Contacts of the strand formed by residues 99 - 109 (chain F) in PDB entry 3F5O
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 ASP 99 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F GLU* 5.1 4.5 - - - +
42F MET 3.5 4.7 - - - +
43F LYS* 3.3 32.1 + - - +
97F GLY 4.5 3.6 - - - +
98F GLU* 1.3 74.4 - - - +
100F ILE* 1.3 63.8 + - - +
122F ASN* 3.8 7.3 + - - +
123F LYS* 2.9 54.4 + - + +
124F ALA 4.7 0.3 + - - -
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Residues in contact with ILE 100 (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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41F GLU* 3.3 8.5 - - - +
42F MET* 2.8 64.1 + - + +
44F VAL* 4.0 17.7 - - + -
55F LEU* 4.1 6.7 - - + -
63F LEU* 3.9 12.3 - - + -
94F ALA* 4.1 7.0 - - + -
98F GLU* 4.5 2.7 - - + +
99F ASP* 1.3 79.9 - - - +
101F VAL* 1.3 64.3 + - - +
102F ILE* 3.8 24.2 - - + -
120F LEU* 4.0 14.4 - - + -
121F THR 3.3 8.3 - - - +
123F LYS* 5.1 0.2 - - - +
129F ILE* 3.4 26.7 - - + -
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Residues in contact with VAL 101 (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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31F VAL* 5.9 0.2 - - + -
39F ILE* 3.5 28.7 - - + -
40F CYS 3.5 4.7 - - - +
41F GLU* 4.6 9.6 - - + +
100F ILE* 1.3 77.5 - - - +
102F ILE* 1.3 63.1 + - - +
103F THR* 3.6 11.4 - - - +
119F ASP 3.6 1.7 - - - +
120F LEU* 3.2 4.9 - - - -
121F THR* 2.8 48.6 + - + +
123F LYS* 4.0 31.4 - - + -
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Residues in contact with ILE 102 (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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28F ILE* 5.3 0.7 - - + -
38F VAL 3.7 1.9 - - - +
39F ILE* 3.3 4.2 - - - -
40F CYS* 2.8 55.8 + - + +
41F GLU* 4.2 9.0 - - - -
42F MET* 4.3 2.7 - - + +
63F LEU* 4.2 24.9 - - + +
67F ILE* 3.8 27.0 - - + +
100F ILE* 3.8 28.5 - - + -
101F VAL* 1.3 75.0 - - - +
103F THR* 1.3 59.0 + - - +
118F VAL* 3.5 28.0 - - + -
119F ASP 3.5 3.6 - - - +
120F LEU* 3.9 21.5 - - + -
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Residues in contact with THR 103 (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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37F LYS* 3.8 30.5 - - - +
38F VAL 3.5 2.7 - - - +
39F ILE* 4.0 16.0 - - + +
101F VAL* 3.6 17.8 + - - +
102F ILE* 1.3 74.2 + - - +
104F ALA* 1.3 60.9 + - - +
105F HIS* 5.2 5.5 + - - +
117F SER 3.9 0.7 - - - +
118F VAL* 3.3 4.1 - - - -
119F ASP* 2.9 47.5 + - - +
121F THR* 5.4 2.9 - - - +
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Residues in contact with ALA 104 (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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37F LYS* 3.3 6.6 - - - +
38F VAL 2.8 33.6 + - - +
67F ILE* 3.5 43.1 - - + +
68F SER* 3.7 11.9 - - - +
71F ALA* 4.1 4.7 - - + +
102F ILE 4.1 0.4 - - - -
103F THR* 1.3 73.5 - - - +
105F HIS* 1.3 64.4 + - - +
117F SER 3.3 4.5 - - - -
118F VAL* 3.8 8.1 - - + -
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Residues in contact with HIS 105 (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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36F GLY 3.2 11.0 - - - +
37F LYS* 4.3 17.5 - - + -
71F ALA* 4.5 2.0 - - - -
103F THR* 5.2 5.8 + - + +
104F ALA* 1.3 76.0 - - - +
106F VAL* 1.3 70.5 + - - +
107F LEU* 3.1 25.9 + - + +
116F THR* 3.2 5.5 - - - -
117F SER* 2.8 59.6 + - - -
119F ASP* 6.5 0.9 - - - -
131G GLN* 5.8 0.7 - - - -
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Residues in contact with VAL 106 (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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36F GLY* 2.8 35.5 + - - +
71F ALA* 3.8 21.5 - - + +
72F LEU* 3.9 26.5 - - + +
75F THR* 4.1 7.4 - - + -
105F HIS* 1.3 81.9 - - - +
107F LEU* 1.3 61.9 + - - +
108F LYS* 3.9 20.2 - - - +
109F GLN* 4.4 9.4 - - + +
115F PHE 3.7 10.3 - - - +
116F THR* 4.2 3.4 - - + -
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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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105F HIS* 3.1 36.8 - - + +
106F VAL* 1.3 73.9 - - - +
108F LYS* 1.3 61.2 + - - +
115F PHE* 2.8 14.3 + - + +
116F THR 4.2 5.6 - - - +
117F SER* 4.0 19.3 - - - +
133F ARG* 4.1 14.6 - - + -
91G MET* 3.7 25.4 - - + -
128G LEU* 3.9 23.9 - - + +
131G GLN* 3.7 32.1 - - - +
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Residues in contact with LYS 108 (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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106F VAL* 3.6 6.7 - - - +
107F LEU* 1.3 83.7 - - - +
109F GLN* 1.3 78.0 + - - +
110F GLY* 4.5 0.6 - - - +
114F ALA* 3.5 0.5 - - - -
115F PHE* 2.8 47.6 + - + +
91G MET* 2.7 41.5 + - + +
92G SER* 4.7 1.8 - - - +
127G LYS* 3.5 26.6 - - - +
128G LEU* 5.8 2.2 - - + +
150H COA 3.0 35.1 + - - -
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Residues in contact with GLN 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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72F LEU* 4.3 10.6 - - - +
75F THR* 3.1 43.1 + - - +
77F ARG* 4.3 18.3 - - - +
79F ALA 5.3 2.4 + - - +
106F VAL* 4.4 7.1 - - + +
108F LYS* 1.3 89.3 - - - +
110F GLY* 1.3 63.3 + - - +
113F LEU 3.7 2.9 - - - +
114F ALA* 3.6 15.5 - - + -
138F LEU* 3.6 20.1 - - - +
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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