Contacts of the strand formed by residues 195 - 204 (chain B) in PDB entry 6BAA
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 ARG 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PRO* 3.8 1.8 - - - -
192B ARG 2.8 35.9 + - - +
193B HIS* 4.2 8.7 - - + +
194B GLY* 1.3 84.5 - - - +
196B LEU* 1.3 64.5 + - - +
197B CYS* 3.3 4.0 + - - +
260B VAL* 3.8 27.6 - - + +
261B ILE 3.1 26.0 + - - -
262B ASP* 3.5 22.0 - - - +
349B LEU* 5.6 0.4 - - - -
350B ASP* 4.3 22.5 + - - -
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Residues in contact with LEU 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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189B ILE* 3.7 24.0 - - + -
190B THR* 4.0 14.6 - - - -
191B PRO* 3.9 12.7 - - + +
194B GLY 4.0 1.6 + - - -
195B ARG* 1.3 74.6 - - - +
197B CYS* 1.3 59.6 + - - +
260B VAL* 4.0 1.9 - - - +
261B ILE* 3.0 36.7 + - + +
267B LEU 5.8 0.2 - - - +
270B LEU* 6.3 0.2 - - + -
311B TRP* 3.6 33.7 - - + -
341B THR* 4.5 7.4 - - - +
342B PRO* 5.3 3.8 - - + +
344B CYS 4.6 2.0 - - - +
345B THR 4.8 0.2 - - - -
346B ALA* 4.0 33.4 - - + +
349B LEU* 4.2 22.4 - - + +
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Residues in contact with CYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL 3.9 0.2 - - - +
189B ILE* 3.3 9.7 - - - +
190B THR 2.8 54.2 + - - -
192B ARG* 3.7 17.5 - - + -
195B ARG 4.1 2.0 - - - +
196B LEU* 1.3 76.7 - - - +
198B PHE* 1.3 59.2 + - - +
199B MET* 3.5 34.9 + - - -
258B TYR* 4.4 9.0 - - + -
259B HIS 3.3 13.9 - - - +
260B VAL* 4.0 14.8 - - + -
261B ILE* 4.4 4.3 - - - +
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Residues in contact with PHE 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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187B ALA* 3.3 26.7 - - + -
188B VAL 3.5 7.9 - - - -
189B ILE* 4.3 14.6 - - + +
197B CYS* 1.3 72.5 - - - +
199B MET* 1.3 62.8 + - - +
200B LEU* 4.5 6.5 - - + -
217B MET* 4.1 36.1 - - + -
257B ILE 5.4 0.4 - - - -
258B TYR* 2.8 8.3 - - - +
259B HIS* 2.8 47.8 + + + +
261B ILE* 4.8 2.2 - - + +
267B LEU* 4.5 23.3 - - + -
283B ILE* 4.0 28.0 - - + -
304B TYR* 5.0 2.0 - + + -
309B ILE* 3.5 30.5 - - + -
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Residues in contact with MET 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU* 6.0 6.1 - - + -
187B ALA* 2.9 10.3 - - - +
188B VAL* 2.7 50.4 + - + -
190B THR* 3.7 22.2 - - + -
191B PRO 5.4 0.2 - - - +
192B ARG* 3.0 43.5 - - + +
197B CYS* 3.5 25.5 + - - -
198B PHE* 1.3 78.6 - - - +
200B LEU* 1.3 60.4 + - - +
256B ILE* 3.9 18.2 - - + -
257B ILE 3.5 2.7 - - - -
258B TYR* 3.8 12.6 - - + -
314B ARG* 5.3 5.4 - - - -
315B PHE* 4.2 9.4 - - + -
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Residues in contact with LEU 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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183B PHE* 4.2 7.6 - - + -
184B SER* 4.6 0.9 - - - +
187B ALA* 4.1 7.6 - - + -
198B PHE* 4.5 7.6 - - + -
199B MET* 1.3 77.6 - - - +
201B ARG* 1.3 75.1 + - - +
202B VAL* 4.0 12.3 - - + +
217B MET* 4.5 7.9 - - + -
256B ILE* 3.4 5.3 - - - -
257B ILE* 2.6 55.9 + - + +
285B VAL* 3.4 27.6 - - + -
304B TYR* 3.3 43.5 - - + +
315B PHE* 4.5 5.1 - - - -
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Residues in contact with ARG 201 (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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183B PHE* 3.6 1.2 - - - -
184B SER* 3.0 34.0 + - - -
200B LEU* 1.3 81.8 - - - +
202B VAL* 1.3 62.2 + - - +
254B PRO* 4.1 17.1 + - + +
255B LEU 3.2 7.2 - - - +
256B ILE* 3.5 19.8 - - + +
315B PHE* 3.2 52.0 - - + +
316B VAL 2.9 27.9 + - - +
317B PRO* 4.9 0.8 - - - +
318B ILE* 3.2 22.4 - - - +
332B LYS 5.0 0.4 + - - -
333B PHE* 3.4 53.3 + - + -
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Residues in contact with VAL 202 (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 ILE 3.1 14.1 - - - +
183B PHE* 4.0 18.4 - - + -
200B LEU* 4.1 8.1 - - + -
201B ARG* 1.3 75.4 - - - +
203B GLY* 1.3 65.5 + - - +
215B ILE* 4.5 5.4 - - + -
251B LEU* 3.7 25.5 - - + +
254B PRO* 3.3 2.6 - - - +
255B LEU* 2.9 33.4 + - + +
257B ILE* 3.5 33.0 - - + -
287B LEU* 4.0 15.3 - - + -
333B PHE* 4.3 4.9 - - - -
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Residues in contact with GLY 203 (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 9.2 - - - +
182B ILE* 2.8 34.2 + - - +
202B VAL* 1.3 77.5 - - - +
204B ASP* 1.3 62.9 + - - +
251B LEU* 3.8 11.3 - - - +
254B PRO* 4.4 6.5 - - - -
333B PHE* 4.0 18.0 - - - -
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Residues in contact with ASP 204 (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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46A HIS* 4.6 6.2 - - - -
177B ARG* 3.3 23.7 + - - -
180B THR* 3.9 6.8 + - - -
181B LEU* 3.3 20.9 - - + +
203B GLY* 1.3 75.1 - - - +
205B LEU* 1.3 63.8 + - - +
206B ARG* 2.9 26.1 + - - +
208B SER 4.3 3.7 - - - +
209B MET* 5.3 0.6 - - - -
210B ILE* 3.4 13.5 + - - +
251B LEU* 3.5 24.6 - - + +
252B VAL 4.7 4.9 + - - +
254B PRO 5.9 0.4 - - - -
330B TYR* 3.4 19.4 + - - -
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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