Contacts of the helix formed by residues 113 - 123 (chain A) in PDB entry 2Q06
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 LYS 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A SER* 2.9 27.6 - - - +
70A ALA* 3.8 25.6 - - - +
72A ASP* 5.2 8.3 - - - +
88A ASP* 5.2 2.0 + - - -
89A PRO 4.2 9.3 + - - -
90A LYS* 3.1 20.8 + - + +
91A LYS 3.5 22.5 + - - +
92A THR* 3.9 6.5 - - + -
111A TYR 3.5 2.6 + - - -
112A ASP* 1.3 68.7 - - - +
114A GLU* 1.3 61.0 + - - +
116A ILE* 2.8 8.1 + - - +
117A ARG* 2.5 53.6 + - - +
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Residues in contact with GLU 114 (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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90A LYS* 3.0 46.3 - - - +
112A ASP* 4.2 16.0 - - + +
113A LYS* 1.3 78.1 + - - +
115A GLU* 1.3 58.4 + - + +
117A ARG* 3.2 30.0 + - - +
118A ARG* 3.2 24.0 + - - +
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Residues in contact with GLU 115 (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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46A GLU* 3.9 15.6 - - - +
111A TYR* 4.0 25.1 - - + -
112A ASP* 2.7 28.5 + - + +
114A GLU* 1.3 80.0 - - - +
116A ILE* 1.3 58.9 + - + +
118A ARG* 3.1 42.3 + - - +
119A ILE* 3.1 22.8 - - + +
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Residues in contact with ILE 116 (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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39A PHE* 4.1 9.6 - - + -
43A MET* 3.7 30.7 - - + -
66A MET* 4.1 9.4 - - + +
67A VAL* 4.0 30.1 - - + +
70A ALA* 4.0 9.2 - - + -
71A PHE* 5.2 0.2 - - - -
92A THR* 4.7 1.8 - - + -
111A TYR* 3.5 46.0 - - + -
112A ASP 3.4 11.2 - - - +
113A LYS* 2.8 7.7 + - - +
115A GLU* 1.3 76.8 - - + +
117A ARG* 1.3 67.3 + - - +
118A ARG 3.0 1.1 - - - -
119A ILE* 3.1 18.1 + - + +
120A TRP* 3.3 12.3 + - - +
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Residues in contact with ARG 117 (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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70A ALA* 2.9 27.3 + - - +
71A PHE* 3.3 41.7 - - + +
90A LYS* 6.1 0.4 - - - +
113A LYS* 2.5 26.9 + - - +
114A GLU* 3.2 46.4 + - - +
116A ILE* 1.3 74.3 - - - +
118A ARG* 1.3 62.2 + - - +
120A TRP* 3.7 2.4 + - - +
121A ARG* 3.3 53.2 + - - +
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Residues in contact with ARG 118 (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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46A GLU* 5.5 1.0 + - - -
114A GLU 3.2 15.6 + - - +
115A GLU* 3.1 40.3 + - - +
117A ARG* 1.3 80.7 - - - +
119A ILE* 1.3 80.8 + - - +
121A ARG* 3.8 7.5 + - - +
122A GLN* 3.5 44.2 + - + +
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Residues in contact with ILE 119 (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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39A PHE* 3.9 19.3 - - + -
42A GLN* 4.2 30.1 - - + -
43A MET* 4.6 12.6 - - - +
46A GLU* 4.3 20.2 - - + +
111A TYR* 6.4 0.7 - - + -
115A GLU* 3.1 33.9 - - + +
116A ILE* 3.1 13.7 + - + +
118A ARG* 1.3 88.5 - - - +
120A TRP* 1.3 70.8 + - - +
121A ARG 2.7 3.8 + - - -
122A GLN* 2.8 16.2 + - + +
123A ALA* 2.8 12.4 + - + -
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Residues in contact with TRP 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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32A MET 5.4 0.7 - - - -
36A ILE* 3.9 34.8 - - + -
39A PHE* 3.5 51.2 - + + -
67A VAL* 4.3 10.5 - - + -
71A PHE* 3.7 22.7 - + + -
116A ILE 3.3 7.8 + - - +
117A ARG 3.7 8.7 - - - +
119A ILE* 1.3 77.9 - - - +
121A ARG* 1.3 56.6 + - - +
123A ALA* 3.2 1.7 + - - -
124A ASN* 2.8 58.8 + - - -
128A ASP* 3.1 46.7 + - + +
129A ALA 4.9 0.2 - - - -
132A GLY* 4.0 4.9 - - - -
133A LEU* 3.6 39.1 - - + +
136A MET* 4.1 8.5 - - + -
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Residues in contact with ARG 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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71A PHE* 4.0 19.2 - - - -
117A ARG* 3.3 46.0 + - - +
118A ARG* 3.9 7.9 - - - +
119A ILE 2.7 5.1 + - - -
120A TRP* 1.3 76.1 - - + +
122A GLN* 1.3 52.7 + - + +
124A ASN 2.9 2.6 + - - -
125A ASN 2.7 31.9 + - - -
126A GLY* 3.2 11.6 + - - +
127A GLU 3.2 24.9 - - - +
128A ASP* 4.2 13.7 - - + +
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Residues in contact with GLN 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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118A ARG* 3.5 34.1 + - + +
119A ILE* 2.8 11.1 + - + +
121A ARG* 1.3 75.2 - - + +
123A ALA* 1.3 58.7 + - - +
124A ASN 3.2 1.2 + - - -
125A ASN 3.9 1.1 - - - +
126A GLY* 4.9 3.2 - - - +
370B ASN* 3.4 54.2 + - - +
372B GLU* 4.0 18.3 + - - +
373B ALA* 4.9 9.3 - - + +
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Residues in contact with ALA 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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35A GLY 4.2 1.4 - - - +
38A ARG* 3.2 35.1 + - + +
39A PHE* 3.7 35.9 - - + +
42A GLN* 5.4 4.0 - - + -
119A ILE* 2.8 15.8 + - + +
120A TRP* 3.4 10.1 - - - +
122A GLN* 1.3 76.3 - - - +
124A ASN* 1.3 64.7 + - - +
125A ASN* 3.7 2.9 - - - -
370B ASN* 5.6 0.4 - - - -
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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