Contacts of the strand formed by residues 148 - 153 (chain A) in PDB entry 1Z6T
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 GLY 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.6 17.3 - - - +
146A GLU 3.7 1.0 + - - -
147A PRO* 1.3 75.8 - - - +
149A TRP* 1.3 73.1 + - - +
258A CYS 3.2 8.4 + - - +
259A GLN* 3.7 1.1 - - - +
260A ILE* 3.0 25.8 + - - +
275A GLY* 5.6 0.2 - - - -
276A PRO* 3.4 15.7 - - - -
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Residues in contact with TRP 149 (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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143A LEU* 4.0 1.0 - - - +
148A GLY* 1.3 80.4 - - - +
150A VAL* 1.3 65.6 + - - +
151A THR* 4.8 2.5 - - - +
251A LEU* 3.5 43.5 - - + -
254A PHE* 4.9 0.2 - - + -
255A ASP* 3.8 20.4 + - - -
258A CYS 5.9 2.7 - - - -
260A ILE* 3.4 49.8 - - + -
262A LEU* 3.9 15.5 - - + -
270A THR* 4.3 9.2 - - - +
273A VAL* 3.1 38.7 - - + +
274A MET 3.1 24.8 + - - -
275A GLY 4.7 0.2 - - - -
276A PRO 2.9 17.1 + - - +
277A LYS* 3.4 13.6 - - + -
278A TYR* 2.9 27.5 + - - -
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 4.7 4.3 - - + +
139A LYS* 3.6 46.9 - - + +
140A LEU* 4.0 17.7 - - + -
143A LEU* 4.0 11.9 - - + -
149A TRP* 1.3 78.5 - - - +
151A THR* 1.3 63.7 + - - +
152A ILE* 5.4 0.4 - - + -
260A ILE 2.9 10.3 + - - +
261A LEU* 3.4 24.6 - - + +
262A LEU* 3.0 28.1 + - - +
278A TYR* 3.4 13.5 - - + +
280A VAL* 4.7 9.6 - - + -
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Residues in contact with THR 151 (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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149A TRP* 4.8 2.9 - - - +
150A VAL* 1.3 75.9 + - - +
152A ILE* 1.3 60.9 + - - +
153A HIS* 3.9 6.8 + - + -
262A LEU* 3.5 29.9 - - + +
264A THR* 3.4 32.1 - - + -
267A LYS* 5.0 9.2 - - + +
269A VAL* 5.3 1.1 - - + -
270A THR* 4.5 15.3 + - - +
278A TYR 2.8 15.0 + - - -
279A VAL* 3.3 12.4 - - + +
280A VAL* 2.8 31.9 + - - +
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Residues in contact with ILE 152 (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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136A ILE* 3.6 34.5 - - + -
150A VAL* 5.4 0.4 - - + -
151A THR* 1.3 73.7 - - - +
153A HIS* 1.3 60.5 + - - +
160A LYS* 3.8 22.2 - - + +
163A LEU* 4.7 3.1 - - + -
164A ALA* 3.8 28.3 - - + +
261A LEU* 3.8 26.2 - - + -
262A LEU 2.9 10.6 + - - +
263A THR* 3.2 8.0 - - + -
264A THR* 3.0 25.8 + - - +
280A VAL* 3.4 8.1 - - + +
282A VAL* 3.5 29.4 - - + -
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Residues in contact with HIS 153 (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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151A THR* 4.3 2.5 - - + -
152A ILE* 1.3 75.2 - - - +
154A GLY* 1.3 57.7 + - - +
160A LYS* 3.8 5.2 - - - -
264A THR* 3.1 26.0 - - + +
265A ARG 5.0 3.4 + - - -
267A LYS* 3.9 44.4 + - + +
279A VAL* 3.2 35.4 - - + +
280A VAL 3.1 7.9 + - - -
281A PRO* 3.6 28.9 - - + +
282A VAL* 2.7 32.9 + - - +
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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