Contacts of the helix formed by residues 137 - 144 (chain D) in PDB entry 1ZXN
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 VAL 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C VAL* 3.8 27.4 - - + -
34C TYR* 3.7 34.3 - - + -
125D ILE* 3.7 21.3 - - + -
126D PRO* 3.2 20.6 - - + +
128D VAL* 3.2 15.5 + - + +
130D HIS* 4.6 10.5 - - + +
135D MET 3.5 2.2 + - - -
136D TYR* 1.3 68.5 - - - +
138D PRO* 1.3 64.7 - - - +
140D LEU* 3.1 9.5 + - + +
141D ILE* 2.9 31.2 + - + +
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Residues in contact with PRO 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ILE* 4.1 9.0 - - + -
126D PRO 3.2 14.1 - - - +
127D VAL* 4.4 4.7 - - - -
136D TYR* 3.4 9.9 - - + -
137D VAL* 1.3 95.5 - - + +
139D ALA* 1.3 60.0 + - - +
141D ILE* 4.2 6.7 - - + -
142D PHE* 3.2 34.0 + - + +
179D VAL* 4.7 3.9 - - + +
181D THR* 3.8 19.7 - - + -
190D PHE* 3.4 44.2 - - + -
194D TRP* 4.4 0.5 - - - -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D MET* 3.8 28.3 - - + +
136D TYR* 2.8 15.2 + - + +
138D PRO* 1.3 76.2 - - - +
140D LEU* 1.3 56.6 + - - +
143D GLY* 2.9 28.8 + - - -
190D PHE* 3.7 9.4 - - + -
192D GLN* 3.5 22.9 - - - +
194D TRP* 3.8 15.0 - - + -
204D MET* 5.5 2.7 - - + -
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C TYR* 5.2 4.0 - - + +
35C GLN 5.8 0.2 - - - -
36C LYS* 4.2 8.3 - - + +
130D HIS* 3.5 26.9 - - + +
133D GLU* 3.5 40.2 - - + +
135D MET* 3.6 15.7 - - + -
136D TYR 2.8 10.8 + - - +
137D VAL* 3.1 11.0 + - - +
139D ALA* 1.3 74.8 - - - +
141D ILE* 1.3 66.5 + - + +
142D PHE 3.1 4.3 - - - -
144D GLN* 3.1 53.1 + - + +
147D THR* 3.3 18.8 + - + -
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Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C TYR* 3.7 30.7 - - + -
35C GLN 5.9 0.4 - - - +
125D ILE* 3.6 34.1 - - + -
137D VAL* 2.9 24.3 + - + +
138D PRO 3.9 0.4 - - - +
140D LEU* 1.3 76.9 - - + +
142D PHE* 1.3 71.9 + - + +
147D THR* 3.3 22.0 - - - +
148D SER 4.9 1.1 - - - +
167D ALA* 4.3 1.7 - - - +
168D LYS* 2.9 25.1 + - - +
907D ADP 3.3 48.4 - - - +
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Residues in contact with PHE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ILE* 5.0 4.0 - - + -
91D ASN* 5.1 0.2 - - - -
125D ILE* 3.5 28.3 - - + -
138D PRO 3.2 23.3 + - - +
140D LEU 3.1 0.4 - - - -
141D ILE* 1.3 86.0 - - + +
143D GLY* 1.3 59.1 + - - +
144D GLN 3.7 0.7 - - - -
167D ALA* 3.5 27.1 - - + -
168D LYS* 3.8 18.8 - - - +
171D ASN* 3.2 20.5 + - - +
177D PHE* 3.7 12.6 - + + -
179D VAL* 3.4 35.0 - - + -
194D TRP* 4.2 6.7 - - + -
198D MET* 4.3 0.3 - - - +
217D ILE* 4.0 27.6 - - + -
907D ADP 3.6 29.8 - + - -
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Residues in contact with GLY 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ALA 2.9 16.3 + - - -
142D PHE* 1.3 81.1 - - - +
144D GLN* 1.3 74.0 + - - +
168D LYS* 4.5 0.4 - - - -
194D TRP* 4.0 20.3 + - - -
198D MET* 3.5 26.3 - - - +
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Residues in contact with GLN 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LYS* 3.3 26.5 - - - +
135D MET* 3.8 27.8 - - - +
139D ALA 4.3 0.2 - - - +
140D LEU* 3.1 36.4 + - + +
142D PHE 3.7 0.6 - - - -
143D GLY* 1.3 87.6 + - - +
145D LEU* 1.3 62.7 + - - +
147D THR* 2.7 31.4 + - + +
168D LYS* 3.5 7.6 - - - +
198D MET* 5.1 0.2 - - - -
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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