Contacts of the strand formed by residues 257 - 266 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B THR* 2.7 31.3 + - - -
195B PHE* 3.7 22.8 - - + -
196B LYS 3.2 4.0 - - - -
197B GLN* 3.9 18.7 + - + +
248B ARG* 3.2 25.8 - - - +
253B ARG* 2.9 48.4 + - + +
254B PRO* 3.2 23.1 + - + +
255B ALA 4.0 1.7 - - - +
256B HIS* 1.3 81.6 + - + +
258B LYS* 1.3 63.1 + - - +
259B LEU 4.0 0.3 + - - -
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Residues in contact with LYS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B PHE* 3.4 2.1 - - - -
196B LYS* 2.8 50.1 + - - +
198B VAL* 4.7 21.8 - - + -
255B ALA 5.2 5.2 - - - +
256B HIS 3.9 0.6 + - - -
257B GLU* 1.3 74.4 - - - +
259B LEU* 1.3 67.6 + - - +
260B LEU* 6.2 0.2 - - + -
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LEU* 4.0 14.4 - - + -
194B ILE 3.3 17.3 - - - +
195B PHE* 3.6 33.7 - - + -
240B PRO* 4.1 27.4 - - + +
241B LEU* 3.2 18.6 - - + +
244B GLY* 3.9 23.4 + - - +
247B LEU* 4.0 29.2 - - + -
248B ARG* 5.7 0.4 - - - +
257B GLU 4.0 0.4 + - - -
258B LYS* 1.3 79.3 - - - +
260B LEU* 1.3 70.1 + - - +
261B MET 3.5 19.3 - - - +
262B LEU* 5.2 0.9 - - + -
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ILE* 4.6 15.2 - - + +
194B ILE* 3.0 16.6 + - + +
196B LYS* 4.6 22.0 - - + +
214B GLU* 4.3 19.1 - - + +
217B VAL* 3.6 32.8 - - + -
218B SER* 3.7 26.0 - - - +
221B CYS* 4.7 5.4 - - - -
239B THR* 3.4 19.2 - - - +
241B LEU* 3.2 24.5 - - + +
258B LYS* 4.7 2.2 - - + +
259B LEU* 1.3 82.9 - - - +
261B MET* 1.3 65.1 - - + +
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Residues in contact with MET 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ILE* 3.9 17.0 - - + -
219A ILE* 3.7 22.4 - - + -
192B ILE 3.8 0.3 - - - +
193B LEU* 3.5 3.1 - - - -
194B ILE* 3.0 36.6 + - + -
218B SER* 5.2 0.4 - - - -
221B CYS* 3.6 41.7 - - + +
225B LEU* 5.3 2.0 - - - -
237B THR* 3.7 19.3 - - + -
238B THR 3.2 16.2 - - - +
239B THR* 4.3 3.6 - - + +
240B PRO* 4.8 0.4 - - - -
259B LEU* 3.5 8.4 - - - +
260B LEU* 1.3 83.3 - - + +
262B LEU* 1.3 59.0 + - - +
263B LEU* 3.8 26.7 - - + -
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ILE* 4.3 6.5 - - + -
153B ILE* 3.5 31.0 - - + -
185B LEU* 4.0 18.8 - - + -
191B LEU* 4.0 11.9 - - + -
192B ILE 3.4 2.7 - - - -
193B LEU* 3.9 32.3 - - + +
236B VAL 3.6 2.8 - - - +
238B THR* 2.6 50.9 + - - +
240B PRO* 4.2 15.7 - - + +
247B LEU* 5.0 3.4 - - + -
259B LEU* 5.2 1.1 - - + -
261B MET* 1.3 74.1 - - - +
263B LEU* 1.3 64.2 + - - +
264B PRO* 3.7 18.2 - - + +
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ILE* 2.8 40.3 + - + +
194B ILE* 4.2 11.7 - - + -
224B LEU* 3.7 30.1 - - + -
225B LEU* 3.9 22.2 - - + -
228B LEU* 4.0 13.7 - - + -
235B THR* 3.3 11.4 - - - +
237B THR* 3.5 34.3 - - - +
261B MET* 3.8 18.4 - - + -
262B LEU* 1.3 77.2 - - - +
264B PRO* 1.3 66.4 - - - +
265B VAL* 3.4 10.0 - - + +
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Residues in contact with PRO 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 4.0 7.5 - - + +
184B TYR* 3.7 24.5 - - + +
185B LEU* 4.4 1.3 - - + -
188B ALA* 4.0 12.1 - - + -
190B ILE 3.7 0.2 - - - +
191B LEU* 3.6 25.4 - - + -
235B THR* 2.4 33.0 + - - +
236B VAL* 3.3 39.3 - - + +
238B THR* 4.9 1.6 - - + +
262B LEU* 3.7 12.7 - - + +
263B LEU* 1.3 84.0 - - - +
265B VAL* 1.3 57.7 + - - +
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 4.3 3.1 - - - -
111B VAL* 4.9 2.2 - - + +
116B ILE* 4.2 22.0 - - + -
188B ALA* 3.9 1.6 - - - +
189B PRO* 3.2 23.9 - - - +
190B ILE* 2.9 25.3 + - + +
192B ILE* 4.0 21.5 - - + -
228B LEU* 4.1 24.5 - - + -
233B LEU* 4.3 9.0 - - + -
234B VAL 3.5 5.8 - - - +
235B THR* 4.1 6.5 - - - +
263B LEU* 3.4 20.4 - - + +
264B PRO* 1.3 80.2 - - - +
266B GLY* 1.3 63.3 + - - +
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Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 3.7 13.3 - - - +
111B VAL* 4.1 9.6 - - - -
189B PRO* 3.9 12.1 - - - -
233B LEU* 3.7 9.2 - - - -
234B VAL* 2.9 33.1 + - - +
265B VAL* 1.3 78.2 - - - +
267B TYR* 1.3 64.2 + - - -
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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