Contacts of the strand formed by residues 132 - 139 (chain C) in PDB entry 6CNB
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 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C VAL* 3.9 19.1 - - + -
106C LEU* 6.1 0.9 - - + -
108C VAL* 4.9 11.2 - - + -
113C LEU* 3.4 40.6 - - + -
131C THR* 1.3 74.8 - - - +
133C VAL* 1.3 59.5 + - - +
134C LEU* 3.6 17.7 - - + -
169C PHE* 3.5 29.4 - - + -
175C GLN* 4.7 11.9 - - - +
179C PHE* 4.7 7.0 - - + -
184C VAL* 4.2 14.8 - - + -
208C CYS* 2.7 45.0 + - + +
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Residues in contact with VAL 133 (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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131C THR* 3.9 4.9 + - + +
132C ILE* 1.3 73.3 - - - +
134C LEU* 1.3 75.0 + - - +
169C PHE* 3.6 17.6 - - - -
170C GLU* 3.2 31.4 + - + +
172C GLN* 3.2 33.1 + - - +
205C LYS* 4.6 15.7 - - + +
206C ALA 3.7 14.8 - - - +
207C HIS* 4.4 26.2 - - + +
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Residues in contact with LEU 134 (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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80C ALA* 5.2 8.7 - - + -
101C ILE* 6.0 0.2 - - + -
104C VAL* 6.3 0.2 - - + -
106C LEU* 3.8 32.5 - - + -
132C ILE* 3.5 28.0 - - + +
133C VAL* 1.3 85.7 - - - +
135C SER* 1.3 60.3 + - - +
167C LEU* 3.5 35.4 - - + -
168C LYS 3.8 13.0 - - - +
169C PHE* 5.1 1.6 - - + -
184C VAL* 5.2 5.8 - - + -
186C PRO* 5.9 0.2 - - + -
204C LEU* 4.3 1.3 - - - +
205C LYS* 3.2 4.7 - - - +
206C ALA* 2.9 41.8 + - + +
208C CYS* 4.1 8.5 - - + -
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Residues in contact with SER 135 (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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134C LEU* 1.3 76.0 - - - +
136C LEU* 1.3 65.9 + - - +
137C ASN* 5.1 4.2 + - - -
166C ASP 4.0 0.5 - - - +
167C LEU* 3.5 1.8 - - - -
168C LYS* 2.8 51.4 + - - +
170C GLU* 3.4 38.7 + - - +
204C LEU 3.9 4.4 + - - -
205C LYS* 4.3 7.8 - - - +
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Residues in contact with LEU 136 (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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97C LEU* 6.3 0.2 - - + -
101C ILE* 5.9 1.1 - - + -
135C SER* 1.3 79.0 + - - +
137C ASN* 1.3 73.4 + - - +
138C VAL* 4.7 5.2 - - + +
162C VAL* 5.5 9.9 - - + -
163C TYR 4.7 0.9 - - - +
166C ASP* 3.7 31.0 - - + +
167C LEU* 3.5 35.7 - - + +
168C LYS* 6.1 1.6 - - - +
193C LEU* 4.5 10.3 - - + -
202C ILE* 3.9 27.4 - - + +
203C SER* 3.6 0.3 + - - -
204C LEU* 2.8 53.9 + - + +
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Residues in contact with ASN 137 (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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135C SER* 5.1 3.5 + - - -
136C LEU* 1.3 79.7 - - - +
138C VAL* 1.3 70.0 + - - +
168C LYS* 5.1 11.3 + - - +
201C GLU* 4.4 3.3 + - - +
202C ILE 2.9 13.9 - - - +
203C SER* 3.7 20.3 + - - +
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Residues in contact with VAL 138 (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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136C LEU* 4.7 5.5 - - + +
137C ASN* 1.3 81.9 - - - +
139C LYS* 1.3 63.4 + - - +
159C ASN* 3.2 38.8 - - + +
162C VAL* 4.1 23.3 - - + -
166C ASP* 3.7 31.9 - - + +
196C LEU* 5.1 6.0 - - + +
200C GLN 4.4 0.3 - - - +
201C GLU* 3.2 6.3 - - - -
202C ILE* 2.9 32.2 + - + +
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Residues in contact with LYS 139 (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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138C VAL* 1.3 77.1 - - - +
140C CYS* 1.3 69.2 + - - +
141C THR* 4.2 20.8 + - + +
158C ASN* 5.1 1.4 - - - +
159C ASN* 3.1 22.4 + - - +
196C LEU* 5.2 0.2 - - - -
199C GLY* 5.7 2.7 - - - -
200C GLN 3.9 4.3 - - - +
201C GLU* 3.5 26.5 - - + -
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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