Contacts of the strand formed by residues 197 - 215 (chain I) in PDB entry 5BRR
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 197 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ARG 3.2 1.2 - - - +
188I LEU* 3.4 5.5 - - - -
189I PHE* 2.8 40.6 + - + +
191I LYS* 3.8 22.2 - - + -
195I SER* 4.8 2.5 - - - +
196I THR* 1.3 78.3 - - - +
198I SER* 1.3 66.2 + - - +
199I VAL* 3.2 25.6 + - + -
378I GLU* 3.7 24.9 - - + +
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Residues in contact with SER 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I ARG* 2.5 58.7 + - - +
187I ARG 3.5 9.7 + - - -
188I LEU* 4.5 12.1 - - - +
196I THR 4.4 0.2 + - - -
197I VAL* 1.3 76.2 - - - +
199I VAL* 1.3 56.5 + - - +
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Residues in contact with VAL 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I ARG* 4.1 3.1 - - - -
187I ARG* 2.6 44.6 + - - +
189I PHE* 4.4 8.5 - - + -
197I VAL* 3.2 25.8 + - + +
198I SER* 1.3 73.1 - - - +
200I PRO* 1.3 86.9 - - + +
201I MET* 3.6 3.3 + - + -
276I PRO* 3.9 10.1 - - + -
277I LYS 4.5 2.2 - - - +
378I GLU* 5.6 0.9 - - + -
379I PRO* 3.7 48.0 - - + -
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Residues in contact with PRO 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I THR* 4.3 15.9 - - + -
185I HIS 3.5 7.0 - - - +
186I ARG* 4.0 32.8 - - + +
199I VAL* 1.3 101.6 - - + +
201I MET* 1.3 60.1 + - - +
202I MET 4.2 0.2 - - - -
276I PRO* 3.5 0.5 - - - +
277I LYS* 3.3 34.1 + - + +
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Residues in contact with MET 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I THR* 3.9 3.1 - - - +
185I HIS* 2.7 44.7 + - + +
187I ARG* 3.8 38.6 - - + +
189I PHE* 3.7 42.4 - - + +
199I VAL* 4.2 4.0 - - + +
200I PRO* 1.3 79.0 - - - +
202I MET* 1.3 60.7 + - - +
274I VAL* 3.9 18.6 - - + -
275I LEU 3.5 7.6 - - - +
276I PRO* 3.6 18.2 - - + -
354I ILE 3.7 26.2 - - - +
355I ASP* 4.2 4.3 - - - -
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Residues in contact with MET 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I PHE* 3.5 35.3 - - + -
183I SER 3.8 7.0 - - - +
184I THR* 3.7 20.0 - - + +
200I PRO 4.2 0.4 + - - -
201I MET* 1.3 72.5 - - - +
203I ALA* 1.3 59.3 + - - +
274I VAL* 3.7 0.9 - - - -
275I LEU* 2.9 49.8 + - + +
277I LYS* 3.7 25.7 - - + +
328I VAL* 3.7 26.5 - - + -
329I ASN* 3.2 34.8 - - - +
330I GLU* 3.6 13.2 - - - +
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Residues in contact with ALA 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I PHE* 4.0 1.1 - - - -
180I PRO* 3.4 9.0 - - - +
183I SER* 3.0 29.2 + - - +
185I HIS* 4.1 15.0 - - + +
201I MET 3.8 0.4 + - - -
202I MET* 1.3 74.8 - - - +
204I GLN* 1.3 65.0 + - - +
272I LEU* 4.8 5.2 - - + -
273I LEU 3.4 5.2 - - - +
274I VAL* 3.8 23.1 - - + -
342I ILE* 3.7 14.7 - - + +
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Residues in contact with GLN 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I THR* 3.2 32.6 + - - +
178I PRO 3.7 9.9 + - - +
179I PHE* 3.1 40.6 - - + -
180I PRO* 4.5 7.0 - - + -
203I ALA* 1.3 77.3 - - - +
205I THR* 1.3 63.9 + - - +
206I ASN* 2.9 31.8 + - + +
208I PHE* 4.0 19.0 - - + -
272I LEU* 3.8 1.6 - - - +
273I LEU* 3.0 32.7 + - - +
341I VAL 5.4 3.8 - - - +
342I ILE* 4.2 8.0 - - - +
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Residues in contact with THR 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E GLN* 3.1 30.3 + - - +
204I GLN* 1.3 72.1 - - - +
206I ASN* 1.3 61.3 + - - +
270I PRO* 5.9 1.1 - - + -
271I ARG 3.5 10.8 - - - +
272I LEU* 3.6 16.3 - - - +
342I ILE* 3.4 21.9 + - - +
343I VAL* 3.6 23.6 - - + +
344I SER* 5.2 1.9 - - - -
345I ALA 5.4 3.8 - - - +
347I MET* 5.7 1.8 - - + +
349I PRO* 3.7 22.0 - - + -
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Residues in contact with ASN 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I THR* 2.8 39.0 + - - +
204I GLN* 2.9 12.1 + - + +
205I THR* 1.3 76.8 + - - +
