Contacts of the strand formed by residues 155 - 159 (chain C) in PDB entry 2QLR
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 ASN 155 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C GLY* 4.8 4.0 - - - +
133C ASP 2.8 10.8 + - - +
134C ASN* 3.4 23.9 - - - +
135C VAL* 2.9 29.6 + - - +
154C CYS* 1.3 72.5 + - - +
156C ILE* 1.3 69.4 + - - +
157C ILE* 3.5 12.5 + - + +
177C ARG* 5.3 3.6 + - - -
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Residues in contact with ILE 156 (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 VAL* 3.5 21.3 - - + +
137C LEU* 3.5 34.8 - - + -
139C GLU* 5.4 1.3 - - - +
146C LEU* 4.4 8.7 - - + +
149C LEU* 3.9 34.8 - - + -
150C HIS* 5.2 2.7 - - - +
154C CYS* 3.7 10.9 + - - +
155C ASN* 1.3 78.5 + - - +
157C ILE* 1.3 65.5 + - - +
158C ASN* 3.8 3.1 + - - +
389C VAL* 3.9 37.8 - - + +
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Residues in contact with ILE 157 (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 ASN* 3.8 28.5 - - + +
135C VAL 2.7 15.7 + - - +
136C LEU* 3.5 18.0 - - + +
137C LEU 3.4 20.5 + - - -
155C ASN* 4.2 15.0 - - - +
156C ILE* 1.3 76.8 - - - +
158C ASN* 1.3 64.9 + - - +
159C VAL 3.5 0.7 + - - -
174C ILE* 3.4 35.9 - - + -
177C ARG* 3.7 36.6 - - - +
178C TRP* 4.8 4.5 - - + -
191C PRO* 5.1 1.6 - - + -
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Residues in contact with ASN 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 3.1 10.4 - - - +
139C GLU* 2.7 65.6 + - - +
156C ILE* 3.8 3.6 + - + +
157C ILE* 1.3 73.9 - - - +
159C VAL* 1.3 69.3 + - - +
160C ALA* 3.9 2.5 + - - +
174C ILE* 3.8 11.3 - - - +
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Residues in contact with VAL 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU* 4.1 12.6 - - + -
137C LEU 3.2 21.5 + - - +
138C ASP* 3.7 10.0 - - + +
139C GLU 4.2 1.7 + - - +
157C ILE 3.5 0.4 + - - +
158C ASN* 1.3 88.8 + - - +
160C ALA* 1.4 70.4 + - - +
161C SER* 3.7 1.4 + - - -
166C ILE* 3.6 32.5 - - + -
167C VAL 4.0 0.7 - - - +
170C SER* 3.8 7.0 - - - +
171C LEU* 3.7 26.2 - - + +
174C ILE* 3.7 9.0 - - + -
194C LEU* 3.9 22.0 - - + -
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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