Contacts of the strand formed by residues 259 - 264 (chain D) 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 GLN 259 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D LEU* 3.3 36.2 - - + +
144D LYS 4.4 0.2 - - - +
145D GLY* 3.5 31.6 - - - +
146D GLU 3.1 25.3 + - - +
147D PRO 4.3 0.2 - - - -
148D GLY 3.7 4.0 - - - -
177D CYS 4.8 2.3 + - - +
178D PHE* 3.6 19.4 - - + -
231D MET* 5.9 0.8 - - - +
237D ARG* 4.2 7.6 - - - -
238D SER 3.6 28.6 + - - +
239D LEU* 3.5 8.9 - - + +
240D LEU* 3.0 25.3 + - - +
258D CYS* 1.3 71.4 - - - +
260D ILE* 1.3 63.2 + - - +
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Residues in contact with ILE 260 (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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143D LEU* 4.6 1.5 - - - +
148D GLY 2.9 8.0 + - - +
149D TRP* 3.4 38.3 - - + -
150D VAL* 2.9 28.5 + - - +
239D LEU* 4.0 4.0 - - - +
240D LEU* 3.3 20.2 - - + +
242D LEU* 3.7 22.7 - - + -
254D PHE* 3.5 35.7 - - + +
258D CYS* 3.7 20.6 - - + +
259D GLN* 1.3 80.8 - - - +
261D LEU* 1.3 69.8 + - - +
262D LEU* 4.1 4.0 - - + -
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Residues in contact with LEU 261 (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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136D ILE* 4.1 8.5 - - + -
140D LEU* 4.2 14.8 - - + -
150D VAL* 3.4 33.9 - - + +
152D ILE* 3.7 25.1 - - + -
164D ALA* 3.9 35.2 - - + +
168D VAL* 4.9 0.7 - - + -
239D LEU* 3.8 22.4 - - + +
240D LEU 2.9 7.6 + - - +
241D ILE* 3.1 22.3 - - + +
242D LEU 2.8 30.5 + - - -
260D ILE* 1.3 75.5 - - - +
262D LEU* 1.3 54.3 + - - +
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Residues in contact with LEU 262 (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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149D TRP* 3.9 31.4 - - + -
150D VAL 3.0 13.6 + - - +
151D THR* 3.4 29.8 - - + +
152D ILE* 2.8 29.1 + - - +
241D ILE* 5.3 0.4 - - - -
242D LEU* 3.1 22.4 - - + +
245D VAL* 4.3 5.8 - - + -
251D LEU* 4.1 17.0 - - + -
260D ILE* 4.1 6.5 - - + -
261D LEU* 1.3 75.2 - - - +
263D THR* 1.3 73.3 + - - +
264D THR* 4.5 0.7 - - - -
269D VAL* 3.8 28.9 - - + -
270D THR* 5.6 0.2 - - - +
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Residues in contact with THR 263 (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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152D ILE* 3.2 16.6 - - + -
160D LYS* 3.7 44.0 - - + +
161D SER* 4.5 0.2 - - - -
164D ALA* 4.1 14.6 - - + -
184D TRP* 6.0 0.2 - - + -
241D ILE* 5.8 1.8 - - + -
242D LEU 2.9 10.4 + - - +
243D ASP* 2.7 26.8 + - - +
244D ASP* 2.8 19.4 + - - +
245D VAL* 3.0 26.2 + - - +
262D LEU* 1.3 78.2 - - - +
264D THR* 1.3 63.5 + - - +
903D ADP 5.3 0.3 + - - -
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Residues in contact with THR 264 (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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151D THR* 3.5 29.8 - - + -
152D ILE 3.0 5.1 + - - +
153D HIS* 3.1 31.5 - - + -
154D GLY 3.2 4.9 + - - +
160D LYS* 3.7 8.1 - - - +
244D ASP* 4.7 3.6 - - - -
245D VAL 2.9 23.5 + - - +
262D LEU* 4.5 1.1 - - + -
263D THR* 1.3 77.4 - - - +
265D ARG* 1.3 57.2 + - - +
266D ASP* 2.8 44.4 + - - +
267D LYS* 4.0 0.4 - - - +
269D VAL* 3.7 12.7 - - + +
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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