207I LYS* 1.3 81.7 + - - +
208I PHE* 3.3 26.1 - - + -
270I PRO* 3.5 4.5 - - - +
271I ARG 3.0 29.6 + - - +
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Residues in contact with LYS 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E GLN* 2.0 39.1 + - - +
96E ASP* 3.4 29.9 + - - +
97E ASP* 5.6 1.1 - - - +
99E TYR* 3.4 16.9 + - - -
206I ASN* 1.3 91.6 + - - +
208I PHE* 1.3 68.8 + - - +
268I ARG* 3.9 42.0 + - + +
269I LEU 3.3 6.1 - - - +
270I PRO* 4.3 14.7 - - + +
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Residues in contact with PHE 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I THR* 5.8 3.4 - - - -
204I GLN* 4.0 24.5 - - - -
206I ASN* 3.3 36.1 - - + -
207I LYS* 1.3 78.4 - - - +
209I ASN* 1.3 65.4 + - - +
210I TYR* 3.3 5.5 + - + +
224I LEU* 4.0 21.5 - - + -
225I GLU 4.7 3.8 - - - +
226I LEU* 3.8 22.0 - - + -
227I PRO* 6.3 0.7 - - + -
267I THR 3.6 0.2 - - - +
268I ARG* 4.3 2.0 - - - +
269I LEU* 2.7 35.6 + - - +
271I ARG* 3.3 37.1 - - + +
273I LEU* 3.9 32.5 - - + -
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Residues in contact with ASN 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208I PHE* 1.3 70.7 - - - +
210I TYR* 1.3 60.5 + - - +
224I LEU* 3.4 6.1 - - - +
225I GLU* 3.1 46.8 + - + +
227I PRO* 5.5 4.0 - - - +
263I LYS* 2.9 29.3 - - - +
266I MET* 3.6 23.2 - - + -
267I THR* 3.8 5.2 - - - -
268I ARG* 3.7 41.1 + - - +
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Residues in contact with TYR 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ARG* 3.5 33.1 - - + +
208I PHE* 3.3 6.7 + - + +
209I ASN* 1.3 75.5 - - - +
211I THR* 1.3 94.6 + - - +
212I GLU* 3.4 17.6 - - + +
222I ASP* 2.6 39.9 + - + -
223I ILE 3.4 17.7 - - - -
224I LEU* 4.8 9.2 - - + -
241I TYR* 3.6 2.3 + - - -
265I ASN 4.1 0.7 - - - +
266I MET* 3.1 20.3 - - - -
267I THR* 3.3 13.1 + - - +
269I LEU* 4.1 26.0 - - + -
271I ARG* 4.7 7.4 - - + +
352I ILE* 4.0 23.1 - - + -
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Residues in contact with THR 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210I TYR* 1.3 93.2 - - - +
212I GLU* 1.3 74.4 + - - +
213I PHE* 5.3 0.2 - - + -
223I ILE* 2.8 54.2 + - + +
262I TRP* 3.8 27.6 - - + +
265I ASN* 3.4 31.0 + - + +
266I MET* 4.0 5.6 - - + -
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Residues in contact with GLU 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ARG* 3.5 21.6 + - - -
210I TYR* 3.4 14.6 - - + +
211I THR* 1.3 84.5 + - - +
213I PHE* 1.3 62.8 + - - +
214I THR* 4.4 2.7 + - + +
220I TYR* 3.0 34.3 - - + -
221I TYR 3.5 9.9 - - - +
241I TYR* 2.7 31.1 + - + +
265I ASN* 5.5 1.2 - - - +
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Residues in contact with PHE 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211I THR* 4.0 1.5 + - + -
212I GLU* 1.3 75.6 - - - +
214I THR* 1.3 86.0 + - - +
215I THR* 4.2 6.7 - - + -
216I PRO* 5.6 1.8 - - + -
219I HIS 3.7 0.3 - - - +
220I TYR* 3.2 4.0 - - - +
221I TYR* 2.7 39.3 + + - +
223I ILE* 3.5 24.5 - - + -
250I LEU* 3.6 30.5 - - + -
253I ILE* 4.4 8.1 - - + -
258I LEU* 3.7 18.6 - - + -
261I HIS* 3.7 29.2 - + - -
262I TRP* 3.4 25.1 - + + +
265I ASN* 5.5 2.0 - - - -
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Residues in contact with THR 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I GLU* 5.0 4.0 - - + +
213I PHE* 1.3 99.0 - - - +
215I THR* 1.3 68.3 + - - +
216I PRO* 4.0 1.6 - - - +
218I GLY* 5.2 1.6 - - - -
219I HIS 3.0 9.9 - - - -
220I TYR* 3.5 44.0 - - + -
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Residues in contact with THR 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213I PHE* 4.3 2.4 - - + -
214I THR* 1.3 83.7 + - - +
216I PRO* 1.3 66.1 - - - +
217I ASP* 2.8 26.2 + - - -
218I GLY* 3.1 11.6 + - - -
219I HIS* 3.0 32.7 + - + +
221I TYR* 4.1 13.9 - - + -
249I ALA 3.8 20.9 - - - +
250I LEU* 3.9 25.4 - - + -
253I ILE* 3.9 9.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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