Contacts of the strand formed by residues 106 - 115 (chain C) in PDB entry 5C16
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 ILE 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C ALA* 5.1 9.9 - - + +
100C LEU* 3.7 37.8 - - + +
105C SER* 1.3 73.2 - - - +
107C LYS* 1.3 66.2 + - - +
108C ALA* 3.9 6.1 - - - +
109C ILE* 3.8 37.5 - - + -
128C THR* 3.8 16.6 - - + -
129C VAL 4.0 2.7 - - - -
130C THR* 4.2 2.7 - - + -
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Residues in contact with LYS 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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105C SER* 3.7 29.3 - - - +
106C ILE* 1.3 77.1 - - - +
108C ALA* 1.3 59.3 + - - +
129C VAL* 2.7 20.7 + - + +
130C THR 4.0 10.1 - - - -
131C ASP* 4.0 17.4 + - - +
194C LEU* 5.9 0.2 - - - +
199C ASN* 4.0 9.4 + - - +
203C HIS* 3.6 39.2 + - + +
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Residues in contact with ALA 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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106C ILE* 3.7 2.5 - - - +
107C LYS* 1.3 81.4 - - - +
109C ILE* 1.3 67.0 + - - +
110C VAL* 4.3 4.0 - - + -
127C LEU 4.4 1.1 - - - -
128C THR* 3.4 5.9 - - - +
129C VAL* 2.9 39.3 + - + +
194C LEU* 4.5 18.4 - - + -
196C ILE* 6.2 1.1 - - + -
199C ASN* 4.2 24.0 - - + +
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Residues in contact with ILE 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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98C ALA 5.8 4.0 - - - +
106C ILE* 3.8 21.3 - - + -
108C ALA* 1.3 79.2 - - - +
110C VAL* 1.3 66.5 + - - +
111C LYS* 4.9 9.4 - - + +
126C THR* 3.8 24.5 - - + -
127C LEU 3.5 3.6 - - - +
128C THR* 3.7 23.6 - - + +
194C LEU* 5.5 5.0 - - - +
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Residues in contact with VAL 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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108C ALA* 5.1 3.6 - - + -
109C ILE* 1.3 81.7 - - - +
111C LYS* 1.3 70.4 + - - +
113C VAL* 3.8 25.0 - - + +
126C THR* 3.4 3.1 - - - +
127C LEU* 2.9 41.6 + - + +
186C TYR* 6.3 1.1 - - + -
194C LEU* 4.6 17.5 - - + -
196C ILE* 4.0 26.5 - - + -
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Residues in contact with LYS 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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109C ILE* 4.9 9.0 - - + +
110C VAL* 1.3 84.6 - - - +
112C ASP* 1.3 72.7 + - + +
113C VAL 3.3 3.5 + - - -
125C GLY 4.2 1.6 - - - -
126C THR* 4.1 22.7 - - + +
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Residues in contact with ASP 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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111C LYS* 1.3 78.9 - - + +
113C VAL* 1.3 62.4 + - - +
114C MET* 4.0 19.5 - - - +
124C SER* 3.4 23.5 + - - -
125C GLY 3.1 14.3 + - - +
126C THR* 5.0 0.6 + - - -
185C ALA 4.9 0.9 - - - +
186C TYR* 5.0 9.0 - - - +
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Residues in contact with VAL 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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110C VAL* 3.8 31.2 - - + +
112C ASP* 1.3 75.5 - - - +
114C MET* 1.3 63.4 + - - +
123C VAL 3.5 0.3 - - - +
124C SER* 3.2 3.5 - - - -
125C GLY 2.8 39.9 + - - +
127C LEU* 3.4 37.5 - - + +
136C PHE* 3.5 14.6 - - + -
184C LEU* 5.7 5.2 - - + -
185C ALA 3.7 9.9 - - - +
186C TYR* 4.7 17.3 - - + +
196C ILE* 5.3 3.1 - - + -
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Residues in contact with MET 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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112C ASP* 4.0 22.2 - - - +
113C VAL* 1.3 80.2 - - - +
115C TYR* 1.3 59.7 + - - +
116C ILE* 3.7 2.4 + - + -
122C ALA* 4.7 21.1 - - + -
123C VAL 3.2 9.0 - - - +
124C SER* 4.6 11.9 - - - -
136C PHE* 4.5 0.2 - - - -
184C LEU* 3.2 9.9 - - - +
185C ALA* 2.7 57.7 + - + +
186C TYR 5.2 9.2 - - - -
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Residues in contact with TYR 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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114C MET* 1.3 70.5 - - - +
116C ILE* 1.3 68.4 + - - +
117C CYS* 2.9 32.0 + - + -
118C PRO* 3.9 15.0 - - + +
123C VAL* 3.0 29.6 + - + +
136C PHE* 3.9 25.7 - - + -
145C PHE* 3.9 32.1 - + - -
147C LEU* 4.1 29.6 - - + +
181C ASN 4.8 3.8 + - - -
182C LEU* 4.2 17.6 - - + +
183C ARG 3.2 28.5 - - - -
184C LEU* 4.1 10.3 - - + -
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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