Contacts of the strand formed by residues 201 - 215 (chain A) in PDB entry 1B3K
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 MET 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A THR* 3.7 3.7 - - - +
185A HIS* 2.9 36.7 + - - -
187A ARG* 3.4 26.0 - - + +
188A LEU 3.3 33.2 - - - +
189A PHE* 3.9 26.0 - - + -
199A VAL* 3.5 14.1 + - + +
200A PRO* 1.3 79.4 - - - +
202A MET* 1.3 63.5 + - - +
274A VAL* 3.8 25.1 - - + -
276A PRO* 3.6 24.7 - - + -
277A LYS 4.2 0.2 - - - +
353A ILE* 5.3 0.4 - - - -
354A ILE 4.3 3.4 - - - +
355A ASP* 4.3 9.2 - - - -
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Residues in contact with MET 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TRP* 4.5 0.9 - - - +
179A PHE* 3.8 29.8 - - + -
180A PRO 5.4 0.2 - - - +
184A THR* 3.2 32.3 - - + +
201A MET* 1.3 73.7 - - - +
203A ALA* 1.3 65.5 + - - +
274A VAL* 3.5 0.7 - - - -
275A LEU* 2.9 51.3 + - + +
277A LYS* 3.8 13.9 - - + +
328A VAL* 3.4 28.7 - - + -
329A ASN* 3.3 39.0 - - - +
330A GLU* 3.4 9.2 - - + +
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A PHE* 3.5 7.4 - - - +
180A PRO* 3.8 7.4 - - - +
183A SER* 3.5 28.5 + - - +
185A HIS* 4.6 7.9 - - + +
201A MET 4.6 2.2 - - - +
202A MET* 1.3 80.5 - - - +
204A GLN* 1.3 60.9 + - - +
272A LEU* 4.1 10.1 - - + -
273A LEU 2.8 19.1 - - - +
274A VAL* 3.7 19.3 - - + -
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Residues in contact with GLN 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A THR* 2.9 50.5 + - - +
178A PRO 4.4 2.2 - - - +
179A PHE* 3.2 34.6 - - + -
180A PRO* 3.9 19.3 - - + -
203A ALA* 1.3 75.7 - - - +
205A THR* 1.3 59.2 + - - +
206A ASN* 3.9 9.7 + - - +
208A PHE* 3.2 33.5 - - + -
226A LEU* 5.5 1.2 - - - +
272A LEU* 4.3 2.2 - - - -
273A LEU 2.8 30.2 + - - -
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Residues in contact with THR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLN* 1.3 74.5 - - - +
206A ASN* 1.3 69.4 + - - +
270A PRO* 5.9 0.7 - - + -
271A ARG 3.2 16.6 - - - +
272A LEU* 3.6 20.8 - - - +
345A ALA* 4.3 16.7 - - - +
346A ARG* 3.6 34.0 + - + +
347A MET 5.2 0.2 - - - +
348A ALA* 3.6 26.2 - - + +
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Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A THR* 3.8 29.6 + - - +
204A GLN* 3.9 4.5 + - - +
205A THR* 1.3 79.5 + - - +
207A LYS* 1.3 83.3 + - - +
208A PHE* 3.0 35.3 - - + -
268A ARG* 4.0 11.4 + - - -
270A PRO* 4.2 1.6 - - - -
271A ARG 3.0 21.3 + - - -
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Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ASN* 1.3 82.7 + - - +
208A PHE* 1.3 63.1 + - - +
268A ARG* 3.2 49.3 + - + +
269A LEU 2.9 17.0 - - - +
270A PRO* 3.6 29.8 - - + -
186C ARG* 5.7 4.4 - - - +
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Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLN* 3.2 50.3 - - + -
206A ASN* 3.0 46.7 - - + -
207A LYS* 1.3 70.8 - - - +
209A ASN* 1.3 58.7 + - - +
210A TYR* 2.9 14.1 + - + +
224A LEU* 3.5 22.2 - - + -
225A GLU 4.6 4.5 - - - +
