Contacts of the strand formed by residues 245 - 254 (chain B) in PDB entry 5E5R
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 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237B LEU* 4.9 7.2 - - + -
239B ALA* 3.5 31.9 - - + -
243B SER* 4.2 4.0 - - - +
244B THR* 1.3 77.4 - - - +
246B ARG* 1.3 61.3 + - - +
247B LEU* 4.2 10.5 - - + -
282B LEU 3.5 0.3 - - - +
283B GLU* 3.4 3.3 - - - +
284B ILE* 2.8 63.9 + - + +
287B PHE* 4.0 19.3 - - + -
312B LEU* 3.8 15.0 - - + -
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Residues in contact with ARG 246 (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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177B GLU* 4.8 8.3 - - - +
233B PHE* 5.5 0.3 - - - +
237B LEU* 5.5 2.3 - - - +
244B THR* 4.0 27.8 + - - +
245B VAL* 1.3 79.0 - - - +
247B LEU* 1.3 65.9 + - - +
248B GLU* 3.6 6.5 + - + +
276B ARG* 4.8 7.1 - - - +
281B MET* 3.7 34.4 - - + -
282B LEU 3.2 5.6 - - - -
283B GLU* 2.7 38.6 + - + +
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PHE* 4.0 19.1 - - + -
237B LEU* 3.5 32.5 - - + -
245B VAL* 4.2 7.6 - - + -
246B ARG* 1.3 72.9 - - - +
248B GLU* 1.3 61.2 + - - +
261B TRP* 3.6 27.3 - - + -
281B MET* 3.1 5.9 - - - -
282B LEU* 2.7 48.9 + - + +
284B ILE* 4.7 1.1 - - + -
295B TYR* 3.8 37.2 - - + -
312B LEU* 3.9 23.6 - - + -
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 3.9 19.6 - - + -
174B VAL 4.4 1.0 - - - +
175B SER* 2.5 31.5 + - - -
176B GLN* 2.8 31.5 + - - +
177B GLU* 3.7 19.1 + - + +
231B VAL* 3.7 15.3 - - + +
232B GLN* 3.1 4.8 - - - -
233B PHE* 3.0 33.1 + - - +
246B ARG 3.6 5.6 + - - +
247B LEU* 1.3 75.2 - - - +
249B CYS* 1.3 64.1 + - - +
261B TRP* 4.1 0.4 - - - -
280B GLY 3.5 3.4 - - - +
281B MET* 4.5 16.9 - - + +
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Residues in contact with CYS 249 (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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173B PHE* 5.0 0.2 - - - -
229B ILE* 3.7 33.7 - - - -
231B VAL* 3.5 4.5 - - - -
232B GLN* 4.6 0.4 - - - -
233B PHE* 5.1 0.4 - - + -
248B GLU* 1.3 76.3 - - - +
250B PHE* 1.3 60.0 + - - +
259B ILE* 3.7 13.9 - - + +
261B TRP* 3.5 13.4 - - + -
280B GLY* 2.6 32.8 + - - +
297B CYS* 2.0 46.7 - - + -
308B ALA* 4.2 4.3 - - - -
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Residues in contact with PHE 250 (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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169B ASP 4.5 3.8 - - - -
170B SER* 3.6 28.5 - - - -
171B ARG 3.8 15.0 - - - -
173B PHE* 3.3 47.1 - + + -
182B TYR* 3.5 37.2 - + + -
184B ALA* 4.0 13.9 - - + -
229B ILE* 3.5 4.3 - - - -
230B GLU* 2.8 23.8 + - - +
231B VAL* 3.1 20.5 + - + +
249B CYS* 1.3 78.6 - - - +
251B ALA* 1.3 85.2 + - - +
252B LEU* 4.7 1.1 - - + -
259B ILE* 4.4 9.6 - - + -
278B PHE 6.2 0.2 - - - -
280B GLY* 4.9 4.5 - - - -
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Residues in contact with ALA 251 (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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184B ALA* 3.5 13.3 - - - +
227B PRO* 4.1 0.2 - - + -
228B LYS 3.1 25.1 - - - +
229B ILE* 3.7 5.2 - - + -
230B GLU 4.1 0.2 - - - +
250B PHE* 1.3 85.6 - - - +
252B LEU* 1.3 66.1 + - - +
257B PRO* 3.4 22.7 - - + +
259B ILE* 4.5 3.4 - - + +
299B ALA* 3.8 27.8 - - + -
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Residues in contact with LEU 252 (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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297A LYS 5.3 0.9 - - - +
298A SER 5.8 0.2 - - - -
299A VAL* 3.7 22.2 - - + +
139B GLY* 3.5 29.4 - - - +
140B VAL* 3.6 8.5 - - - +
141B VAL* 4.2 17.7 - - + -
182B TYR* 4.7 10.8 - - + -
183B ILE 3.4 29.6 - - - +
184B ALA* 3.5 9.2 - - - +
225B TYR* 4.2 5.5 - - + +
226B GLU 3.9 1.0 - - - +
227B PRO* 3.2 2.9 - - - +
228B LYS* 2.7 42.1 + - + +
230B GLU* 4.3 19.9 - - + +
250B PHE* 4.7 0.2 - - + -
251B ALA* 1.3 75.6 - - - +
253B GLY* 1.3 58.2 + - - +
257B PRO* 3.8 0.7 - - - -
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Residues in contact with GLY 253 (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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184B ALA 3.4 16.9 + - - +
185B LYS* 3.7 5.2 - - - +
225B TYR* 3.7 14.5 + - - -
227B PRO* 4.3 0.7 - - - -
252B LEU* 1.3 77.2 - - - +
254B ASN* 1.3 60.8 + - - +
255B PRO 3.1 16.0 - - - +
256B VAL* 3.6 2.9 + - - -
257B PRO* 3.5 20.6 - - - +
301B ASN* 4.2 5.6 - - - -
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Residues in contact with ASN 254 (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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137B GLY* 3.7 22.5 + - - +
185B LYS* 3.9 21.4 - - + +
222B MET 3.5 11.1 + - - -
223B GLY 3.0 28.5 + - - +
224B GLU* 3.0 14.7 - - - +
225B TYR* 2.8 45.7 + - + +
253B GLY* 1.3 74.1 - - - +
255B PRO* 1.4 71.4 + - - +
301B ASN* 3.7 1.6 - - - -
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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