Contacts of the helix formed by residues 128 - 133 (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 PRO 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ALA* 3.1 19.6 - - + +
125B LYS* 4.6 3.8 - - - +
126B ALA* 3.4 7.9 - - - +
127B LEU* 1.3 87.8 - - - +
129B GLU* 1.3 64.1 + - - +
131B PHE* 2.8 37.0 + - + +
132B GLU* 3.5 12.8 + - + +
51D ARG* 4.9 0.9 - - - +
68D PHE* 6.2 4.0 - - + -
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 2.8 5.4 + - - +
128B PRO* 1.3 93.6 - - + +
130B ILE* 1.3 60.7 + - - +
132B GLU* 3.4 15.0 + - - +
133B VAL* 3.3 19.3 - - - +
220B ILE* 3.6 37.8 - - + +
224B ARG* 5.1 3.0 + - - +
51D ARG* 2.6 30.8 + - - -
68D PHE* 4.3 8.2 - - - -
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 4.7 1.6 - - + -
123B LEU* 4.4 7.2 - - + -
127B LEU* 2.9 27.0 + - + +
128B PRO 2.9 1.6 + - - -
129B GLU* 1.3 68.5 - - - +
131B PHE* 1.3 83.0 + - + +
132B GLU 2.8 11.7 + - - -
133B VAL* 2.9 17.8 + - + +
134B ALA 3.0 15.7 + - - +
136B VAL* 3.8 23.7 - - + +
219B LEU* 3.9 24.9 - - + -
220B ILE* 3.8 31.4 - - + +
223B VAL* 3.5 28.8 - - + +
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Residues in contact with PHE 131 (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* 3.7 25.8 - - + -
88B LYS* 3.6 26.0 - - - +
91B LEU* 3.6 10.6 - - - +
120B ALA* 3.3 21.1 - - + -
123B LEU* 3.3 17.7 - - + -
124B ALA* 3.1 40.6 - - + -
127B LEU 3.9 3.8 - - - -
128B PRO* 2.8 15.7 + - + +
130B ILE* 1.3 81.9 - - + +
132B GLU* 1.3 58.6 + - + +
133B VAL 3.6 0.2 - - - -
134B ALA 3.6 7.5 - - - +
135B ASN* 5.0 4.4 + - - -
136B VAL* 3.7 41.3 - - + -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LYS* 2.7 33.3 + - - +
91B LEU* 3.9 15.0 - - - +
128B PRO* 3.7 17.9 - - + +
129B GLU* 3.4 13.0 - - - +
130B ILE 2.8 0.4 - - - -
131B PHE* 1.3 78.2 - - + +
133B VAL* 1.3 63.2 + - + +
134B ALA 3.7 0.2 - - - -
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Residues in contact with VAL 133 (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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91B LEU* 3.5 14.7 - - - +
92B PRO* 3.6 8.5 - - - +
129B GLU 3.3 19.3 - - - +
130B ILE* 2.9 7.3 + - - +
132B GLU* 1.3 83.0 - - + +
134B ALA* 1.3 59.4 + - - +
220B ILE* 5.3 3.6 - - + +
223B VAL* 4.1 19.1 - - + -
224B ARG* 3.7 58.6 - - + +
227B THR* 4.4 11.7 + - + +
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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