Contacts of the strand formed by residues 119 - 123 (chain A) in PDB entry 3QNQ
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 VAL 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLN* 1.3 79.7 - - - +
120A ALA* 1.3 60.0 + - - +
121A TYR* 3.8 16.8 + - + +
130A ILE 4.0 0.7 - - - +
131A LEU* 3.7 7.0 - - - +
132A VAL* 3.1 52.1 + - + +
135A VAL* 3.8 14.8 - - + -
137A PRO* 4.1 17.7 - - + -
132B VAL* 4.3 5.8 - - + -
134B GLY 5.7 0.9 - - - +
135B VAL* 4.2 11.9 - - + -
123D MET* 3.3 24.7 - - + -
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLN* 6.0 0.7 - - + +
119A VAL* 1.3 74.1 - - - +
121A TYR* 1.3 63.6 + - - +
129A SER* 6.1 2.0 - - - -
130A ILE 4.0 4.5 - - - +
131A LEU* 4.7 10.5 - - + -
123D MET* 3.1 26.7 - - - +
124D PRO* 3.3 15.4 - - + +
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Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A VAL* 3.8 18.9 - - + +
120A ALA* 1.3 77.0 - - - +
122A ILE* 1.3 61.8 + - - +
129A SER* 3.3 26.9 - - - -
130A ILE* 3.1 38.5 + - + -
132A VAL* 4.8 3.4 - - + -
132B VAL* 3.4 28.1 - - + +
133B ASP 4.1 9.0 + - - -
121D TYR* 3.8 11.7 - - + -
122D ILE 3.5 3.6 - - - -
123D MET* 3.4 48.2 - - + +
124D PRO* 4.9 0.4 - - - -
128D GLU* 4.0 7.8 - - - +
129D SER* 3.9 13.8 + - - -
130D ILE* 3.3 34.6 - - + +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 1.3 77.5 - - - +
123A MET* 1.3 56.8 + - - +
124A PRO* 3.2 15.7 - - + +
127A LYS* 4.6 22.0 - - + +
128A GLU 3.4 20.0 - - - +
129A SER* 4.3 6.3 - - - -
121D TYR* 3.8 2.5 - - - -
122D ILE* 2.5 50.9 + - + +
124D PRO* 4.8 19.3 - - + -
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Residues in contact with MET 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 1.3 70.0 - - - +
124A PRO* 1.3 77.4 - - + +
125A GLY 3.3 0.3 + - - -
126A THR* 2.8 36.9 + - + +
127A LYS 4.3 2.1 + - - -
128A GLU* 2.9 27.6 + - - +
132C VAL* 5.7 1.1 - - + -
133C ASP 5.4 3.8 - - - +
134C GLY 5.5 5.6 - - - +
119D VAL* 3.5 38.8 - - + -
120D ALA 4.2 13.9 - - - +
121D TYR* 3.4 27.8 - - + -
139D ALA* 6.0 7.0 - - + -
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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