Contacts of the helix formed by residues 114 - 121 (chain A) in PDB entry 1QZZ
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 GLY 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ALA 5.1 4.5 - - - -
111A ASP* 2.7 22.4 + - - +
113A ASN* 1.3 81.7 - - - +
115A ALA* 1.3 62.5 + - - -
116A VAL 3.5 2.4 + - - -
117A SER 4.4 0.2 - - - -
118A HIS* 3.0 29.4 + - - +
155A LEU* 4.1 0.7 - - - -
158A SER* 3.5 16.2 - - - -
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Residues in contact with ALA 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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114A GLY* 1.3 69.6 - - - -
116A VAL* 1.3 60.1 + - - +
118A HIS* 3.5 2.6 + - - +
119A ALA* 2.8 32.4 + - - +
137A TYR* 5.2 0.3 - - - -
145A PHE* 4.7 2.7 - - + -
149A LEU* 4.2 13.9 - - + -
155A LEU* 3.3 38.7 - - - +
158A SER* 2.8 10.7 + - - +
159A PHE* 3.6 23.7 - - + +
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Residues in contact with VAL 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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108A ALA 5.8 0.4 - - - +
109A TRP* 3.7 39.5 - - + +
114A GLY 3.5 0.6 - - - -
115A ALA* 1.3 74.8 - - - +
117A SER* 1.3 60.2 + - - +
119A ALA* 3.3 5.9 + - - +
120A ASP* 2.8 34.8 + - - +
158A SER 5.5 0.2 - - - +
159A PHE* 4.1 26.0 - - + -
162A LEU* 3.9 23.1 - - + +
163A MET* 4.3 7.2 - - + -
307A ARG* 4.1 24.2 - - - +
311A PHE* 3.7 8.6 - - + -
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Residues in contact with SER 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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34A ARG* 3.1 23.4 + - - -
109A TRP 3.5 13.3 + - - -
110A LEU 2.8 22.1 + - - -
111A ASP 3.2 23.3 - - - -
112A LEU* 3.4 6.5 - - - +
114A GLY 3.7 1.4 + - - -
115A ALA 3.4 0.2 - - - -
116A VAL* 1.3 75.9 - - - +
118A HIS* 1.3 67.6 + - - +
120A ASP* 3.0 25.0 + - - +
121A LEU* 3.3 13.5 + - - +
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Residues in contact with HIS 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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112A LEU* 3.9 17.3 + - - +
114A GLY 3.0 22.3 + - - +
115A ALA* 3.5 5.1 + - - +
117A SER* 1.3 76.5 - - - +
119A ALA* 1.3 61.8 + - - +
121A LEU* 3.4 14.8 + - + +
137A TYR* 3.5 19.1 + - - -
141A TYR* 2.5 75.5 + + - -
148A ASP* 4.1 6.3 - - - -
155A LEU* 4.1 19.5 - - + +
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Residues in contact with ALA 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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115A ALA 2.8 18.4 + - - +
116A VAL 3.6 0.4 - - - +
118A HIS* 1.3 73.8 + - - +
120A ASP* 1.3 59.2 - - - +
121A LEU 3.0 2.2 - - - -
122A ALA* 2.8 29.3 + - - +
123A PHE 4.2 0.3 + - - -
137A TYR* 3.8 26.5 - - + -
145A PHE* 4.1 4.7 - - + -
311A PHE* 3.4 42.4 - - + -
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Residues in contact with ASP 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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34A ARG* 2.8 29.2 + - - +
109A TRP 5.2 1.4 - - - +
116A VAL* 2.8 18.3 + - - +
117A SER* 3.2 15.9 - - - +
119A ALA* 1.3 76.6 - - - +
121A LEU* 1.3 56.2 + - + +
123A PHE* 2.9 37.1 + - + +
307A ARG* 2.7 47.5 + - - +
311A PHE* 3.2 14.1 - - - -
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Residues in contact with LEU 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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31A MET* 3.6 36.8 - - + -
34A ARG* 4.5 4.0 - - - -
112A LEU* 4.1 18.2 - - + +
117A SER 3.5 14.6 - - - +
118A HIS* 3.4 11.2 - - + +
119A ALA 3.0 0.2 - - - -
120A ASP* 1.3 74.1 - - - +
122A ALA* 1.3 58.4 + - - +
123A PHE 2.9 10.7 + - - -
124A THR* 3.2 27.7 + - + +
140A ARG* 3.4 41.0 + - - +
141A TYR* 3.6 7.9 - - - +
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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