Contacts of the strand formed by residues 203 - 210 (chain A) in PDB entry 4BZ5
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 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ILE* 3.7 24.2 - - + -
165A VAL* 3.4 33.2 - - + -
180A VAL* 3.2 11.2 - - + +
182A TYR* 4.9 1.1 - - + -
197A PHE* 3.6 51.5 - - + +
200A SER* 3.5 19.2 + - - +
201A PRO 3.3 0.2 - - - -
202A ARG* 1.3 79.8 - - + +
204A VAL* 1.3 63.5 + - - +
205A THR* 3.7 12.1 + - + +
243A SER* 4.3 2.8 + - - +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A VAL 2.8 12.0 + - - +
181A LEU* 3.5 9.3 - - + +
182A TYR* 2.8 27.2 + - - +
201A PRO 3.9 4.7 - - - +
202A ARG 5.2 0.9 - - - -
203A VAL* 1.3 71.9 - - - +
205A THR* 1.3 63.6 + - - +
243A SER* 3.4 14.8 - - - +
245A PHE* 3.7 24.2 - - + -
269A LEU* 4.4 1.3 - - + -
273A ILE* 3.6 38.1 - - + -
418A TYR* 3.4 41.1 - - + +
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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
----------------------------------------------------------
182A TYR* 3.6 28.9 - - + -
193A VAL* 4.1 22.9 - - + +
194A GLU* 4.0 19.5 + - - +
197A PHE* 4.6 4.5 - - + -
203A VAL* 3.7 15.0 + - + +
204A VAL* 1.3 76.9 - - - +
206A PHE* 1.3 57.6 + - - +
207A SER* 4.3 0.4 - - - -
243A SER 3.1 7.1 + - - +
244A ALA* 3.6 20.1 - - - +
245A PHE* 2.7 36.6 + - - +
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Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 4.8 2.7 - - + -
182A TYR* 2.8 15.1 + - - +
183A VAL* 3.4 11.5 - - + -
184A ASP* 2.8 27.3 + - - +
205A THR* 1.3 76.0 - - - +
207A SER* 1.3 74.7 + - - +
208A VAL* 4.3 19.5 - - + -
245A PHE* 3.3 21.8 - - + -
246A ASN 4.6 1.6 - - - -
247A LEU* 4.0 15.0 - - + -
262A ILE* 4.4 12.3 - - + -
265A ILE* 3.6 35.9 - - + -
266A LEU* 3.9 26.5 - - + -
269A LEU* 3.8 26.9 - - + -
411A ILE* 4.9 1.3 - - + -
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TYR* 5.9 0.9 - - - -
184A ASP* 3.7 15.3 + - - +
188A HIS 4.3 1.2 + - - -
189A HIS* 3.6 8.4 - - - -
190A GLY* 3.2 23.2 + - - -
194A GLU* 5.4 0.7 - - - -
205A THR* 4.3 0.4 - - - -
206A PHE* 1.3 79.8 - - - +
208A VAL* 1.3 60.8 + - - +
209A HIS* 2.7 27.9 + - - +
245A PHE 3.1 7.5 + - - -
246A ASN* 3.4 14.4 - - - -
247A LEU 2.9 24.3 + - - -
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Residues in contact with VAL 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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184A ASP 3.2 15.8 + - - +
185A LEU* 4.1 11.3 - - + +
186A ASP 3.2 15.8 - - - +
206A PHE* 4.3 11.8 - - + -
207A SER* 1.3 73.7 + - - +
209A HIS* 1.3 64.5 + - - +
247A LEU* 3.3 12.3 - - + +
249A LEU* 3.5 30.5 - - + -
258A TRP* 3.9 30.8 + - + +
262A ILE* 3.7 25.8 - - + -
286A CYS* 5.7 0.2 - - - -
295A PHE* 5.5 0.5 - - - -
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Residues in contact with HIS 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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186A ASP 4.0 1.8 - - - -
187A LEU 3.3 15.7 - - - +
188A HIS 3.6 3.1 - - - +
189A HIS* 3.4 30.2 - + + +
207A SER* 2.7 31.7 + - - +
208A VAL* 1.3 75.2 - - - +
210A HIS* 1.3 71.3 + - - +
211A ALA* 4.2 4.5 - - + -
219A THR 4.5 0.9 - - - -
220A GLY* 2.8 27.6 + - - -
246A ASN* 3.2 29.6 - - + -
247A LEU 3.1 6.2 + - - +
248A PRO* 3.3 15.2 - - + +
249A LEU* 2.8 25.3 + - - +
295A PHE* 3.7 10.8 - - - -
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 2.9 19.0 + - + +
189A HIS* 4.9 2.9 + - - +
209A HIS* 1.3 80.4 - - - +
211A ALA* 1.3 71.5 + - - +
212A SER* 2.8 28.0 + - - -
215A PHE* 3.5 51.7 - + + -
216A PHE 5.0 0.7 - - - +
217A PRO* 6.0 0.2 - - - +
249A LEU 3.0 21.9 + - - -
250A GLU* 4.0 5.4 - - - -
251A GLU* 3.7 30.0 + - + +
294A ILE* 3.5 23.9 - - + +
295A PHE* 3.5 14.9 - - + -
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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
------------------------------------------------------------
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