Contacts of the strand formed by residues 113 - 122 (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 LEU 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A VAL* 3.8 34.5 - - + -
113A LEU* 4.2 24.0 - - + -
137A HIS* 4.1 10.8 - - - +
150A COA 3.2 28.8 + - - +
84C VAL* 4.8 1.8 - - + -
110C GLY* 2.7 34.0 + - - +
111C LYS 3.8 0.2 - - - -
112C THR* 1.3 92.8 - - - +
114C ALA* 1.3 57.6 + - - +
115C PHE* 3.9 17.7 - - + -
135C THR* 4.1 13.0 - - + -
136C LYS 3.3 13.2 - - - +
137C HIS* 4.2 7.9 - - + +
138C LEU* 4.3 4.4 - - - +
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Residues in contact with ALA 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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72C LEU* 3.5 33.9 - - + -
108C LYS 3.5 5.6 - - - -
109C GLN* 4.0 12.3 - - + -
113C LEU* 1.3 73.9 - - - +
115C PHE* 1.3 64.4 + - - +
116C THR* 5.1 1.1 - - - -
134C HIS 3.9 0.7 - - - +
135C THR* 3.4 5.7 - - - +
136C LYS* 2.9 33.5 + - + +
138C LEU* 4.1 18.6 - - + +
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Residues in contact with PHE 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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84A VAL* 3.7 22.7 - - + -
150A COA 3.5 39.0 - - + -
89B THR* 3.3 32.3 - - + -
90B TYR 3.7 6.1 - - - -
91B MET* 3.5 23.3 - - + -
106C VAL* 3.6 2.3 - - - +
107C LEU* 2.7 33.5 + - + -
108C LYS* 2.9 35.5 + - + +
113C LEU* 3.9 25.1 - - + -
114C ALA* 1.3 73.3 - - - +
116C THR* 1.3 61.5 + - - +
133C ARG* 5.9 1.1 - - + -
134C HIS 3.7 4.0 - - - -
135C THR* 3.3 19.1 - - + -
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Residues in contact with THR 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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68C SER* 3.2 32.7 + - - +
71C ALA* 5.3 0.2 - - + -
72C LEU* 3.9 36.8 - - + -
105C HIS 3.2 13.0 - - - +
106C VAL* 4.1 8.1 - - + -
107C LEU* 4.1 4.9 - - - +
114C ALA 5.1 0.2 - - - -
115C PHE* 1.3 81.7 - - - +
117C SER* 1.3 60.0 + - - +
118C VAL* 5.3 0.2 - - - -
133C ARG* 3.2 9.6 - - - +
134C HIS* 2.9 48.5 + - - +
136C LYS* 5.9 0.7 - - + -
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Residues in contact with SER 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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131B GLN* 3.9 15.4 + - - -
133B ARG* 5.5 0.2 + - - -
103C THR 3.9 1.1 - - - +
104C ALA* 3.4 2.6 - - - -
105C HIS* 2.9 37.6 + - - +
107C LEU* 4.0 24.7 - - - +
116C THR* 1.3 73.6 - - - +
118C VAL* 1.3 66.1 + - - +
119C ASP* 4.7 2.3 + - - -
131C GLN* 4.4 13.7 + - - +
132C GLY 3.4 12.3 + - - -
133C ARG* 4.6 0.4 - - - -
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Residues in contact with VAL 118 (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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63C LEU 4.9 0.4 - - - +
64C VAL* 3.6 46.0 - - + +
67C ILE* 5.2 0.2 - - + -
68C SER* 3.7 17.3 - - - +
102C ILE* 3.5 32.1 - - + -
103C THR 3.2 8.5 - - - +
104C ALA* 3.8 9.9 - - + -
116C THR* 5.1 0.2 - - - +
117C SER* 1.3 81.6 + - - +
119C ASP* 1.3 67.4 + - - +
120C LEU* 4.1 10.9 - - + +
131C GLN* 3.3 5.2 - - - +
132C GLY 2.8 35.7 + - - +
134C HIS* 5.8 0.7 - - + -
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Residues in contact with ASP 119 (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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101C VAL 3.5 1.4 - - - +
102C ILE* 3.5 1.9 - - - -
103C THR* 2.9 42.6 + - - +
117C SER* 4.7 2.9 + - - -
118C VAL* 1.3 73.9 - - - +
120C LEU* 1.3 62.5 + - - +
121C THR* 4.1 8.8 + - + +
128C LEU* 3.7 22.3 - - + +
130C ALA 3.6 3.6 - - - -
131C GLN* 3.0 32.4 - - - +
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Residues in contact with LEU 120 (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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55C LEU* 4.1 13.0 - - + -
60C THR* 3.9 26.9 - - + +
63C LEU* 4.1 11.4 - - + -
64C VAL* 4.0 26.9 - - + -
100C ILE* 4.0 23.3 - - + -
101C VAL 3.2 4.7 - - - +
102C ILE* 4.0 17.0 - - + -
118C VAL* 4.1 9.4 - - + +
119C ASP* 1.3 75.5 - - - +
121C THR* 1.3 59.5 + - - +
128C LEU* 3.6 1.7 - - - +
129C ILE* 2.8 42.1 + - + -
130C ALA* 2.9 20.5 + - + +
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Residues in contact with THR 121 (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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100C ILE* 3.3 6.8 - - - +
101C VAL* 2.8 53.0 + - - +
103C THR* 5.3 2.6 + - - +
119C ASP* 4.5 10.5 - - + +
120C LEU* 1.3 79.6 - - - +
122C ASN* 1.3 61.9 + - - +
126C GLY* 3.7 23.4 - - - +
127C LYS 3.2 9.6 - - - +
128C LEU* 4.0 16.6 - - + -
129C ILE* 3.6 5.8 - - - +
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Residues in contact with ASN 122 (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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98C GLU* 2.8 43.6 + - - +
99C ASP 3.9 2.5 - - - -
121C THR* 1.3 72.6 + - - +
123C LYS* 1.3 56.9 + - - +
124C ALA* 2.7 37.0 + - - +
125C THR* 2.9 31.6 + - - +
126C GLY* 2.7 32.6 + - - -
127C LYS* 2.8 15.4 + - + +
129C ILE* 3.7 4.9 - - + +
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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