Contacts of the strand formed by residues 123 - 131 (chain A) in PDB entry 2QCB
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 THR 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LEU* 4.2 23.3 - - + -
110A LEU 3.2 10.3 - - - +
111A THR* 3.7 19.0 + - - +
120A TRP 5.2 1.0 + - - -
121A LYS* 3.4 4.9 + - - -
122A SER* 1.3 93.1 + - - +
124A LEU* 1.3 74.6 + - - +
125A VAL* 4.2 0.9 + - - +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A TRP* 3.7 19.2 - - + -
109A LEU* 3.3 4.9 - - - -
110A LEU* 2.8 49.2 + - + +
122A SER 4.2 0.4 + - - -
123A THR* 1.3 78.6 - - - +
125A VAL* 1.3 62.1 + - - +
400A KYS 3.5 42.4 - - + +
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Residues in contact with VAL 125 (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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107A GLN* 5.4 7.9 - - + +
108A TRP* 3.3 20.6 - - - +
109A LEU* 4.0 16.8 - - + -
123A THR* 4.2 1.1 + - + +
124A LEU* 1.3 78.0 - - - +
126A GLY* 1.3 67.0 + - - +
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Residues in contact with GLY 126 (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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107A GLN* 3.3 8.3 - - - +
108A TRP* 2.9 50.8 + - - +
125A VAL* 1.3 81.3 - - - +
127A HIS* 1.3 70.2 + - - +
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Residues in contact with HIS 127 (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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24A GLN* 3.4 10.2 + - - -
106A THR 3.3 14.6 - - - +
107A GLN* 4.4 11.9 - - + +
108A TRP* 3.4 4.3 + - - +
126A GLY* 1.3 80.8 - - - +
128A ASP* 1.3 68.2 + - - +
129A THR* 5.9 1.2 + - - -
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Residues in contact with ASP 128 (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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23A ASN* 3.0 17.6 + - - +
24A GLN* 2.9 21.8 + - - +
25A LEU* 4.4 1.7 - - - +
92A TRP* 2.9 14.9 + - - -
104A ILE 3.8 1.6 - - - +
106A THR* 2.7 48.5 + - - +
108A TRP* 3.0 21.8 + - - -
127A HIS* 1.3 73.9 - - - +
129A THR* 1.3 63.0 + - - +
130A PHE* 3.6 14.1 - - + -
400A KYS 2.9 26.3 + - - -
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Residues in contact with THR 129 (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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22A TYR 3.8 0.5 - - - +
23A ASN* 3.2 19.6 - - - -
24A GLN* 3.0 16.1 + - - +
103A ARG* 3.9 26.0 - - + +
104A ILE 3.6 3.4 - - - +
105A ASN* 2.9 29.7 + - - +
127A HIS* 5.9 1.0 + - - -
128A ASP* 1.3 75.3 + - - +
130A PHE* 1.3 67.1 + - - +
131A THR* 4.7 3.8 - - + +
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Residues in contact with PHE 130 (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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21A TRP* 3.7 19.6 - - + -
22A TYR 3.2 7.0 - - - +
23A ASN* 3.6 30.7 - - + -
27A SER 5.0 1.8 - - - -
29A PHE* 3.8 31.4 - + + -
43A TYR* 3.4 24.2 - + - -
75A TRP* 3.8 30.1 - + - -
92A TRP* 3.9 6.7 - + - -
103A ARG* 3.3 8.5 - - - +
104A ILE* 2.9 46.0 + - + +
106A THR* 3.8 12.3 - - + -
128A ASP* 3.6 18.2 - - + -
129A THR* 1.3 73.0 - - - +
131A THR* 1.3 64.9 + - - +
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Residues in contact with THR 131 (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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21A TRP* 3.5 10.2 - - - -
22A TYR* 2.9 34.9 + - - +
102A ALA 4.0 5.8 - - - -
103A ARG* 3.5 45.3 - - + +
129A THR* 4.7 5.6 - - + +
130A PHE* 1.3 78.8 - - - +
132A LYS* 1.3 61.3 + - - +
133A VAL* 2.7 31.6 + - - +
134A LYS* 4.4 2.6 - - - +
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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