Contacts of the strand formed by residues 109 - 117 (chain C) in PDB entry 1F80
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 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A THR* 3.9 16.0 + - + -
108A GLU* 3.9 15.1 + - - +
109A TYR* 3.2 27.8 - + - -
9B ILE* 5.5 9.6 - - + -
109B TYR* 3.5 38.1 - + - -
9C ILE* 3.9 25.8 - - + -
10C THR 3.5 1.1 - - - -
11C GLU* 3.4 35.1 - - + +
12C LEU* 4.2 6.2 - - - +
105C HIS* 3.6 3.3 + - - +
106C THR* 2.8 43.1 + - + +
107C LYS 3.6 1.2 - - - -
108C GLU* 1.3 105.7 + - + +
110C ALA* 1.3 61.9 + - - +
111C ALA* 4.2 1.1 - - + +
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Residues in contact with ALA 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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9C ILE* 3.6 0.6 - - - -
10C THR 2.8 40.1 + - - +
12C LEU* 4.7 2.4 - - + +
51C ALA* 3.4 43.1 - - + +
52C GLY* 4.1 1.1 - - - +
55C ALA* 3.7 8.3 - - - +
104C THR 3.7 4.3 - - - -
105C HIS* 3.7 18.4 - - + +
109C TYR* 1.3 74.3 - - - +
111C ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 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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7B LEU* 4.1 7.0 - - + -
9B ILE* 3.8 29.2 - - + -
8C ASP 3.3 9.0 - - - +
9C ILE* 4.2 9.9 - - + -
55C ALA* 4.1 2.0 - - - -
103C ILE* 3.5 4.9 - - - +
104C THR* 2.9 45.1 + - + +
109C TYR* 5.6 1.1 - - + -
110C ALA* 1.3 76.1 - - - +
112C ALA* 1.3 63.6 + - - +
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Residues in contact with ALA 112 (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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7B LEU* 4.1 4.4 - - - +
7C LEU* 3.2 7.8 - - - +
8C ASP 2.9 32.0 + - - -
52C GLY 4.8 0.2 - - - +
55C ALA* 3.7 6.3 - - + +
56C ALA* 3.6 36.3 - - + +
59C ALA* 3.7 3.2 - - + +
101C VAL* 5.2 0.9 - - + -
102C SER 3.2 11.4 - - - +
103C ILE* 4.1 9.4 - - + -
111C ALA* 1.3 77.5 - - - +
113C GLN* 1.3 64.5 + - - +
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Residues in contact with GLN 113 (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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113A GLN* 3.3 13.6 + - - +
5B ILE* 3.8 19.1 - - + +
6B GLY 2.9 47.9 + - - +
7B LEU* 3.3 12.4 - - + +
113B GLN* 3.2 28.8 + - - +
114B VAL 4.5 1.2 + - - -
115B VAL* 5.9 2.5 - - - +
6C GLY 3.1 10.1 - - - +
7C LEU* 4.3 5.2 - - + -
59C ALA* 4.2 0.4 - - - -
101C VAL* 3.3 5.2 - - - +
102C SER* 3.0 38.0 + - - +
112C ALA* 1.3 77.9 - - - +
114C VAL* 1.3 67.5 + - - +
115C VAL* 5.6 2.6 - - - +
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Residues in contact with VAL 114 (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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113A GLN* 4.5 1.0 + - - -
5B ILE* 4.3 0.4 - - - -
5C ILE* 3.2 6.2 - - - +
6C GLY 2.8 30.8 + - - +
56C ALA 4.0 2.9 - - - +
59C ALA* 3.9 8.5 - - + +
60C PHE* 3.7 44.9 - - + +
63C ALA* 3.7 19.1 - - + -
89C ILE* 3.9 19.7 - - + -
99C VAL* 4.0 3.4 - - + -
100C HIS 3.2 11.4 - - - +
101C VAL* 4.1 6.5 - - + -
113C GLN* 1.3 82.0 - - - +
115C VAL* 1.3 74.4 + - - +
116C ILE* 3.9 2.7 - - + -
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Residues in contact with VAL 115 (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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113A GLN* 5.9 1.1 - - - +
115A VAL* 5.6 4.0 - - + -
2B ALA* 5.7 2.9 - - + -
5B ILE* 3.9 27.4 - - + -
115B VAL* 5.9 3.6 - - + -
3C TYR* 3.5 34.8 - - + +
4C GLY 3.6 3.1 - - - +
5C ILE* 3.8 14.8 - - + -
98C ALA 3.9 0.9 - - - +
99C VAL* 3.5 3.8 - - - +
100C HIS* 3.0 37.7 + - + +
113C GLN* 5.6 2.9 - - - +
114C VAL* 1.3 80.8 - - - +
116C ILE* 1.3 65.6 + - - +
117C GLU* 4.0 13.9 - - - +
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Residues in contact with ILE 116 (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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3C TYR* 2.5 46.2 - - - +
4C GLY 2.9 13.4 + - - +
60C PHE* 3.6 34.1 - - + -
63C ALA* 3.7 5.6 - - + -
64C PHE* 3.6 41.5 - - + +
97C ALA* 4.0 21.3 - - + -
98C ALA 3.7 4.7 - - - +
99C VAL* 4.1 6.5 - - + -
114C VAL* 3.9 8.3 - - + -
115C VAL* 1.3 76.7 - - - +
117C GLU* 1.3 58.2 + - - +
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Residues in contact with GLU 117 (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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117A GLU* 4.9 0.7 - - - +
2B ALA* 2.6 35.8 + - - +
3C TYR* 3.5 38.6 + - + -
97C ALA* 2.9 28.1 - - - +
98C ALA* 3.1 23.3 + - + +
100C HIS* 3.0 25.7 - - + -
115C VAL* 4.0 5.7 - - + +
116C ILE* 1.3 77.3 - - - +
118C ARG* 1.3 67.1 + - - +
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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