Contacts of the strand formed by residues 142 - 147 (chain C) in PDB entry 4QPL
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 PHE 142 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C TRP* 3.2 32.5 - + + -
138C LEU* 3.5 5.5 - - - +
139C ILE 2.8 28.6 + - - +
140C ALA 3.6 7.0 - - - -
141C GLY* 1.3 85.7 - - - +
143C LEU* 1.3 62.8 + - - +
144C TYR* 3.4 8.5 - - + -
155C ARG* 3.2 59.9 - - + +
158C GLU* 3.9 17.0 - - - -
-3D HIS* 5.9 3.4 - + - -
-2D HIS* 5.6 7.0 - - - -
0D ALA* 4.7 1.8 - - - -
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Residues in contact with LEU 143 (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 GLU* 3.6 25.8 - - + +
137C MET 3.5 7.0 - - - +
138C LEU* 3.8 31.2 - - + +
142C PHE* 1.3 72.5 - - - +
144C TYR* 1.3 62.2 + - - +
155C ARG* 3.6 7.8 - - - +
156C ARG* 3.0 35.5 + - + +
-4D HIS 5.7 3.1 - - - +
-3D HIS* 5.4 17.2 + - + +
0D ALA* 3.9 18.9 - - + +
3D LEU* 5.9 5.4 - - + -
4D LYS* 4.0 24.0 - - + +
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Residues in contact with TYR 144 (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 GLU* 3.3 9.0 - - - +
137C MET* 2.7 55.1 + - + +
139C ILE* 3.6 35.0 - - + -
142C PHE* 3.4 13.5 - - + -
143C LEU* 1.3 75.5 - - - +
145C VAL* 1.3 64.2 + - - +
153C GLN* 3.5 28.0 - - - -
154C TYR* 3.4 23.6 - - - +
155C ARG* 3.1 33.8 + - + -
156C ARG* 5.0 0.2 - - - -
161C ARG 5.6 0.2 - - - -
201C V3L 2.7 53.9 + + - -
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Residues in contact with VAL 145 (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* 4.0 16.4 - - + +
135C THR 3.5 7.4 - - - +
136C GLU* 4.6 7.0 - - + +
137C MET* 4.3 1.8 - - - -
144C TYR* 1.3 76.1 - - - +
146C ALA* 1.3 74.7 + - - +
147C ASP* 3.8 3.9 + - + +
153C GLN* 3.1 25.6 - - - +
154C TYR* 2.9 44.6 + - + +
156C ARG* 3.9 34.5 - - + +
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Residues in contact with ALA 146 (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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124C LEU* 3.5 32.3 - - + -
134C ASN* 3.1 7.1 - - - +
135C THR* 2.8 40.4 + - + +
137C MET* 3.6 16.1 - - + +
144C TYR 4.0 0.8 + - - -
145C VAL* 1.3 71.7 - - - +
147C ASP* 1.3 61.5 + - - +
148C LEU* 3.5 7.6 + - + +
152C VAL 3.8 4.5 - - - -
153C GLN* 4.5 0.4 - - - +
165C ILE* 4.5 5.2 - - + -
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Residues in contact with ASP 147 (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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133C LYS 3.8 5.8 - - - +
134C ASN* 4.2 6.5 - - + -
145C VAL* 3.8 4.6 - - + -
146C ALA* 1.3 71.4 - - - +
148C LEU* 1.3 57.6 + - - +
149C GLU* 3.0 13.5 + - - +
150C ASN* 2.8 45.7 + - - +
151C MET* 2.9 28.6 + - - -
152C VAL* 2.8 28.6 + - + +
154C TYR* 4.4 17.1 + - + +
162C ARG* 5.2 2.3 + - - -
165C ILE* 4.2 1.7 - - - +
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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