226A LEU* 3.4 25.1 - - + -
227A PRO* 6.1 1.3 - - + -
268A ARG* 5.0 0.9 - - - +
269A LEU 3.0 23.6 + - - +
271A ARG* 3.5 17.0 - - + -
273A LEU* 3.5 28.0 - - + -
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Residues in contact with ASN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LYS 3.6 2.0 + - - -
208A PHE* 1.3 70.5 - - - +
210A TYR* 1.3 57.8 + - - +
224A LEU* 3.7 3.3 - - - +
225A GLU* 3.2 52.8 + - + +
263A LYS* 5.1 5.1 + - - +
266A MET* 2.9 43.1 - - - +
267A THR* 3.7 5.7 + - - -
268A ARG* 3.5 37.7 + - + +
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Residues in contact with TYR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PHE 2.9 11.0 + - - +
209A ASN* 1.3 74.3 - - - +
211A THR* 1.3 94.2 + - - +
212A GLU* 3.4 22.3 + - + +
222A ASP* 2.5 40.7 + - + -
223A ILE 3.5 11.0 - - - -
224A LEU* 3.8 11.4 - - + -
241A TYR* 3.8 7.4 + - - -
265A ASN 4.3 0.3 - - - +
266A MET* 3.1 4.1 - - - -
267A THR* 2.7 41.7 + - - +
269A LEU* 3.9 23.8 - - + -
271A ARG* 4.2 22.2 - - - +
352A ILE* 4.0 19.7 - - + -
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Residues in contact with THR 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 1.3 92.1 - - - +
212A GLU* 1.3 71.0 + - - +
213A PHE* 5.5 0.4 - - + +
223A ILE* 2.8 52.2 + - + +
262A TRP* 4.0 9.4 - - + +
265A ASN* 3.6 21.5 + - - -
266A MET* 3.2 34.3 - - + -
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 3.4 13.5 + - + +
211A THR* 1.3 82.6 + - - +
213A PHE* 1.3 65.0 + - - +
214A THR* 5.3 0.8 + - - +
220A TYR* 3.9 23.0 - - + +
221A TYR 3.5 12.6 - - - +
241A TYR* 2.9 42.0 + - + -
265A ASN* 4.8 4.9 + - - -
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Residues in contact with PHE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A THR* 4.0 1.7 + - + +
212A GLU* 1.3 76.3 - - - +
214A THR* 1.3 79.7 + - - +
215A THR* 3.8 20.4 - - + -
216A PRO* 5.0 0.2 - - + -
219A HIS 3.6 0.2 - - - +
220A TYR* 3.3 5.5 - - - +
221A TYR* 2.9 37.3 + + + +
223A ILE* 3.6 23.6 - - + -
250A LEU* 3.4 31.6 - - + -
253A ILE* 4.6 3.6 - - + -
258A LEU* 3.5 22.9 - - + -
261A HIS* 4.4 9.4 - + - -
262A TRP* 3.4 22.2 - + + +
152B LEU* 3.4 26.5 - - + -
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Residues in contact with THR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLU* 5.3 0.5 + - - +
213A PHE* 1.3 93.1 - - - +
215A THR* 1.3 77.7 + - - +
216A PRO* 3.6 2.8 - - - +
218A GLY* 4.4 3.1 - - - +
219A HIS 3.1 11.2 - - - +
220A TYR* 3.2 43.1 - - + +
152B LEU* 5.3 0.5 - - - +
283B GLU 5.5 2.4 - - - +
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Residues in contact with THR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PHE* 3.8 16.7 - - + -
214A THR* 1.3 88.0 - - - +
216A PRO* 1.3 59.9 - - - +
217A ASP* 2.4 40.2 + - - -
218A GLY 3.2 1.7 + - - -
219A HIS* 2.8 34.6 + - + +
221A TYR* 3.8 25.8 - - + -
249A ALA 4.1 18.8 - - - +
250A LEU* 4.2 5.4 - - + -
253A ILE* 4.4 5.6 - - + -
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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