Contacts of the strand formed by residues 204 - 211 (chain A) in PDB entry 5B4N
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 ILE 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A LEU* 4.6 10.3 - - + -
197A LEU* 5.2 2.5 - - + -
202A PRO* 3.6 8.3 - - + +
203A ALA* 1.3 72.7 - - - +
205A VAL* 1.3 58.3 + - - +
206A VAL* 4.5 4.3 - - + -
226A LEU* 4.1 24.9 - - + -
258A THR* 3.5 0.4 - - - -
259A PHE* 2.8 55.2 + - + -
262A TYR* 3.6 32.5 - - + +
266A VAL* 4.4 9.6 - - + -
269A VAL* 4.5 5.8 - - + -
294A VAL* 4.2 19.7 - - + -
295A TRP 3.3 9.4 - - - +
296A VAL* 4.3 17.3 - - + -
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Residues in contact with VAL 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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203A ALA* 4.5 0.7 - - + -
204A ILE* 1.3 75.1 - - - +
206A VAL* 1.3 64.7 + - - +
207A LYS* 3.9 33.8 + - + +
256A SER* 4.6 2.0 - - - +
257A HIS 3.5 8.7 - - - +
258A THR* 4.0 23.8 - - + +
293A SER 3.8 1.0 - - - +
294A VAL* 3.4 3.3 - - - -
295A TRP* 2.9 56.4 + - + +
297A GLU* 3.9 24.9 - - + +
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Residues in contact with VAL 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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204A ILE* 4.5 5.4 - - + -
205A VAL* 1.3 80.3 - - - +
207A LYS* 1.3 63.4 + - - +
222A LEU* 5.2 3.9 - - + +
224A VAL* 3.7 43.7 - - + -
237A PHE* 4.6 4.3 - - + -
255A ILE 4.0 0.3 - - - +
256A SER* 3.5 2.3 - - - -
257A HIS* 2.8 55.4 + - + +
259A PHE* 4.2 15.0 - - + -
269A VAL* 4.7 0.7 - - + -
271A PHE* 4.9 3.4 - - + -
293A SER 3.3 5.4 - - - +
294A VAL* 3.8 23.8 - - + -
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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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205A VAL* 3.9 14.7 - - + +
206A VAL* 1.3 81.6 - - - +
208A ASP* 1.3 64.4 + - - +
209A TRP* 5.4 3.8 - - - +
222A LEU* 5.8 2.0 - - - -
254A GLU* 3.2 27.1 + - + +
255A ILE 3.2 8.1 - - - +
256A SER* 3.0 27.8 + - - +
271A PHE* 4.0 6.4 - - - -
291A ASN 4.8 1.8 - - - +
292A SER* 3.6 1.8 - - - -
293A SER* 2.9 42.0 + - - +
295A TRP* 3.9 34.5 - - + -
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Residues in contact with ASP 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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207A LYS* 1.3 74.4 - - - +
209A TRP* 1.3 73.6 + - - +
220A TYR* 2.6 30.5 + - - +
222A LEU* 4.7 3.1 - - + -
254A GLU* 3.2 5.7 - - - +
255A ILE* 2.8 40.0 + - + +
271A PHE* 3.9 10.3 - - + -
273A HIS* 2.5 30.7 + - - +
289A VAL* 4.2 1.0 - - - +
290A THR 3.7 3.5 - - - +
292A SER* 2.6 30.8 + - - +
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Residues in contact with TRP 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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162A GLU 3.5 24.7 - - - -
163A PHE* 3.7 23.3 - + + -
164A PRO* 3.8 19.9 - - + +
207A LYS* 5.4 3.6 - - + +
208A ASP* 1.3 82.5 + - - +
210A TYR* 1.3 61.3 + - - +
252A TRP* 3.7 29.8 - - + -
253A ARG* 3.1 20.6 - - - -
254A GLU* 3.7 42.0 + - + +
289A VAL* 3.3 6.1 - - - +
290A THR 3.0 31.1 + - - +
291A ASN* 3.2 35.5 + - + +
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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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209A TRP* 1.3 75.6 - - - +
211A SER* 1.3 65.7 + - - +
220A TYR* 3.5 51.1 - + + -
242A ALA* 3.4 18.8 - - + +
244A ILE* 3.7 24.2 - - + -
252A TRP* 3.5 3.7 - - - -
253A ARG* 2.9 57.2 + - + -
254A GLU 4.7 1.3 - - - -
255A ILE* 4.1 24.9 - - + +
287A PRO* 4.8 0.7 - - + -
288A ARG 3.1 11.2 - - - +
289A VAL* 4.0 0.7 - - + -
260B ILE* 3.5 15.4 + - - +
261B ASP* 2.6 30.9 + - - +
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Residues in contact with SER 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 81.5 - - - +
212A GLY* 1.3 71.4 + - - +
218A SER* 4.5 0.5 - - - -
244A ILE* 4.4 6.9 - - - +
250A ALA 3.7 11.5 + - - -
251A LYS 3.5 18.6 - - - -
252A TRP* 3.7 16.2 - - - -
253A ARG* 4.5 3.1 - - - +
287A PRO* 3.4 9.7 - - - +
288A ARG* 2.9 46.5 + - - +
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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