Contacts of the helix formed by residues 120 - 130 (chain B) in PDB entry 2ZQK
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 GLN 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B THR* 1.3 71.2 - - - +
121B THR* 1.3 69.5 + - + +
122B VAL 3.2 2.0 - - - -
123B LEU* 3.1 7.7 + - - +
124B SER* 2.9 24.6 + - - -
149B ILE* 3.6 28.9 - - + +
162B SER* 5.9 4.0 - - - -
164B TYR* 4.1 19.0 - - + -
171B PRO* 3.2 33.5 - - - +
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Residues in contact with THR 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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119B THR* 3.3 13.3 + - - +
120B GLN* 1.3 76.0 - - + +
122B VAL* 1.3 72.9 + - - +
123B LEU 2.7 2.8 + - - -
124B SER* 2.8 14.1 - - - +
125B ASP* 2.7 44.2 + - - +
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Residues in contact with VAL 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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95B TYR* 2.7 37.4 + - + +
97B ILE* 4.4 0.7 - - - +
117B PRO* 3.9 22.2 - - + -
118B SER* 4.1 13.9 - - - +
119B THR* 3.3 34.3 - - - +
121B THR* 1.3 83.4 + - - +
123B LEU* 1.3 60.8 + - + +
125B ASP* 4.7 2.2 - - - -
126B ILE* 3.7 8.5 + - - +
187B VAL* 4.2 19.7 - - + -
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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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97B ILE* 3.6 26.0 - - + -
117B PRO* 3.6 41.7 - - + -
119B THR 5.1 0.4 - - - +
120B GLN 3.1 7.2 + - - +
121B THR 2.7 3.2 + - - -
122B VAL* 1.3 77.1 - - + +
124B SER* 1.3 63.8 + - - +
125B ASP 3.3 0.4 - - - -
126B ILE* 3.0 21.3 - - - +
127B TYR 3.4 3.3 + - - -
147B ALA* 4.2 14.4 - - + -
148B TRP 4.0 11.0 - - - +
149B ILE* 4.2 6.5 - - + -
164B TYR* 3.9 34.4 - - + +
166B LEU* 4.2 17.6 - - + +
185B VAL* 4.3 9.4 - - + -
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLN* 2.9 19.5 + - - -
121B THR* 2.8 31.3 + - - +
123B LEU* 1.3 74.3 - - - +
125B ASP* 1.3 72.9 + - - -
127B TYR* 2.9 15.6 + - - +
128B ASP* 2.9 20.9 + - - +
164B TYR* 3.5 31.0 + - - -
169B GLN* 5.6 0.7 - - - -
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Residues in contact with ASP 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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30B ILE* 5.1 9.9 - - + -
95B TYR* 4.7 7.3 + - - +
121B THR* 2.7 38.9 + - - +
122B VAL* 4.4 6.1 + - - +
124B SER* 1.3 78.0 + - - +
126B ILE* 1.3 51.1 + - - +
128B ASP* 3.0 17.3 + - - +
129B SER* 2.8 37.2 + - - +
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Residues in contact with ILE 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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30B ILE* 3.7 35.4 - - + +
31B TRP 4.1 13.7 - - - +
32B LEU* 4.1 27.4 - - + -
95B TYR* 4.0 4.7 - - + +
97B ILE* 3.4 33.2 - - + -
122B VAL 3.7 13.2 - - - +
123B LEU 3.0 11.7 - - - +
124B SER 3.0 0.2 - - - -
125B ASP* 1.3 72.8 - - - +
127B TYR* 1.3 59.7 + - - +
128B ASP 3.0 1.3 - - - -
129B SER* 3.0 1.7 + - - +
130B TRP* 2.8 36.5 + - + +
131B GLY 5.8 0.9 - - - +
166B LEU* 5.0 8.7 - - + -
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Residues in contact with TYR 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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21B ASN* 4.5 1.0 - - - +
123B LEU 3.4 2.4 + - - +
124B SER 2.9 12.2 + - - +
126B ILE* 1.3 77.3 - - - +
128B ASP* 1.3 65.5 + - - +
130B TRP 3.7 0.2 - - - -
131B GLY* 2.7 62.4 + - - +
132B ALA* 3.5 17.4 + - - +
164B TYR* 3.9 17.5 - - + +
165B ASN 5.1 0.4 - - - -
166B LEU* 3.8 15.4 - - + +
167B ILE 3.8 16.3 + - - -
168B THR* 5.6 0.6 - - - -
169B GLN* 3.5 45.8 + - + -
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Residues in contact with ASP 128 (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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21B ASN* 4.0 6.1 - - - +
23B VAL* 5.9 0.9 - - - +
124B SER* 2.9 23.8 + - - +
125B ASP* 3.0 20.7 - - - +
127B TYR* 1.3 87.3 - - - +
129B SER* 1.3 57.3 + - - +
169B GLN* 5.0 6.0 + - - -
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Residues in contact with SER 129 (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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18B ILE* 4.1 12.5 - - - +
21B ASN* 3.2 16.5 + - - +
23B VAL* 5.6 0.9 - - - +
28B PRO* 4.1 14.8 - - - +
30B ILE* 3.4 26.2 - - - +
125B ASP* 2.8 15.9 + - - +
126B ILE* 3.0 1.3 + - - -
128B ASP* 1.3 75.1 - - - +
130B TRP* 1.3 80.0 + - - +
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Residues in contact with TRP 130 (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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18B ILE* 3.4 14.6 - - + -
20B GLY* 3.1 15.9 - - - -
21B ASN* 3.1 13.5 + - - -
27B LEU* 4.2 6.5 - - + -
28B PRO* 4.1 18.6 - - + +
30B ILE 2.9 26.8 + - - -
31B TRP* 4.2 4.9 - + - -
32B LEU* 3.9 21.6 - - + +
35B GLY* 3.9 3.8 - - - -
36B GLN 3.7 30.7 - - - -
37B PHE* 4.0 12.1 - + - -
68B LEU* 3.5 33.0 - - + -
126B ILE* 2.8 34.9 + - + +
129B SER* 1.3 85.2 - - - +
131B GLY* 1.3 58.8 + - - +
136B TYR* 3.1 53.9 + + + +
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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