Contacts of the strand formed by residues 242 - 251 (chain B) in PDB entry 5MJ6
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 GLN 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PHE* 3.8 19.9 - - + -
163B TRP* 3.4 21.1 - - - +
165B GLN 3.1 22.6 + - - +
166B ILE* 3.2 20.0 + - - +
168B LEU* 3.9 14.3 - - + +
208B ILE* 3.7 12.6 - - + +
209B LEU 3.1 11.7 - - - +
210B HIS* 4.0 7.5 + - + -
211B SER 4.6 0.9 - - - +
236B GLU* 3.8 1.9 - - - +
237B TYR* 2.8 36.9 + - - +
238B ALA* 5.1 0.5 - - - -
240B HIS* 3.1 27.2 + - + +
241B GLY* 1.3 81.1 - - - +
243B ILE* 1.3 60.7 + - - +
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Residues in contact with ILE 243 (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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161B PHE* 3.9 3.1 - - - -
207B ILE 3.8 0.3 - - - +
208B ILE* 3.5 6.4 - - - +
209B LEU* 2.9 57.7 + - + +
211B SER* 3.6 37.0 - - - +
216B ILE* 4.2 13.7 - - + -
234B ILE* 4.2 14.6 - - + -
235B LEU 3.2 12.6 - - - +
236B GLU* 4.4 17.0 - - + +
241B GLY 4.2 0.4 + - - -
242B GLN* 1.3 78.5 - - - +
244B ALA* 1.3 60.7 + - - +
245B ILE* 4.2 1.3 - - + +
261B ILE* 4.0 24.9 - - + -
304B PRO* 4.2 2.2 - - + -
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 3.5 23.1 - - + -
162B PRO* 3.7 24.0 - - + -
206B ASN* 5.5 0.7 - - - +
207B ILE 3.4 4.3 - - - -
208B ILE* 3.8 10.1 - - + -
234B ILE* 3.2 10.1 - - - +
235B LEU* 2.8 39.3 + - + +
243B ILE* 1.3 74.6 - - - +
245B ILE* 1.3 63.5 + - - +
246B VAL* 3.5 2.6 + - + +
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Residues in contact with ILE 245 (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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206B ASN* 3.5 5.9 - - - +
207B ILE* 2.8 60.5 + - + +
209B LEU* 4.9 6.7 - - + -
219B VAL* 3.5 22.2 - - + -
221B PHE* 5.0 3.6 - - + -
232B ALA* 4.1 20.6 - - + -
233B GLU 3.8 2.5 - - - -
234B ILE* 3.4 22.7 - - + -
243B ILE* 4.2 1.1 - - + -
244B ALA* 1.3 68.7 - - - +
246B VAL* 1.3 59.6 + - - +
247B ALA* 3.0 13.2 + - + +
259B LEU* 3.7 27.6 - - + -
261B ILE* 4.2 11.2 - - + -
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Residues in contact with VAL 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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162B PRO* 5.9 0.7 - - + -
205B TRP 5.4 0.2 - - - +
206B ASN* 3.6 13.7 - - - +
232B ALA* 3.7 12.3 - - - +
233B GLU* 3.1 40.8 + - + +
235B LEU* 3.8 32.5 - - + -
244B ALA* 4.2 4.3 - - + +
245B ILE* 1.3 70.3 - - - +
247B ALA* 1.3 67.0 + - - +
248B PRO* 3.4 2.3 - - - +
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Residues in contact with ALA 247 (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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205B TRP* 3.2 35.3 + - - +
207B ILE* 4.5 10.3 - - + -
221B PHE* 4.6 4.0 - - + -
245B ILE* 3.0 13.8 + - - +
246B VAL* 1.3 76.5 - - - +
248B PRO* 1.3 71.4 - - + +
249B GLU 3.1 11.0 + - - +
251B LEU* 3.8 24.5 - - + -
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Residues in contact with PRO 248 (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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205B TRP* 3.8 9.4 - - - -
221B PHE* 3.9 36.6 - - + -
230B LYS* 4.3 27.4 - - + -
231B GLN 4.5 10.3 - - - +
232B ALA* 4.0 7.6 - - + -
246B VAL 3.4 5.1 - - - +
247B ALA* 1.3 85.4 - - + +
249B GLU* 1.3 61.3 + - + +
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Residues in contact with GLU 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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205B TRP* 3.5 7.8 - - - -
221B PHE* 3.9 20.4 - - + -
223B SER* 3.5 26.2 + - - -
230B LYS* 4.2 23.3 + - - +
247B ALA* 3.1 6.0 + - - +
248B PRO* 1.3 87.8 - - + +
250B ALA* 1.3 73.9 + - - +
251B LEU* 3.3 15.8 + - - +
257B TYR* 3.9 10.4 + - - -
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Residues in contact with ALA 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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203B VAL* 4.8 10.3 - - + -
204B THR 3.7 8.3 - - - +
205B TRP* 3.2 44.5 - - + +
249B GLU* 1.3 82.3 - - - +
251B LEU* 1.3 66.0 + - - +
252B LEU* 3.6 14.8 + - + +
257B TYR* 4.0 2.8 + - - -
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Residues in contact with LEU 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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172B VAL* 4.4 14.8 - - + -
198B VAL* 4.9 5.2 - - + -
200B ALA* 4.0 9.6 - - + -
202B GLN 3.8 0.5 - - - +
203B VAL* 3.2 10.7 - - - +
204B THR* 2.8 50.0 + - + +
205B TRP 4.4 2.5 - - - -
207B ILE* 4.1 22.7 - - + -
221B PHE* 4.0 22.9 - - + -
247B ALA* 3.8 19.5 - - + -
249B GLU 3.7 11.2 - - - +
250B ALA* 1.3 71.3 - - - +
252B LEU* 1.3 60.0 + - - +
257B TYR* 3.3 32.8 - - + -
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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