Contacts of the strand formed by residues 172 - 184 (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 VAL 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B PRO* 4.4 6.2 + - + +
170B THR 4.2 0.5 - - - +
171B ALA* 1.3 82.8 - - + +
173B VAL* 1.3 69.1 + - - +
198B VAL* 3.6 35.0 - - + -
199B GLN 3.6 6.3 - - - +
200B ALA* 4.8 3.1 - - - -
204B THR* 4.1 21.8 - - + -
206B ASN 4.3 11.0 - - - +
207B ILE* 4.4 12.1 - - + -
251B LEU* 4.4 12.8 - - + -
306B PHE* 3.7 32.1 - - + -
311B PHE* 3.9 8.3 - - - -
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B THR 3.8 13.2 - - - +
172B VAL* 1.3 79.4 - - - +
174B PRO* 1.3 75.6 - - + +
175B LEU* 3.8 10.6 - - + +
198B VAL* 4.3 3.4 - - - -
199B GLN* 3.0 37.4 + - + +
201B LEU* 3.9 25.1 - - + -
311B PHE* 3.7 20.0 - - + -
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Residues in contact with PRO 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL* 1.3 93.2 - - + +
175B LEU* 1.3 66.1 + - - +
177B TYR* 3.7 32.1 - - + +
196B ILE* 4.2 3.8 - - + -
197B SER 3.6 6.5 - - - +
198B VAL* 4.3 5.6 - - + -
306B PHE* 3.6 34.5 - - + -
311B PHE* 3.8 34.8 - - + +
312B LYS 3.8 11.1 - - - +
313B ALA* 4.3 2.7 - - + -
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL* 3.8 17.5 - - + +
174B PRO* 1.3 86.1 - - - +
176B ARG* 1.3 72.6 + - + +
197B SER* 2.6 24.2 + - - +
198B VAL 4.2 6.1 - - - +
199B GLN* 4.2 17.7 - - + +
256B ASN* 4.1 15.5 - - - +
313B ALA* 3.4 8.2 - - - +
314B THR* 3.1 23.6 + - - +
353B LYS* 5.8 0.2 - - - +
1109B NAG 4.0 31.4 - - - +
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Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 1.3 93.9 - - + +
177B TYR* 1.3 67.0 + - - +
178B GLU* 5.7 5.7 + - - +
195B THR 3.5 2.0 + - - +
196B ILE* 3.5 3.3 - - - +
197B SER* 2.8 53.9 + - - +
313B ALA* 4.2 0.2 - - - +
314B THR* 3.4 18.6 - - + +
316B ILE* 4.0 19.2 - - - +
350B GLU* 3.4 21.1 + - - +
1109B NAG 5.3 12.3 - - - -
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PRO* 3.7 15.2 - - + +
176B ARG* 1.3 81.4 + - - +
178B GLU* 1.3 63.7 + - - +
179B LEU* 4.1 2.7 - - + +
194B VAL* 4.0 20.2 - - + -
195B THR 3.6 2.7 - - - -
196B ILE* 3.7 19.5 - - + -
303B PHE* 4.3 5.6 - + + -
304B PRO 4.1 0.4 - - - -
305B CYS* 3.5 23.7 - - + +
306B PHE* 3.0 39.8 + - - +
311B PHE 5.2 1.1 + - - -
313B ALA* 3.6 27.4 - - + -
314B THR 2.8 7.7 + - - +
315B PHE* 3.5 41.6 - + + -
316B ILE* 3.0 27.1 + - - +
356B THR* 4.1 6.1 - - + +
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG* 5.7 5.9 + - - +
177B TYR* 1.3 74.3 - - - +
179B LEU* 1.3 64.4 + - - +
180B SER* 5.1 3.4 - - - +
193B SER* 3.3 6.2 + - - +
194B VAL* 3.3 1.9 - - - -
195B THR* 2.8 51.0 + - - +
316B ILE* 3.5 28.4 - - + +
318B LYS* 3.5 33.3 + - + +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 4.1 4.9 - - + -
178B GLU* 1.3 73.4 - - - +
180B SER* 1.3 62.6 + - - +
181B LEU* 3.6 33.7 - - + -
193B SER 3.4 4.0 - - - +
194B VAL* 3.8 15.9 - - + +
263B TYR* 3.7 11.9 - - - +
303B PHE* 3.6 52.3 - - + -
315B PHE* 5.9 1.1 - - + -
316B ILE 2.8 13.1 + - - +
317B ILE* 3.4 23.0 - - + +
318B LYS* 2.8 26.0 + - - +
359B VAL* 5.2 0.2 - - + -
361B PHE* 4.0 8.3 - - + -
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 4.0 4.2 + - - -
179B LEU* 1.3 73.7 - - - +
181B LEU* 1.3 63.4 + - - +
191B ARG 4.0 0.2 - - - +
192B GLY* 3.3 5.4 - - - -
193B SER* 2.9 47.5 + - - -
318B LYS* 3.4 29.4 - - - -
320B ILE* 6.4 1.3 - - - -
345B GLN* 5.7 2.0 - - - -
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Residues in contact with LEU 181 (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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179B LEU* 3.6 23.3 - - + -
180B SER* 1.3 80.4 - - - +
182B HIS* 1.3 60.7 + - - +
183B PRO* 3.4 8.9 - - + +
190B PHE* 3.6 35.0 - - + -
191B ARG 3.7 3.6 - - - +
192B GLY* 4.3 1.3 - - - -
263B TYR* 3.9 14.1 - - - +
274B PHE* 5.0 2.7 - - + -
302B ALA* 5.2 1.6 - - + +
317B ILE* 5.0 1.1 - - + -
318B LYS 2.5 15.0 + - - +
319B ILE* 3.7 20.4 - - + -
320B ILE* 2.9 33.4 + - - +
361B PHE* 3.5 35.2 - - + -
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Residues in contact with HIS 182 (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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181B LEU* 1.3 74.7 - - - +
183B PRO* 1.3 62.9 - - - +
184B ASN* 3.8 0.7 + - + +
190B PHE* 3.2 5.7 - - - -
191B ARG* 2.9 45.4 + - + +
320B ILE* 3.2 48.4 - - + +
341B ASP* 5.7 1.1 - - - -
343B LEU* 3.8 12.0 - - + +
1M NAG 3.4 25.4 + - + -
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Residues in contact with PRO 183 (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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181B LEU* 3.4 12.3 - - + +
182B HIS* 1.3 91.2 - - - +
184B ASN* 1.3 61.8 + - - +
185B LEU* 4.0 15.8 + - + +
190B PHE* 3.6 9.2 - - + -
267B ILE* 4.3 7.2 - - + -
274B PHE* 4.1 34.5 - - + -
319B ILE* 4.1 16.8 - - + -
320B ILE 3.1 22.3 - - - +
321B ARG* 5.3 0.3 - - - -
363B VAL* 4.7 5.2 - - + -
1M NAG 3.6 21.1 - - - +
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Residues in contact with ASN 184 (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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182B HIS 3.8 1.0 + - - -
183B PRO* 1.3 72.6 - - - +
185B LEU* 1.3 61.3 + - - +
186B THR* 3.2 8.1 - - - -
187B SER* 2.9 40.8 + - - +
188B MET* 2.9 26.2 + - - -
189B THR* 2.8 20.2 + - - +
267B ILE* 4.4 2.1 - - - +
1M NAG 1.4 68.8 + - - +
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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