Contacts of the strand formed by residues 203 - 209 (chain A) in PDB entry 6PXC
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 SER 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 3.9 9.4 - - - +
198A ALA* 3.7 18.4 - - - +
200A LYS* 2.7 30.6 + - - +
201A SER 3.3 0.2 - - - -
202A GLY* 1.3 78.7 - - - +
204A TYR* 1.3 62.1 + - - +
220A PHE* 3.5 1.4 - - - -
221A LEU* 2.9 34.2 + - - +
270A TYR* 3.2 16.4 - - - +
272A VAL* 3.8 16.8 - - - -
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Residues in contact with TYR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PRO* 3.7 14.2 - - - +
181A TRP* 4.0 14.8 - - + +
195A LEU* 3.8 6.0 - - - +
202A GLY 3.7 9.9 - - - -
203A SER* 1.3 75.6 - - - +
205A LEU* 1.3 70.0 + - - +
206A ILE* 5.1 0.4 - - + -
218A LEU* 4.1 14.8 - - + -
219A SER 3.1 13.2 - - - +
220A PHE* 4.3 1.8 - - + -
253A ILE* 3.4 44.4 - - + +
257A SER* 4.7 1.8 + - - -
268A LEU* 3.7 37.9 - - + -
269A LEU 4.1 1.8 - - - -
270A TYR 2.9 19.5 + - - -
271A PRO* 3.4 32.2 - - + +
272A VAL* 2.9 26.7 + - - +
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TRP* 3.6 5.2 - - - +
183A HIS* 3.5 41.7 - - + +
186A LEU* 4.8 0.9 - - + -
191A ALA* 3.9 17.0 - - + +
194A ARG* 4.1 7.9 - - + -
195A LEU* 3.8 26.7 - - + -
204A TYR* 1.3 78.3 - - - +
206A ILE* 1.3 81.1 + - - +
207A ARG* 4.0 20.6 - - + -
218A LEU* 3.6 3.8 - - - +
219A SER* 3.0 47.0 + - - +
272A VAL* 3.9 2.9 - - + +
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Residues in contact with ILE 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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181A TRP* 2.9 25.9 + - + +
182A TYR* 3.4 15.6 - - + -
183A HIS* 3.0 26.9 + - - +
204A TYR* 5.2 0.9 - - + -
205A LEU* 1.3 80.6 - - - +
207A ARG* 1.3 68.5 + - - +
216A PHE* 4.4 10.1 - - + -
217A VAL 3.3 11.4 - - - +
218A LEU* 3.9 15.7 - - + -
232A ILE* 4.0 18.6 - - + -
249A LEU* 4.1 24.5 - - + -
252A LEU* 4.9 2.2 - - + -
253A ILE* 3.9 30.5 - - + -
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Residues in contact with ARG 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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182A TYR* 4.1 7.4 - - - -
183A HIS* 4.5 2.0 - - + +
184A GLY 3.4 14.1 - - - +
186A LEU* 3.0 36.3 + - + +
187A ASP 4.0 0.2 - - - -
188A ARG* 3.9 13.6 - - - +
191A ALA* 3.4 21.4 - - - +
205A LEU* 4.0 10.1 - - + -
206A ILE* 1.3 75.6 - - - +
208A GLU* 1.3 60.7 + - - +
209A SER* 4.3 2.8 - - - +
216A PHE* 3.2 5.8 - - - +
217A VAL* 2.8 53.4 + - + +
219A SER* 3.2 13.5 + - - -
229A HIS* 3.1 26.9 + - - -
1105U PTR 2.8 43.8 + - - -
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Residues in contact with GLU 208 (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 19.8 + - - +
184A GLY* 2.8 7.9 + - - -
185A LYS* 3.3 34.5 + - + +
186A LEU 3.0 28.2 + - - +
207A ARG* 1.3 72.5 - - - +
209A SER* 1.3 68.7 + - - +
210A ASP 3.4 0.2 + - - -
213A PRO* 3.7 6.6 - - - +
214A GLY* 2.8 30.7 + - - +
215A SER 3.5 13.2 - - - +
216A PHE* 3.8 13.2 - - + -
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Residues in contact with SER 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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185A LYS* 3.9 5.3 - - - +
207A ARG* 3.8 6.7 + - - +
208A GLU* 1.3 72.8 - - - +
210A ASP* 1.3 60.3 + - - +
211A ARG* 3.1 5.9 + - - +
212A ARG* 3.1 30.0 + - - +
213A PRO* 3.4 22.0 - - - +
215A SER* 2.9 17.7 + - - -
216A PHE* 4.4 0.4 - - - +
217A VAL* 3.9 13.2 - - - +
231A ARG* 4.7 2.2 + - - -
1105U PTR 3.1 29.6 + - - -
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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