Contacts of the strand formed by residues 257 - 266 (chain A) in PDB entry 4TTB
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 GLU 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A THR* 2.7 31.8 + - - -
195A PHE* 3.8 19.9 - - + +
196A LYS 3.2 6.1 - - - +
197A GLN* 4.1 12.2 + - + +
248A ARG* 3.2 24.6 - - - +
253A ARG* 2.8 41.7 + - + +
254A PRO* 3.3 25.7 - - + +
255A ALA 3.1 4.8 - - - +
256A HIS* 1.3 92.4 + - + +
258A LYS* 1.3 63.9 + - - +
259A LEU 4.1 0.5 + - - -
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Residues in contact with LYS 258 (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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195A PHE* 3.2 4.9 - - - -
196A LYS* 2.7 68.4 + - - +
198A VAL* 4.7 12.3 - - + -
241A LEU* 6.2 3.1 - - - -
255A ALA 6.0 0.7 - - - +
256A HIS 4.0 1.1 + - - +
257A GLU* 1.3 76.4 - - - +
259A LEU* 1.3 68.1 + - - +
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Residues in contact with LEU 259 (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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193A LEU* 4.0 12.8 - - + -
194A ILE 3.3 21.5 - - - +
195A PHE* 3.7 31.4 - - + -
240A PRO* 4.0 28.3 - - + +
241A LEU* 3.2 20.6 - - + +
244A GLY* 3.9 23.6 - - - +
247A LEU* 3.7 31.9 - - + -
248A ARG* 5.8 0.4 - - - +
257A GLU 4.1 0.4 + - - -
258A LYS* 1.3 80.6 - - - +
260A LEU* 1.3 64.7 + - - +
261A MET 3.5 17.0 - - - +
262A LEU* 5.2 0.4 - - + -
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Residues in contact with LEU 260 (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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194A ILE* 2.8 18.1 + - + +
196A LYS* 4.5 18.4 - - + +
214A GLU* 4.2 24.7 - - + +
217A VAL* 4.2 19.1 - - + -
218A SER* 4.0 22.9 - - - +
221A CYS* 4.1 10.3 - - - -
239A THR* 3.4 26.0 - - - +
241A LEU* 3.8 10.2 - - + +
258A LYS 3.6 0.6 + - - -
259A LEU* 1.3 77.7 - - - +
261A MET* 1.3 84.6 + - + +
215B ILE* 4.2 16.1 - - + +
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Residues in contact with MET 261 (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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193A LEU* 3.4 3.3 - - - -
194A ILE* 2.8 41.0 + - + -
218A SER* 5.5 0.2 - - - -
221A CYS* 3.5 36.3 - - + -
225A LEU* 5.1 3.4 - - - -
237A THR* 3.7 18.4 - - + -
238A THR 3.3 12.3 - - - +
239A THR* 4.3 3.1 - - + +
240A PRO* 4.6 1.1 - - - -
259A LEU* 3.5 7.4 - - - +
260A LEU* 1.3 93.2 - - + +
262A LEU* 1.3 63.9 + - - +
263A LEU* 3.9 24.5 - - + -
215B ILE* 4.1 6.5 - - + -
219B ILE* 3.6 25.8 - - + -
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Residues in contact with LEU 262 (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 ILE* 4.3 5.6 - - + -
153A ILE* 3.4 32.1 - - + -
185A LEU* 4.1 17.0 - - + -
191A LEU* 4.4 13.7 - - + -
192A ILE 3.5 3.1 - - - -
193A LEU* 3.8 29.6 - - + +
236A VAL 3.7 1.9 - - - +
238A THR* 2.6 50.9 + - - +
240A PRO* 3.9 18.2 - - + -
247A LEU* 4.8 2.0 - - + -
259A LEU* 5.2 0.7 - - + -
261A MET* 1.3 74.3 - - - +
263A LEU* 1.3 65.6 + - - +
264A PRO* 3.7 17.7 - - + +
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Residues in contact with LEU 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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192A ILE* 2.8 44.5 + - + +
194A ILE* 4.2 5.4 - - + -
224A LEU* 3.5 36.6 - - + -
225A LEU* 4.1 17.0 - - + -
228A LEU* 4.2 8.1 - - + -
235A THR* 3.3 13.5 - - - +
237A THR* 3.5 35.2 - - - +
261A MET* 3.9 20.6 - - + -
262A LEU* 1.3 77.4 - - - +
264A PRO* 1.3 66.4 - - - +
265A VAL* 3.5 10.5 + - + +
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Residues in contact with PRO 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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106A ILE* 4.0 7.6 - - + +
184A TYR* 3.7 25.6 - - + +
185A LEU* 4.4 1.8 - - + -
188A ALA* 4.1 11.0 - - + -
190A ILE 3.6 6.7 - - - +
191A LEU* 3.7 17.5 - - + -
234A VAL 3.7 0.2 - - - +
235A THR* 2.5 31.7 + - - -
236A VAL* 3.3 39.9 - - + +
238A THR* 4.8 2.0 - - - +
262A LEU* 3.7 13.4 - - + +
263A LEU* 1.3 83.1 - - - +
265A VAL* 1.3 58.2 + - - +
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Residues in contact with VAL 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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106A ILE* 4.4 0.2 - - - -
111A VAL* 5.1 1.3 - - + -
116A ILE* 4.5 14.4 - - + -
188A ALA* 3.8 4.7 - - - +
189A PRO* 3.3 22.0 - - - +
190A ILE* 2.7 30.5 + - + +
192A ILE* 3.9 20.9 - - + -
228A LEU* 4.1 31.9 - - + -
233A LEU* 4.4 14.8 - - + -
234A VAL 3.6 5.2 - - - +
235A THR* 4.2 0.9 - - - +
263A LEU* 3.5 20.2 - - + +
264A PRO* 1.3 81.0 - - - +
266A GLY* 1.3 64.0 + - - +
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Residues in contact with GLY 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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106A ILE* 3.8 13.8 - - - +
111A VAL* 4.1 8.7 - - - -
189A PRO* 3.9 12.1 - - - -
233A LEU* 3.7 9.6 - - - -
234A VAL* 3.0 33.4 + - - +
265A VAL* 1.3 78.2 - - - +
267A TYR* 1.3 64.0 + - - -
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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