Contacts of the helix formed by residues 138 - 148 (chain A) in PDB entry 1ZP2
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 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A HIS 4.5 0.7 - - - +
137A HIS* 1.3 86.4 - - + +
139A TYR* 1.3 63.3 + - - -
140A THR 3.3 0.7 - - - -
141A SER* 3.4 4.7 + - - +
142A LEU* 3.2 23.0 + - - +
163A VAL* 3.4 29.6 - - + -
167A TYR* 3.6 9.2 - - + +
177A PRO* 2.9 37.2 - - + +
180A LEU* 3.7 20.0 - - + -
181A ALA* 3.5 19.7 - - + +
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Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLN* 2.6 26.0 + - + -
51A ARG* 5.1 9.4 - - + -
54A ALA* 4.3 10.3 - - + -
137A HIS* 3.0 24.9 - + + -
138A PRO* 1.3 78.2 - - - +
140A THR* 1.3 63.9 + - - +
142A LEU* 3.0 10.4 + - + +
143A GLU* 3.0 23.7 + - - +
160A TRP* 3.5 46.5 - + + -
163A VAL* 3.4 19.5 - - + -
164A ASN* 2.4 38.6 + - - -
167A TYR* 3.3 24.7 - + - -
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Residues in contact with THR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A HIS 3.8 12.4 + - - -
138A PRO 3.3 0.4 - - - -
139A TYR* 1.3 77.1 - - - +
141A SER* 1.3 65.4 - - - +
143A GLU* 3.3 6.3 + - + +
144A GLN* 2.9 24.8 + - + +
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A HIS 4.8 1.0 + - - -
138A PRO* 3.6 6.2 + - - +
139A TYR 3.3 0.4 - - - -
140A THR* 1.3 76.5 - - - +
142A LEU* 1.3 64.8 + - - +
144A GLN* 3.1 10.0 + - - +
145A ALA* 3.0 22.8 + - - +
177A PRO* 4.1 0.9 + - - +
178A HIS* 3.5 29.9 + - - +
181A ALA* 3.5 21.0 - - - +
182A TYR* 5.3 9.2 - - - -
185A LEU* 5.3 2.0 - - - -
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Residues in contact with LEU 142 (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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138A PRO 3.2 12.3 + - - +
139A TYR* 3.0 12.2 + - + +
141A SER* 1.3 80.2 - - - +
143A GLU* 1.3 64.3 + - - +
145A ALA* 3.1 10.6 + - - +
146A PHE 3.1 8.8 + - - -
151A ILE* 4.2 1.0 - - - +
156A LEU* 3.8 19.1 - - + +
159A ALA* 4.1 10.5 - - + -
160A TRP* 3.5 46.7 - - + +
163A VAL* 3.7 18.4 - - + -
181A ALA* 3.9 15.5 - - + +
184A ALA* 4.9 0.2 - - + -
185A LEU* 3.6 35.9 - - + -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR 3.0 9.3 + - - +
140A THR* 3.9 8.5 - - - +
142A LEU* 1.3 77.1 - - - +
144A GLN* 1.3 53.2 + - - +
146A PHE* 3.0 18.8 + - + +
147A HIS* 2.8 60.5 + - - +
156A LEU* 4.3 6.9 - - + +
160A TRP* 4.5 12.9 - - + -
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Residues in contact with GLN 144 (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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140A THR* 2.9 14.4 + - + +
141A SER* 3.1 13.9 + - - +
143A GLU* 1.3 77.8 - - - +
145A ALA* 1.3 64.8 + - - +
147A HIS* 2.8 13.9 + - - +
148A ASP* 2.8 54.2 + - - +
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Residues in contact with ALA 145 (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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141A SER 3.0 11.5 + - - +
142A LEU 3.1 8.3 + - - +
144A GLN* 1.3 77.4 - - - +
146A PHE* 1.3 58.9 + - - +
148A ASP* 3.7 1.4 + - - -
149A GLY 3.5 1.0 + - - -
150A ILE* 2.9 50.3 + - + +
151A ILE* 3.3 24.8 + - + -
185A LEU* 4.1 17.0 - - + -
199A LEU* 5.0 0.2 - - + -
202A LEU* 4.9 8.3 - - + -
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Residues in contact with PHE 146 (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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142A LEU 3.1 10.2 + - - +
143A GLU* 3.0 19.9 + - + +
144A GLN 3.0 0.4 - - - -
145A ALA* 1.3 76.1 - - - +
147A HIS* 1.3 69.0 + + - +
149A GLY* 3.0 14.6 + - - -
151A ILE* 3.4 26.7 - - + +
152A ASN* 4.0 6.7 - - - -
153A GLN* 3.6 38.4 - - + -
156A LEU* 3.8 26.9 - - + -
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Residues in contact with HIS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLU* 2.8 33.9 + - - +
144A GLN* 3.3 17.0 - - - +
146A PHE* 1.3 80.9 - + - +
148A ASP* 1.3 65.3 + - - +
149A GLY* 3.0 5.2 + - - -
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Residues in contact with ASP 148 (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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144A GLN* 2.8 55.6 + - - +
145A ALA* 4.3 0.3 + - - -
146A PHE 3.3 0.2 - - - -
147A HIS* 1.3 77.0 + - - +
149A GLY* 1.3 59.8 + - - +
150A ILE* 3.1 31.0 + - + +
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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