Contacts of the helix formed by residues 119 - 127 (chain B) in PDB entry 1ZQ1
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 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PHE* 3.9 13.1 + - + +
82B GLU 2.7 40.2 - - - +
83B ALA* 3.5 8.0 - - - +
118B PHE* 1.3 78.6 - - - +
120B ALA* 1.3 58.6 + - - +
121B GLU* 3.0 15.5 - - + +
122B GLU* 3.1 27.3 + - - +
123B LEU* 2.8 31.1 + - - +
138B PRO* 5.1 0.2 - - - -
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 2.5 24.4 + - - +
84B LEU* 3.6 15.9 - - - -
85B ILE* 3.7 21.3 - - + +
118B PHE 3.9 0.6 + - - -
119B THR* 1.3 72.5 - - - +
121B GLU* 1.3 56.9 + - - +
123B LEU* 4.3 0.2 - - - -
124B ALA* 2.8 32.2 + - - +
131B PHE* 3.3 9.4 - - + -
136B VAL 4.2 5.8 - - - +
138B PRO* 3.9 21.7 - - + +
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PHE* 3.4 25.1 - - + -
82B GLU* 2.6 58.0 + - + +
85B ILE* 4.3 10.2 - - + +
119B THR* 3.0 5.8 - - + +
120B ALA* 1.3 79.9 - - - +
122B GLU* 1.3 56.9 + - - +
124B ALA* 3.2 6.5 + - - +
125B LYS* 2.9 31.1 + - + +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PHE* 3.7 28.8 - - + -
106B ARG* 3.0 42.0 + - - +
116B PRO 4.6 0.2 - - - +
117B ALA* 3.3 22.7 - - + +
118B PHE 3.1 18.2 + - - -
119B THR* 3.1 29.1 + - - +
120B ALA 3.3 0.2 - - - -
121B GLU* 1.3 76.5 - - - +
123B LEU* 1.3 59.4 + - - +
125B LYS* 3.2 2.9 + - - -
126B ALA* 2.9 25.9 + - - +
54D MET* 3.0 18.8 - - - +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 3.9 27.8 - - + -
103B ILE* 4.9 6.3 - - + +
104B ALA* 4.0 24.7 - - + -
117B ALA 4.4 11.2 - - - +
118B PHE* 4.2 13.9 - - + +
119B THR 2.8 25.5 + - - +
120B ALA 3.7 1.3 - - - +
122B GLU* 1.3 73.6 - - - +
124B ALA* 1.3 53.7 + - - +
126B ALA* 4.5 1.6 - - - -
127B LEU* 2.5 41.3 + - + +
130B ILE* 4.4 6.3 - - + -
131B PHE* 3.3 14.7 - - + -
136B VAL* 4.3 4.5 - - + -
138B PRO* 3.9 20.2 - - + -
219B LEU* 4.8 12.8 - - + -
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ILE* 4.3 11.7 - - + -
120B ALA 2.8 17.7 + - - +
121B GLU* 3.5 5.2 - - - +
123B LEU* 1.3 72.5 - - - +
125B LYS* 1.3 63.6 + - - +
126B ALA 3.0 6.3 + - - -
128B PRO* 3.1 28.7 - - + +
131B PHE* 3.1 28.0 - - + -
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PHE* 6.2 2.2 - - + -
121B GLU* 2.9 20.0 + - + +
122B GLU* 3.6 6.7 - - - +
124B ALA* 1.3 76.2 - - - +
126B ALA* 1.3 57.5 + - - +
128B PRO* 4.6 3.5 - - - +
54D MET* 3.5 21.1 - - + +
58D GLY* 3.0 30.2 + - - +
59D GLU* 4.4 1.8 - - - +
60D ILE* 3.5 45.6 - - + +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA* 4.3 15.3 - - + -
105B SER 6.1 0.2 - - - +
122B GLU 2.9 9.7 + - - +
123B LEU 4.0 1.1 - - - +
125B LYS* 1.3 78.0 - - - +
127B LEU* 1.3 65.8 + - + +
128B PRO* 3.4 8.6 - - - +
51D ARG* 2.5 30.5 + - - -
54D MET* 3.1 22.4 - - + -
60D ILE* 5.7 0.9 - - - -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ILE* 4.5 13.9 - - + +
104B ALA* 4.8 2.7 - - + -
123B LEU* 2.5 25.7 + - + +
124B ALA 4.5 0.2 - - - -
126B ALA* 1.3 93.4 - - + +
128B PRO* 1.3 68.5 - - - +
129B GLU* 2.8 9.4 + - + +
130B ILE* 2.9 27.4 + - + +
131B PHE* 3.9 0.9 - - - -
216B ALA* 3.6 22.4 - - + +
219B LEU* 3.2 41.7 - - + -
220B ILE* 4.3 8.1 - - + -
51D ARG* 3.4 15.5 - - - +
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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