +
47F ALA* 3.8 23.1 - - + +
50F ALA* 3.5 25.8 - - + -
51F TYR* 3.8 8.8 + + - -
73F TRP* 3.5 20.6 - - + -
103F ALA* 1.3 72.2 - - - +
105F VAL* 1.3 58.5 + - - +
122F LEU* 4.0 6.3 - - + -
124F GLN 3.3 5.2 - - - -
125F ARG* 3.5 29.2 + - + -
126F PRO* 3.5 22.2 - - + -
129F ALA* 3.6 19.4 - - - +
131F ASP* 3.7 14.2 + - - -
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Residues in contact with VAL 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F LEU* 4.0 13.2 - - + -
43F GLU 3.4 10.5 - - - +
44F PHE* 4.0 10.8 - - + -
73F TRP* 4.1 0.2 - - - -
93F ILE 5.7 0.2 - - - +
96F CYS* 3.8 25.6 - - + -
97F THR* 4.1 11.0 - - + -
100F PHE* 4.6 5.4 - - + +
103F ALA* 4.0 2.7 - - + +
104F TYR* 1.3 81.2 - - - +
106F ARG* 1.3 64.8 + - - +
122F LEU* 3.3 6.1 - - - +
123F VAL* 2.8 39.1 + - + -
124F GLN* 2.9 43.6 + - + +
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Residues in contact with ARG 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS* 5.9 0.4 - - - +
187B ARG* 5.9 0.4 - - - +
163E ASN* 4.0 21.7 + - - +
12F PHE* 5.3 5.9 - - + -
42F LEU* 3.6 9.1 - - - +
43F GLU* 2.8 62.3 + - + +
70F ASN 5.3 0.4 + - - -
71F ARG 3.0 24.4 + - - -
73F TRP* 3.3 62.3 - - + +
105F VAL* 1.3 75.6 - - - +
107F LEU* 1.3 60.4 + - - +
108F VAL* 4.0 15.0 + - + +
117F GLN* 5.8 1.5 + - - +
120F GLY 6.4 0.2 - - - -
121F PHE 3.4 19.7 - - - +
122F LEU* 4.1 4.5 - - + -
123F VAL* 4.1 0.7 - - - +
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Residues in contact with LEU 107 (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* 5.4 0.2 - - + -
30F VAL* 3.8 28.5 - - + -
33F ILE* 3.9 19.1 - - + -
40F PRO* 4.6 0.7 - - + -
41F CYS 3.7 20.6 - - - +
42F LEU* 3.9 16.4 - - + -
89F VAL* 3.8 22.4 - - + -
93F ILE* 4.5 7.0 - - + -
106F ARG* 1.3 72.1 - - - +
108F VAL* 1.3 68.4 + - - +
119F MET* 4.4 1.8 - - - +
120F GLY* 3.1 3.1 - - - -
121F PHE* 3.0 52.8 + - + +
123F VAL* 4.0 18.3 - - + +
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Residues in contact with VAL 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F ILE* 4.6 0.3 - - - +
40F PRO* 3.4 4.9 - - - +
41F CYS* 2.9 53.4 + - + +
43F GLU* 3.8 25.1 - - - +
106F ARG* 4.0 18.8 - - + +
107F LEU* 1.3 83.2 - - - +
109F ALA* 1.3 61.9 + - - +
110F PHE* 3.9 20.0 - - + -
117F GLN* 3.3 32.5 - - - +
119F MET* 3.5 9.6 - - - -
120F GLY* 4.1 1.8 - - - -
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Residues in contact with ALA 109 (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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33F ILE* 3.8 25.6 - - + -
38F TRP* 4.0 10.3 - - + -
39F ILE 3.0 11.0 - - - +
108F VAL* 1.3 77.9 - - - +
110F PHE* 1.3 59.0 + - - +
117F GLN* 3.4 5.2 - - - +
118F ILE* 2.8 32.8 + - + +
119F MET* 3.3 28.2 + - + -
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Residues in contact with PHE 110 (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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74A LEU* 4.0 24.5 - - + +
184B ASN* 4.9 4.5 - - - -
187B ARG* 3.7 45.3 - - - -
38F TRP* 3.5 5.9 - - - +
39F ILE* 2.8 56.3 + - + +
41F CYS* 3.6 30.7 - - + -
43F GLU* 4.7 1.6 - - - -
75F MET* 5.7 0.2 - - + -
79F PRO* 4.4 12.8 - - + -
108F VAL* 3.9 13.0 - - + -
109F ALA* 1.3 73.4 - - - +
111F ASP* 1.3 61.7 + - - +
112F ASN 4.0 0.2 - - - -
116F VAL* 3.7 3.8 - - - +
117F GLN* 3.7 33.9 - - + -
118F ILE* 4.2 3.4 - - - -
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Residues in contact with ASP 111 (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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74A LEU 4.4 0.5 - - - +
38F TRP* 3.3 26.7 + - + +
110F PHE* 1.3 74.4 - - - +
112F ASN* 1.3 58.5 + - - +
113F GLN* 2.7 37.6 + - - +
114F LYS* 2.9 27.0 + - + +
115F GLN* 2.9 26.0 + - - -
116F VAL 2.9 16.2 + - - +
118F ILE* 4.0 22.7 - - + +
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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