Contacts of the strand formed by residues 189 - 200 (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 THR 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B PRO* 3.7 0.3 - - - +
184B ASN* 2.8 29.2 + - - +
187B SER* 3.3 26.7 + - - +
188B MET* 1.3 84.3 - - - +
190B PHE* 1.3 67.5 + - - +
265B ALA 3.5 11.7 - - - -
266B ASN* 4.1 13.7 - - - +
267B ILE* 3.9 4.9 - - - +
1123B NAG 6.0 0.7 - - - +
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Residues in contact with PHE 190 (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* 3.6 28.9 - - + -
182B HIS 3.2 16.2 - - - +
183B PRO* 3.6 14.8 - - + -
189B THR* 1.3 78.1 - - - +
191B ARG* 1.3 67.0 + - - +
263B TYR* 3.9 9.9 - + - -
264B SER* 3.6 2.6 - - - -
265B ALA* 3.0 52.3 + - + +
266B ASN 3.0 24.7 - - - -
267B ILE* 3.5 19.1 - - + -
274B PHE* 4.2 21.8 - + + -
301B SER 4.5 2.7 - - - -
302B ALA* 3.5 35.0 - - + -
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Residues in contact with ARG 191 (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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180B SER 4.0 0.3 - - - +
181B LEU* 3.7 4.0 - - - +
182B HIS* 2.9 46.6 + - + +
190B PHE* 1.3 81.9 - - - +
192B GLY* 1.3 65.1 + - - +
217B SER* 5.0 8.7 + - - -
262B GLU* 5.0 13.5 + - - +
263B TYR 3.5 25.0 + - - +
264B SER* 4.2 15.0 - - - +
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Residues in contact with GLY 192 (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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180B SER 3.3 9.0 - - - -
181B LEU* 4.3 4.9 - - - -
191B ARG* 1.3 82.4 + - - +
193B SER* 1.3 61.7 + - - -
262B GLU* 3.4 4.7 - - - +
263B TYR* 2.8 61.8 + - - +
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 3.3 4.3 + - - +
179B LEU* 3.4 1.4 - - - +
180B SER* 2.9 48.9 + - - -
192B GLY* 1.3 75.9 - - - -
194B VAL* 1.3 62.8 + - - +
195B THR* 4.3 3.6 + - - -
260B LYS* 3.9 23.4 - - - +
261B ILE 3.5 5.4 - - - -
262B GLU* 4.6 11.6 - - - +
263B TYR* 4.1 0.2 - - - -
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 4.0 14.8 - - + -
178B GLU 3.3 7.4 - - - +
179B LEU* 3.8 9.0 - - + +
193B SER* 1.3 74.1 - - - +
195B THR* 1.3 65.2 + - - +
196B ILE* 3.7 24.2 - - + +
259B LEU 3.6 0.7 - - - +
260B LYS* 3.4 4.3 - - - +
261B ILE* 3.1 35.1 + - + +
263B TYR* 3.7 24.7 - - + -
303B PHE* 3.7 24.2 - - + -
304B PRO* 3.8 20.9 - - + +
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Residues in contact with THR 195 (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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176B ARG* 3.5 5.4 + - - +
177B TYR 3.6 0.2 - - - -
178B GLU* 2.8 49.9 + - + +
193B SER* 4.3 3.8 + - - -
194B VAL* 1.3 76.7 + - - +
196B ILE* 1.3 62.6 + - - +
197B SER* 3.8 4.8 + - - +
258B THR* 3.6 27.8 - - + -
259B LEU 3.1 4.7 - - - +
260B LYS* 3.5 25.0 - - + +
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Residues in contact with ILE 196 (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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174B PRO* 4.2 10.5 - - + -
176B ARG 3.5 4.7 - - - +
177B TYR* 3.7 28.3 - - + +
194B VAL* 3.7 19.7 - - + -
195B THR* 1.3 71.6 - - - +
197B SER* 1.3 62.2 + - - +
198B VAL* 3.6 20.9 + - + -
209B LEU* 4.1 12.1 - - + -
258B THR* 3.4 2.9 - - - -
259B LEU* 2.6 67.0 + - + +
261B ILE* 5.6 2.2 - - + -
304B PRO* 3.9 15.5 - - + +
305B CYS* 4.4 1.1 - - - -
306B PHE* 3.9 14.8 - - + -
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Residues in contact with SER 197 (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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174B PRO* 3.5 1.7 - - - +
175B LEU* 2.6 43.2 + - - +
176B ARG* 2.8 50.0 + - - +
195B THR* 4.7 5.0 + - - +
196B ILE* 1.3 72.9 - - - +
198B VAL* 1.3 55.5 + - - +
257B TYR 3.7 7.0 - - - -
258B THR* 4.1 11.7 + - - +
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Residues in contact with VAL 198 (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* 3.6 28.5 - - + -
173B VAL 3.5 7.2 - - - +
174B PRO* 4.4 1.8 - - + -
175B LEU* 4.2 3.7 - - - +
196B ILE* 3.6 28.3 - - + +
197B SER* 1.3 78.8 - - - +
199B GLN* 1.3 64.5 + - - +
207B ILE* 5.7 4.5 - - + -
251B LEU* 4.9 4.5 - - + -
256B ASN* 3.5 7.6 - - - +
257B TYR* 2.8 56.0 + - + +
258B THR* 5.4 0.2 - - - -
259B LEU* 4.8 9.6 - - + -
306B PHE* 4.1 11.9 - - + -
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Residues in contact with GLN 199 (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* 3.6 4.8 - - - +
173B VAL* 3.0 34.4 + - + +
175B LEU* 4.2 19.4 - - + +
198B VAL* 1.3 78.5 - - - +
200B ALA* 1.3 73.9 + - - +
201B LEU* 3.8 15.9 + - + +
254B GLY* 3.8 17.7 + - - +
255B HIS 3.4 10.5 - - - +
256B ASN* 2.6 27.2 + - - +
1109B NAG 3.8 14.6 + - - -
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Residues in contact with ALA 200 (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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171B ALA 3.5 5.4 - - - +
172B VAL* 4.5 4.9 - - + +
199B GLN* 1.3 79.0 - - - +
201B LEU* 1.3 62.4 + - - +
202B GLN 3.5 16.4 - - - +
204B THR* 5.1 0.2 - - + -
251B LEU* 4.0 24.5 - - + -
252B LEU 3.4 20.0 - - - +
254B GLY* 2.8 25.7 + - - -
255B HIS 3.1 8.1 + - - -
257B TYR* 4.2 4.9 - - + -
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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