Contacts of the strand formed by residues 261 - 268 (chain A) in PDB entry 4RTL
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 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU* 4.2 28.7 - - + -
228A HIS* 4.4 26.5 - - + +
229A ASP 4.5 9.9 - - - +
230A THR* 5.5 1.1 - - + -
247A VAL* 4.3 5.5 - - - +
248A ARG 3.7 12.3 + - - -
249A ARG* 3.5 17.8 + - + +
251A ILE 5.7 4.0 - - - +
259A LYS* 4.4 9.2 - - + +
260A LYS* 1.3 79.8 - - - +
262A ASP* 1.3 78.8 + - - +
263A GLU* 4.6 4.0 - - - +
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A HIS* 4.1 0.2 - - - -
229A ASP* 3.2 30.2 + - + +
244A VAL* 4.4 14.6 - - + +
245A VAL 3.4 14.8 - - - +
246A LYS* 4.1 10.1 - - - +
247A VAL* 3.8 6.5 + - - +
248A ARG* 3.6 22.0 + - - +
260A LYS* 5.3 2.5 - - - +
261A VAL* 1.3 85.7 + - - +
263A GLU* 1.3 70.9 + - - +
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Residues in contact with GLU 263 (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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17A LEU* 4.6 20.2 - - + +
184A TYR* 4.1 12.2 + - - -
227A ASN 3.3 19.3 - - - +
228A HIS* 3.1 32.5 + - - -
229A ASP* 4.1 5.1 - - - +
244A VAL* 3.9 3.8 - - - -
245A VAL* 3.1 41.4 + - + +
247A VAL* 4.1 22.7 - - + +
249A ARG* 5.8 1.7 + - - -
261A VAL* 4.6 5.2 - - - +
262A ASP* 1.3 82.0 - - - +
264A LEU* 1.3 63.3 + - - +
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Residues in contact with LEU 264 (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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226A SER* 3.5 9.2 - - - -
227A ASN 3.0 33.4 + - - +
228A HIS 4.1 3.8 - - - +
229A ASP* 4.0 21.1 - - + +
233A THR* 4.2 23.6 - - - +
234A ARG* 4.8 10.5 - - + +
237A TYR* 4.4 22.7 - - + -
242A LEU* 4.1 25.6 - - + -
243A HIS 3.5 16.2 - - - +
244A VAL* 4.8 7.6 - - + +
245A VAL* 5.1 0.2 - - - -
263A GLU* 1.3 80.6 - - - +
265A LEU* 1.3 82.4 + - - +
266A ALA 4.9 0.2 - - - +
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Residues in contact with LEU 265 (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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17A LEU* 6.4 2.2 - - + -
20A ASP* 4.0 29.4 - - + +
21A ILE* 4.7 16.6 - - + +
24A HIS* 4.3 17.5 - - + +
179A TYR* 5.4 0.9 - - + -
224A LEU* 4.7 18.8 - - + -
225A ILE 3.5 5.8 - - - +
226A SER* 3.6 27.4 - - - -
241A LYS 3.8 0.7 - - - +
242A LEU* 3.6 5.0 - - - -
243A HIS* 3.1 43.7 + - + +
245A VAL* 4.4 19.3 - - + -
264A LEU* 1.3 79.7 - - - +
266A ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 266 (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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223A VAL 4.0 0.9 - - - +
224A LEU* 3.3 6.6 - - - +
225A ILE* 3.0 40.4 + - + +
237A TYR* 4.2 24.5 - - + -
240A ALA* 4.1 10.3 - - + -
241A LYS 3.6 4.0 - - - -
242A LEU* 3.6 20.9 - - + -
264A LEU* 4.9 0.4 - - + +
265A LEU* 1.3 74.7 - - - +
267A LEU* 1.3 61.2 + - - +
268A TYR* 4.2 6.1 + - + -
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Residues in contact with LEU 267 (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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24A HIS* 3.9 29.2 - - + +
26A PRO* 4.4 17.9 - - + -
222A PRO* 6.1 0.2 - - + -
223A VAL 3.8 9.4 - - - +
224A LEU* 4.0 15.0 - - + -
240A ALA* 3.6 6.6 - - - +
241A LYS* 3.1 43.1 + - + +
243A HIS* 5.5 12.3 - - + +
265A LEU 4.4 0.4 - - - -
266A ALA* 1.3 72.6 - - - +
268A TYR* 1.3 69.3 + - - +
269A LYS* 3.8 16.8 + - + +
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Residues in contact with TYR 268 (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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210A ALA* 4.4 9.4 + - - +
213A ALA* 4.1 23.8 - - + +
214A GLU* 4.0 27.8 + - + +
217A VAL* 4.0 26.8 - - + +
222A PRO* 3.7 8.7 - - - +
223A VAL* 3.1 44.7 + - + +
225A ILE* 4.4 15.7 - - + -
236A TRP 4.3 3.3 + - - -
237A TYR* 3.9 28.8 - + - -
239A ARG* 4.2 17.9 - - + -
240A ALA* 3.8 23.1 - - + +
266A ALA* 4.6 9.0 - - + -
267A LEU* 1.3 75.3 - - - +
269A LYS* 1.3 59.5 + - - +
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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