Contacts of the helix formed by residues 114 - 125 (chain A) in PDB entry 3QZS
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 ASP 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.7 7.2 - - - +
95A GLU 3.6 21.7 - - - +
96A PRO* 3.3 29.9 - - + +
97A VAL 5.4 0.2 - - - +
113A MET* 1.3 79.3 - - - +
115A LEU* 1.3 59.3 + - - +
116A ALA* 2.9 19.2 + - - +
117A THR* 2.4 45.2 + - - -
118A MET* 3.1 28.4 + - - +
140A ILE* 3.6 10.5 - - - -
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Residues in contact with LEU 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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81A LEU* 3.9 18.0 - - + +
84A LEU* 4.3 10.5 - - + +
85A GLN* 3.8 35.2 + - + +
90A ALA* 4.1 13.5 - - + -
93A PHE* 2.9 37.7 + - + +
94A LEU* 4.1 17.3 - - + +
114A ASP* 1.3 71.9 - - - +
116A ALA* 1.3 56.4 + - - +
118A MET* 3.4 5.0 + - - +
119A GLU* 2.9 27.9 + - - +
137A MET* 3.8 20.6 - - + -
140A ILE* 3.6 22.2 - - + +
161A LEU* 4.7 4.5 - - + -
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Residues in contact with ALA 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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85A GLN* 4.6 4.0 - - - +
94A LEU 3.1 19.1 + - - +
95A GLU* 3.7 21.8 - - - +
96A PRO* 4.4 2.5 - - + -
114A ASP* 2.9 13.0 + - - +
115A LEU* 1.3 73.0 - - - +
117A THR* 1.3 59.8 + - - +
119A GLU* 3.2 10.6 + - - +
120A GLU* 3.0 27.0 + - - +
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Residues in contact with THR 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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96A PRO* 4.5 4.5 - - - +
113A MET* 3.7 22.0 - - + -
114A ASP* 2.4 38.5 + - - -
116A ALA* 1.3 68.4 - - - +
118A MET* 1.3 66.2 + - - +
120A GLU* 3.2 16.6 + - - +
121A ARG* 3.0 41.0 + - + +
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Residues in contact with MET 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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81A LEU* 4.0 11.2 - - + -
113A MET* 3.8 13.2 - - - -
114A ASP 3.1 12.4 + - - +
115A LEU* 3.7 8.5 - - - +
116A ALA 3.3 0.2 - - - -
117A THR* 1.3 75.0 - - - +
119A GLU* 1.3 57.2 + - - +
121A ARG* 3.3 2.1 + - - +
122A VAL* 2.8 34.3 + - - +
127A TYR* 3.6 22.6 - - - +
133A PHE* 3.5 51.4 - - + +
136A ASP* 3.7 2.7 - - + -
137A MET* 3.6 34.5 - - + +
140A ILE* 3.7 20.2 - - - -
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Residues in contact with GLU 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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78A LYS* 4.5 9.2 + - - -
81A LEU* 3.4 21.0 - - + +
82A ARG* 3.0 43.2 + - - +
85A GLN* 3.2 11.1 + - - +
115A LEU 2.9 15.0 + - - +
116A ALA* 3.5 12.1 - - - +
117A THR 3.2 0.4 - - - -
118A MET* 1.3 76.9 - - - +
120A GLU* 1.3 57.9 + - - +
122A VAL* 3.2 2.3 + - - +
123A GLN* 2.9 35.4 + - + +
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Residues in contact with GLU 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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116A ALA 3.0 12.9 + - - +
117A THR* 3.2 17.1 + - - +
119A GLU* 1.3 79.1 - - - +
121A ARG* 1.3 58.9 + - + +
123A GLN* 3.2 15.3 + - - +
124A ARG* 2.9 67.9 + - + +
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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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113A MET* 3.5 18.0 - - - +
117A THR* 3.0 31.9 + - + +
118A MET* 3.6 2.2 - - - +
120A GLU* 1.3 75.6 - - + +
122A VAL* 1.3 63.8 + - - +
124A ARG* 3.6 3.1 + - - +
125A ARG 3.1 2.6 + - - -
126A TYR* 2.9 78.0 + - + +
127A TYR* 3.6 28.4 - - + -
136A ASP* 2.7 37.7 + - - -
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Residues in contact with VAL 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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74A TYR* 3.4 35.9 - - + +
77A LEU* 5.0 3.6 - - + -
78A LYS* 4.5 26.5 - - + +
81A LEU* 4.4 8.3 - - + -
118A MET 2.8 25.6 + - - +
119A GLU* 3.7 6.1 - - - +
121A ARG* 1.3 72.4 - - - +
123A GLN* 1.3 55.3 + - - +
125A ARG* 2.8 36.9 + - - +
127A TYR* 3.9 10.3 - - + -
133A PHE* 3.9 29.2 - - + -
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Residues in contact with GLN 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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78A LYS* 5.8 5.1 - - - +
119A GLU* 2.9 23.3 + - + +
120A GLU* 3.5 15.5 - - - +
122A VAL* 1.3 78.8 - - - +
124A ARG* 1.3 67.7 + - + +
125A ARG* 3.6 17.5 + - - +
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Residues in contact with ARG 124 (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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120A GLU* 2.9 50.9 + - + +
121A ARG* 4.2 4.9 - - - +
123A GLN* 1.3 85.3 + - + +
125A ARG* 1.3 71.3 + - - +
126A TYR* 4.4 5.5 - - + +
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Residues in contact with ARG 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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71A GLU* 2.8 40.8 + - - +
74A TYR* 3.3 50.8 + - + +
75A GLU* 3.7 20.0 + - - -
121A ARG 3.1 4.3 + - - -
122A VAL* 2.8 34.1 + - - +
123A GLN* 3.8 15.7 + - - +
124A ARG* 1.3 81.3 - - - +
126A TYR* 1.3 64.4 + - - +
127A TYR 4.1 2.9 - - - +
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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