Contacts of the strand formed by residues 99 - 109 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C GLU* 6.3 1.1 - - + -
42C MET 3.6 3.9 - - - +
43C LYS* 3.5 32.1 + - - +
97C GLY 3.8 4.1 + - - +
98C GLU* 1.3 81.8 - - - +
100C ILE* 1.3 61.8 + - - +
122C ASN* 3.8 0.9 - - - +
123C LYS* 2.8 48.1 + - + +
124C ALA 4.6 0.3 + - - -
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Residues in contact with ILE 100 (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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41C GLU* 3.2 8.7 - - - +
42C MET* 2.7 71.8 + - + +
44C VAL* 3.9 19.7 - - + -
55C LEU* 4.0 9.9 - - + -
63C LEU* 4.0 7.0 - - + -
94C ALA* 4.1 5.2 - - + -
98C GLU* 4.1 5.2 - - + +
99C ASP* 1.3 78.6 - - - +
101C VAL* 1.3 62.3 - - - +
102C ILE* 4.1 9.1 - - + +
120C LEU* 4.0 26.5 - - + -
121C THR 3.3 7.2 - - - +
123C LYS* 4.7 0.2 - - - -
129C ILE* 3.5 25.4 - - + -
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Residues in contact with VAL 101 (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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39C ILE* 3.5 28.7 - - + -
40C CYS 3.5 4.0 - - - +
41C GLU* 3.6 23.8 - - + +
100C ILE* 1.3 76.1 - - - +
102C ILE* 1.3 63.5 + - - +
103C THR* 3.7 12.3 - - - +
119C ASP 3.5 1.2 - - - +
120C LEU* 3.2 4.7 - - - +
121C THR* 2.8 45.3 + - - +
123C LYS* 3.8 27.4 - - + +
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Residues in contact with ILE 102 (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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28C ILE* 5.1 0.9 - - + -
38C VAL 3.7 1.9 - - - +
39C ILE* 3.4 3.3 - - - -
40C CYS* 2.8 49.8 + - + +
41C GLU 4.2 0.7 - - - -
42C MET* 4.2 11.4 - - + +
63C LEU* 4.1 20.6 - - + +
67C ILE* 3.3 41.2 - - + +
100C ILE* 4.1 22.4 - - + -
101C VAL* 1.3 78.0 - - - +
103C THR* 1.3 58.8 + - - +
118C VAL* 3.5 27.6 - - + -
119C ASP 3.5 2.0 - - - -
120C LEU* 4.0 22.0 - - + -
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Residues in contact with THR 103 (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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37C LYS* 3.9 16.2 - - - -
38C VAL 3.6 2.9 - - - +
39C ILE* 4.0 13.9 - - + +
101C VAL* 3.7 17.5 + - - +
102C ILE* 1.3 73.9 - - - +
104C ALA* 1.3 61.5 + - - +
105C HIS* 3.4 30.6 - - + +
117C SER 3.9 0.7 - - - +
118C VAL* 3.2 4.3 - - - -
119C ASP* 2.9 44.8 + - - +
121C THR* 5.3 2.3 + - - +
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Residues in contact with ALA 104 (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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36C GLY 3.9 0.2 - - - +
37C LYS* 3.2 9.0 - - - +
38C VAL 2.9 33.6 + - - +
67C ILE* 3.5 42.4 - - + +
68C SER* 3.7 11.7 - - - +
71C ALA* 4.1 6.0 - - + +
102C ILE 4.1 0.4 - - - -
103C THR* 1.3 73.9 - - - +
105C HIS* 1.3 60.4 + - - +
117C SER 3.4 4.9 - - - -
118C VAL* 3.8 8.1 - - + -
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Residues in contact with HIS 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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36C GLY 3.3 5.6 + - - +
37C LYS* 3.4 33.9 + - + +
71C ALA* 4.7 0.7 - - - -
103C THR* 3.4 29.3 - - + +
104C ALA* 1.3 81.0 - - - +
106C VAL* 1.3 67.1 + - - +
107C LEU* 3.6 11.1 + - + +
116C THR* 3.2 5.8 - - - -
117C SER* 2.9 38.2 + - - +
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Residues in contact with VAL 106 (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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36C GLY* 2.8 36.4 + - - +
71C ALA* 3.7 21.5 - - + +
72C LEU* 3.8 20.6 - - + -
75C THR* 4.1 7.0 - - + -
105C HIS* 1.3 75.0 - - - +
107C LEU* 1.3 62.4 - - - +
108C LYS 3.9 9.9 - - - +
109C GLN* 4.0 25.8 - - + +
115C PHE 3.6 10.3 - - - +
116C THR* 4.1 3.6 - - + -
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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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91B MET* 3.8 24.5 - - + -
128B LEU* 4.0 26.5 - - + +
131B GLN* 3.8 30.7 - - - +
105C HIS* 4.6 8.3 - - + +
106C VAL* 1.3 76.9 - - - +
108C LYS* 1.3 60.4 + - - +
115C PHE* 2.7 15.9 + - + +
116C THR 4.1 7.4 - - - +
117C SER* 4.0 27.6 - - - +
133C ARG* 4.0 14.1 - - + -
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Residues in contact with LYS 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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150A COA 3.1 37.5 + - - +
91B MET* 2.8 38.7 + - + +
92B SER* 4.4 10.0 - - - -
93B PRO* 6.0 0.4 - - - +
127B LYS* 6.3 4.0 - - + +
128B LEU* 5.7 2.7 - - + +
106C VAL* 3.6 4.5 - - - +
107C LEU* 1.3 82.7 - - - +
109C GLN* 1.3 82.1 + - - +
110C GLY 4.0 0.7 - - - +
114C ALA* 3.5 1.9 - - - +
115C PHE* 2.9 50.3 + - + +
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Residues in contact with GLN 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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72C LEU* 4.3 8.3 - - + +
75C THR* 3.3 37.7 + - - +
76C GLU 5.1 0.2 - - - +
77C ARG* 4.1 20.9 - - - +
79C ALA* 5.1 3.3 - - - +
106C VAL* 4.0 12.7 - - + +
108C LYS* 1.3 87.8 - - - +
110C GLY* 1.3 59.3 + - - +
113C LEU 3.9 1.3 - - - -
114C ALA* 4.0 12.7 - - + +
138C LEU* 3.4 24.4 - - - +
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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