Contacts of the helix formed by residues 120 - 131 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A THR* 1.3 71.4 - - - +
121A THR* 1.3 57.7 + - - +
122A VAL 3.0 6.1 - - - -
123A LEU* 3.0 7.8 + - - +
124A SER* 2.9 28.5 + - - -
149A ILE* 4.1 18.3 - - + +
162A SER* 5.9 3.0 - - - -
163A THR 4.5 2.8 - - - +
164A TYR* 3.6 38.3 - - + -
171A PRO* 3.2 26.4 - - - +
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Residues in contact with THR 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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119A THR* 3.3 12.2 + - - -
120A GLN* 1.3 77.9 + - - +
122A VAL* 1.3 61.2 + - - +
123A LEU 3.1 0.2 - - - -
124A SER* 3.1 11.9 - - - +
125A ASP* 2.7 60.8 + - - +
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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
----------------------------------------------------------
95A TYR* 2.6 50.7 + - + +
97A ILE* 4.7 0.7 - - + -
117A PRO* 4.0 10.3 - - + -
118A SER* 3.9 12.8 - - - +
119A THR* 3.4 35.7 - - - +
120A GLN 3.0 1.0 - - - -
121A THR* 1.3 80.2 - - - +
123A LEU* 1.3 58.9 + - - +
125A ASP* 4.6 0.7 - - - -
126A ILE* 3.6 9.7 + - - +
187A VAL* 4.0 23.1 - - + -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 3.7 29.4 - - + -
117A PRO* 3.7 26.9 - - + -
120A GLN 3.0 6.9 + - - +
122A VAL* 1.3 79.0 - - - +
124A SER* 1.3 64.9 + - - +
125A ASP 3.2 1.8 - - - -
126A ILE* 3.0 16.0 + - - +
127A TYR* 3.1 10.7 + - - +
147A ALA* 3.8 27.1 - - + -
148A TRP 4.4 0.2 - - - +
149A ILE* 3.5 25.8 - - + -
164A TYR* 3.9 23.0 - - + -
166A LEU* 3.9 18.5 - - + +
185A VAL* 4.4 6.5 - - + -
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLN* 2.9 16.7 + - - -
121A THR* 3.1 25.6 + - - +
123A LEU* 1.3 78.1 - - - +
125A ASP* 1.3 60.4 + - - +
127A TYR* 3.1 3.0 + - - +
128A ASP* 2.9 39.6 + - - +
164A TYR* 3.6 33.1 - - - -
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Residues in contact with ASP 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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30A ILE* 4.8 8.1 - - + -
95A TYR* 4.1 12.8 + - - +
121A THR* 2.7 50.1 + - - +
122A VAL* 4.6 0.5 - - - -
124A SER* 1.3 77.9 + - - +
126A ILE* 1.3 58.0 + - - +
128A ASP* 3.3 15.4 + - - +
129A SER* 2.9 36.0 + - - +
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Residues in contact with ILE 126 (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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30A ILE* 3.5 30.3 - - + +
31A TRP 3.6 28.3 - - - +
32A LEU* 3.9 34.1 - - + +
95A TYR* 4.0 5.4 - - + +
97A ILE* 3.8 20.4 - - + -
122A VAL 3.6 15.9 - - - +
123A LEU* 3.0 11.9 + - - +
125A ASP* 1.3 74.9 - - - +
127A TYR* 1.3 60.9 + - - +
130A TRP* 2.9 32.8 + - + +
131A GLY 5.9 1.1 - - - +
166A LEU* 4.9 8.3 - - + -
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Residues in contact with TYR 127 (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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21A ASN* 4.6 0.3 - - - +
123A LEU 3.1 9.4 + - - +
124A SER 3.1 11.0 + - - +
126A ILE* 1.3 77.7 - - - +
128A ASP* 1.3 72.8 + - - +
129A SER 2.9 0.5 + - - -
131A GLY* 2.6 45.9 + - - +
132A ALA* 3.3 26.0 + - - +
164A TYR* 4.1 10.1 - + + +
165A ASN 5.0 1.1 - - - -
166A LEU* 4.1 13.4 - - + +
167A ILE 3.5 21.3 + - - -
168A THR 5.7 0.2 - - - -
169A GLN* 3.2 46.7 + - + +
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Residues in contact with ASP 128 (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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21A ASN* 3.6 11.1 - - - +
23A VAL* 5.5 1.9 - - - +
124A SER* 2.9 26.3 + - - +
125A ASP* 3.7 15.9 - - - +
127A TYR* 1.3 87.4 - - - +
129A SER* 1.3 60.4 + - - +
164A TYR* 5.3 0.3 + - - -
169A GLN* 5.2 2.8 + - - -
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Residues in contact with SER 129 (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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18A ILE* 3.9 12.8 - - - +
21A ASN* 3.6 7.9 + - - +
23A VAL* 5.6 0.5 - - - +
28A PRO* 4.0 20.0 - - - +
30A ILE* 3.4 25.1 - - - +
125A ASP* 2.9 18.0 + - - +
127A TYR 2.9 0.2 + - - -
128A ASP* 1.3 79.1 - - - +
130A TRP* 1.3 79.0 + - - +
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Residues in contact with TRP 130 (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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18A ILE* 3.8 12.8 - - + -
20A GLY* 3.3 17.8 - - - -
21A ASN* 3.5 8.5 + - - -
27A LEU* 4.1 15.0 - - + -
28A PRO* 4.0 15.6 - - + +
30A ILE 2.9 26.4 + - - -
31A TRP* 4.1 9.2 - + - -
32A LEU* 3.9 27.3 - - + +
35A GLY* 3.7 8.3 - - - -
36A GLN 3.5 30.1 - - - -
37A PHE* 4.2 2.2 - + - -
68A LEU* 3.7 29.8 - - + -
126A ILE* 2.9 26.0 + - + +
127A TYR 2.9 1.2 + - - -
129A SER* 1.3 90.6 - - - +
131A GLY* 1.3 61.0 + - - +
136A TYR* 2.8 51.6 + + + +
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Residues in contact with GLY 131 (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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20A GLY 4.4 8.5 - - - -
21A ASN* 4.7 5.4 - - - -
32A LEU* 5.0 2.4 - - - +
126A ILE* 4.8 1.0 - - - +
127A TYR* 2.6 43.2 + - - -
130A TRP* 1.3 79.4 - - - +
132A ALA* 1.3 68.4 + - - -
133A ALA* 3.2 4.0 + - - +
136A TYR* 4.7 0.2 - - - -
166A LEU 4.1 1.6 - - - +
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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