Contacts of the strand formed by residues 255 - 263 (chain B) in PDB entry 6E7P
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 THR 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B VAL* 5.6 4.7 - - + -
236B ARG* 4.7 15.5 - - + -
237B LEU 3.4 9.0 - - - +
238B LYS* 3.1 36.5 + - + +
253B CYS 4.8 0.7 + - - -
254B TYR* 1.3 84.3 + - - +
256B PHE* 1.3 71.4 + - - +
257B SER* 5.1 0.3 - - - -
278B GLN 3.5 1.2 - - - +
279B ALA* 4.8 0.2 - - - -
280B HIS* 3.3 47.3 + - + +
282B GLN* 4.3 4.8 + - - +
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Residues in contact with PHE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 3.9 13.7 - + - -
94B ARG* 4.7 15.3 - - + -
97B ASN* 3.3 39.3 - - + -
98B THR* 5.7 0.2 - - + -
101B PHE* 4.4 24.0 - + + -
147B TYR* 4.6 6.7 - + - -
236B ARG* 3.3 9.9 - - - +
237B LEU* 2.8 43.4 + - + +
239B THR* 3.9 26.0 - - + -
254B TYR* 4.4 5.6 - + + -
255B THR* 1.3 77.0 - - - +
257B SER* 1.3 60.3 + - - +
258B VAL* 4.1 3.4 - - + -
277B THR* 4.4 21.1 - - + -
278B GLN 4.0 2.2 - - - -
279B ALA* 4.2 22.9 - - + -
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Residues in contact with SER 257 (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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157B TRP* 5.3 4.9 - - - -
234B HIS* 5.9 0.7 + - - -
235B PHE 3.7 5.5 + - - -
236B ARG* 4.2 14.8 - - - +
255B THR 5.1 0.4 - - - -
256B PHE* 1.3 77.6 - - - +
258B VAL* 1.3 64.4 + - - +
259B LEU* 3.8 1.2 + - - +
276B GLU 3.3 12.0 - - - +
277B THR* 3.3 10.5 - - - +
278B GLN* 3.4 34.8 + - - +
280B HIS* 6.5 0.2 - - - -
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Residues in contact with VAL 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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101B PHE* 4.2 27.6 - - + -
105B PHE* 5.0 2.2 - - + -
233B ILE 3.5 3.8 - - - +
234B HIS* 3.6 5.0 + - - +
235B PHE* 2.9 73.0 + - + +
236B ARG* 5.7 0.2 - - - -
237B LEU* 5.3 2.2 - - + -
256B PHE* 4.9 3.1 - - + -
257B SER* 1.3 79.9 + - - +
259B LEU* 1.3 62.1 + - - +
260B ILE* 4.1 19.5 - - + +
275B LEU* 4.3 14.1 - - + -
276B GLU 3.3 7.6 - - - +
277B THR* 4.5 4.5 - - + -
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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
----------------------------------------------------------
232B THR* 3.9 19.1 - - + -
233B ILE 3.4 9.2 - - - +
234B HIS* 3.5 35.2 - - + +
257B SER 3.8 1.1 + - - +
258B VAL* 1.3 73.7 - - - +
260B ILE* 1.3 62.4 + - - +
261B THR* 3.4 19.1 + - - +
275B LEU* 3.4 4.5 + - - -
276B GLU* 3.2 46.8 + - + +
278B GLN* 5.9 3.8 - - - +
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Residues in contact with ILE 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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105B PHE* 3.9 35.9 - - + +
106B LEU* 4.4 11.4 - - + -
132B ALA* 4.3 14.1 - - + +
231B VAL 3.9 1.0 - - - +
232B THR* 3.5 4.5 - - - -
233B ILE* 3.0 48.4 + - + +
235B PHE* 4.5 4.7 - - + -
258B VAL* 4.1 12.3 - - + -
259B LEU* 1.3 73.3 - - - +
261B THR* 1.3 62.8 + - - +
262B PHE* 3.8 28.5 - - + -
273B ILE* 4.8 2.2 - - + -
274B SER 3.6 11.0 - - - +
275B LEU* 4.1 18.2 - - + -
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Residues in contact with THR 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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230B ASN* 5.2 4.7 - - + +
231B VAL 3.9 2.0 - - - -
232B THR* 4.7 12.1 - - + +
259B LEU* 3.4 31.1 + - - +
260B ILE* 1.3 73.3 - - - +
262B PHE* 1.3 64.0 + - - +
263B ASP* 3.5 27.4 + - + +
272B PRO 3.6 0.5 - - - +
273B ILE* 3.5 6.9 - - - +
274B SER* 3.2 40.9 + - - +
276B GLU* 5.5 2.3 - - - +
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Residues in contact with PHE 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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106B LEU* 5.8 1.1 - - + -
125B LEU* 3.6 25.4 - - + -
128B ALA* 3.7 30.3 - - + -
129B ILE* 4.0 17.5 - - + -
132B ALA* 5.5 1.1 - - + -
230B ASN* 3.4 4.4 - - - -
231B VAL* 2.8 57.5 + - + +
233B ILE* 4.2 13.2 - - + -
260B ILE* 3.8 27.1 - - + -
261B THR* 1.3 71.6 - - - +
263B ASP* 1.3 62.2 + - - +
264B ASN* 3.6 1.6 + - - +
271B ILE* 3.8 12.1 - - + +
272B PRO 3.7 3.4 - - - -
273B ILE* 3.7 37.0 - - + -
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Residues in contact with ASP 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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230B ASN* 4.0 20.2 + - - +
261B THR* 3.5 17.4 - - + +
262B PHE* 1.3 73.9 - - - +
264B ASN* 1.3 59.9 + - - +
265B LYS* 2.6 53.2 + - - +
271B ILE* 3.3 6.0 - - - +
272B PRO* 3.2 43.8 + - + +
274B SER* 6.0 1.8 - - - +
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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