Contacts of the helix formed by residues 159 - 171 (chain A) in PDB entry 2ZA6
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 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A LEU 3.2 7.1 + - - +
156A VAL 3.8 2.9 - - - -
157A GLY 3.7 0.2 - - - -
158A SER* 1.3 84.8 + - - +
160A ALA* 1.3 62.0 + - - +
161A GLY 3.6 0.9 - - - +
162A LEU* 4.1 31.6 - - + +
163A GLY 2.8 26.9 + - - -
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Residues in contact with ALA 160 (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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156A VAL* 3.6 31.2 + - + +
159A GLN* 1.3 74.7 - - - +
161A GLY* 1.3 63.9 + - - +
164A GLU* 3.0 26.2 + - - +
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Residues in contact with GLY 161 (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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159A GLN* 5.6 0.4 - - - +
160A ALA* 1.3 78.1 - - - +
162A LEU* 1.3 62.1 + - - +
164A GLU* 3.2 12.7 + - - +
165A TYR* 3.1 22.1 + - - +
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Residues in contact with LEU 162 (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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159A GLN* 3.7 34.0 + - + +
161A GLY* 1.3 75.0 - - - +
163A GLY* 1.3 58.4 + - - +
165A TYR* 3.3 8.8 + - + +
166A LEU* 2.9 52.3 + - + +
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Residues in contact with GLY 163 (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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152A ILE* 6.3 0.2 - - - -
155A LEU* 3.6 38.4 - - - +
156A VAL* 4.4 2.0 - - - -
159A GLN 2.8 22.9 + - - -
160A ALA 3.7 0.7 - - - -
162A LEU* 1.3 74.7 - - - +
164A GLU* 1.3 60.1 + - - +
166A LEU* 3.4 2.7 + - - +
167A PHE* 3.1 24.3 + - - +
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Residues in contact with GLU 164 (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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38A PHE* 5.0 0.2 - - - -
45A LEU* 3.8 19.3 - - + +
92A THR* 3.8 17.2 - - - +
93A THR* 2.7 52.5 + - - +
94A PRO* 4.6 0.7 - - + -
152A ILE* 5.2 1.8 - - + -
156A VAL* 3.9 16.1 - - + +
160A ALA* 3.0 17.5 + - - +
161A GLY* 3.2 13.0 + - - +
163A GLY* 1.3 75.0 - - - +
165A TYR* 1.3 63.7 + - - +
167A PHE* 3.5 5.7 + - - +
168A GLU* 3.1 24.8 + - - +
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Residues in contact with TYR 165 (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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45A LEU* 4.6 13.0 - - + +
161A GLY 3.1 10.3 + - - +
162A LEU* 3.6 11.9 - - + +
164A GLU* 1.3 77.4 - - - +
166A LEU* 1.3 78.6 + - + +
168A GLU* 3.3 6.9 + - - +
169A ARG* 3.0 64.4 + - + +
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Residues in contact with LEU 166 (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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155A LEU* 4.4 21.1 - - + -
162A LEU* 2.9 41.4 + - + +
163A GLY* 3.8 4.0 - - - +
164A GLU 3.4 0.2 - - - -
165A TYR* 1.3 90.1 - - + +
167A PHE* 1.3 56.9 + - - +
169A ARG* 3.3 2.2 + - + -
170A LEU* 2.8 57.9 + - + +
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Residues in contact with PHE 167 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A VAL* 5.5 0.4 - - + -
93A THR* 4.4 8.7 - - + -
97A MET* 4.8 2.0 - - + -
148A HIS* 3.6 32.1 - + + -
151A ASN* 3.8 22.4 - - + -
152A ILE* 3.5 39.3 - - + -
155A LEU* 3.6 26.4 - - + +
163A GLY 3.1 11.2 + - - +
164A GLU* 3.9 5.6 - - - +
166A LEU* 1.3 76.2 - - - +
168A GLU* 1.3 60.6 + - - +
170A LEU* 5.4 0.2 - - - -
171A THR* 2.9 58.0 + - + +
172A LEU* 3.3 32.9 + - + -
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Residues in contact with GLU 168 (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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44A ALA 5.4 0.4 - - - +
45A LEU* 3.9 29.7 - - + +
46A GLU 3.4 7.7 + - - -
47A GLY* 2.8 37.4 + - - +
48A VAL* 4.0 9.2 - - + +
164A GLU 3.1 16.6 + - - +
165A TYR* 3.8 6.3 - - - +
167A PHE* 1.3 77.9 - - - +
169A ARG* 1.3 108.9 + - - +
172A LEU* 3.3 29.7 + - - +
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Residues in contact with ARG 169 (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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46A GLU* 4.5 10.7 - - - +
165A TYR* 3.0 60.7 + - + +
166A LEU* 3.8 4.9 - - + +
168A GLU* 1.3 115.1 + - - +
170A LEU* 1.3 73.9 + - + +
171A THR 3.6 0.2 - - - -
172A LEU 4.2 6.3 - - - +
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Residues in contact with LEU 170 (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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166A LEU* 2.8 39.6 + - + +
169A ARG* 1.3 90.7 - - + +
171A THR* 1.3 65.4 + - - +
172A LEU 5.1 0.2 - - - -
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Residues in contact with THR 171 (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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148A HIS* 3.6 25.1 - - + +
151A ASN* 5.5 4.3 - - - +
167A PHE* 2.9 46.3 + - + -
170A LEU* 1.3 83.3 + - - +
172A LEU* 1.3 64.0 + - + +
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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