Contacts of the strand formed by residues 207 - 217 (chain A) in PDB entry 2B25
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 LEU 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A PHE* 3.5 20.4 - - - +
188A ALA* 4.1 17.7 - - - -
189A VAL* 4.2 10.1 - - + -
203A PHE* 3.2 21.0 + - + +
204A TYR* 3.2 12.9 + - + +
205A PRO 4.3 0.7 - - - +
206A HIS* 1.3 76.0 - - - +
208A LYS* 1.3 71.6 + - - +
209A HIS* 5.5 0.2 + - - -
211A GLY* 3.6 35.0 - - - +
212A VAL 4.2 0.7 - - - +
213A CYS* 4.2 22.9 - - + +
237A LEU* 4.4 8.5 - - + -
328A LYS* 2.9 39.7 + - + -
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Residues in contact with LYS 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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105A ASP* 4.7 4.2 + - - -
185A THR* 4.6 14.4 - - + -
186A PHE 2.9 20.1 + - - +
187A ASP* 2.8 46.6 + - - +
206A HIS 3.4 2.9 + - - -
207A LEU* 1.3 84.2 - - - +
209A HIS* 1.3 70.7 + - - +
210A GLY 3.5 1.3 + - - -
211A GLY* 3.1 25.6 + - - +
328A LYS* 3.8 2.6 - - - +
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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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204A TYR* 5.2 1.4 + - - -
207A LEU 3.6 0.4 + - - -
208A LYS* 1.3 83.8 - - - +
210A GLY* 1.3 60.2 + - - +
211A GLY 3.3 0.5 + - - -
328A LYS* 3.5 38.8 + - + +
329A VAL 3.8 20.0 + - - -
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Residues in contact with GLY 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 LYS* 5.1 2.8 - - - -
209A HIS* 1.3 72.0 - - - +
211A GLY* 1.3 58.2 + - - +
327A ARG* 2.9 38.0 + - - -
328A LYS 2.7 22.3 + - - -
329A VAL* 5.9 0.4 - - - -
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Residues in contact with GLY 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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187A ASP 3.9 14.6 - - - -
207A LEU* 3.6 13.8 - - - +
208A LYS* 3.1 24.0 + - - -
209A HIS 3.2 1.8 + - - -
210A GLY* 1.3 78.7 - - - +
212A VAL* 1.3 60.7 + - - -
327A ARG* 3.5 1.6 - - - -
328A LYS 2.9 24.8 + - - -
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Residues in contact with VAL 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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98A MET 3.6 29.4 - - - +
99A MET* 4.0 20.5 + - - +
100A ASP* 5.6 2.0 - - + -
187A ASP 4.1 5.9 + - - -
188A ALA* 3.3 7.1 - - - +
189A VAL 3.0 23.7 + - - +
207A LEU* 4.2 3.0 - - - +
210A GLY 4.7 0.2 - - - +
211A GLY* 1.3 73.0 - - - -
213A CYS* 1.3 72.4 + - - +
214A ALA* 3.9 7.4 - - + +
325A LYS* 3.9 13.9 - - + +
326A LEU 3.2 14.4 - - - +
327A ARG* 3.6 33.9 - - + +
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Residues in contact with CYS 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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189A VAL* 3.4 17.5 - - + -
191A LEU* 4.0 9.4 - - - -
200A LEU* 5.2 1.1 - - - -
203A PHE* 3.6 35.0 - - + -
207A LEU* 4.2 7.5 - - + +
211A GLY 4.0 2.0 + - - -
212A VAL* 1.3 73.1 - - - +
214A ALA* 1.3 60.1 + - - +
215A VAL* 3.9 19.9 + - - -
237A LEU* 4.8 4.5 - - + -
324A VAL 3.7 1.9 - - - +
326A LEU* 2.8 52.8 + - + +
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Residues in contact with ALA 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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95A ILE* 3.9 29.7 - - + +
98A MET* 4.4 7.6 - - + -
99A MET* 3.7 25.6 - - + -
189A VAL 2.9 10.0 + - - +
190A ALA* 3.5 3.5 - - - +
191A LEU* 3.0 25.3 + - - +
212A VAL* 3.9 7.1 - - + +
213A CYS* 1.3 72.0 - - - +
215A VAL* 1.3 62.6 + - - +
324A VAL 3.3 7.0 - - - +
325A LYS* 4.8 0.4 - - - +
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Residues in contact with VAL 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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95A ILE* 4.2 4.6 - - - +
191A LEU* 3.5 17.5 - - + +
193A MET 5.9 0.2 - - - +
196A PRO* 3.8 25.6 - - + -
200A LEU* 6.2 0.2 - - + -
213A CYS* 3.9 24.0 - - - +
214A ALA* 1.3 78.2 - - - +
216A TYR* 1.3 64.2 + - - +
217A VAL* 3.5 20.6 - - + -
226A LEU* 3.9 24.9 - - + -
322A PHE 3.6 1.7 - - - +
323A LEU* 3.4 5.7 - - - -
324A VAL* 2.8 43.5 + - + +
326A LEU* 4.4 5.2 - - + -
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Residues in contact with TYR 216 (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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86A ILE 4.2 13.5 + - - -
87A THR* 4.0 25.9 - - + -
88A PHE 5.0 0.2 + - - -
91A ASP* 3.8 25.8 + - + -
95A ILE* 4.8 8.9 - - + +
117A MET* 6.0 4.5 - - + -
191A LEU 2.8 19.4 + - - +
192A ASP* 3.2 43.7 - - + +
193A MET 4.6 8.0 + - - +
215A VAL* 1.3 72.3 - - - +
217A VAL* 1.3 66.0 + - - +
218A VAL* 4.4 15.0 - - + +
222A GLN* 5.5 0.5 + - - -
320A THR* 3.9 11.8 + - - -
321A ALA* 3.4 24.6 - - + +
322A PHE 3.8 2.5 - - - -
323A LEU* 3.7 18.8 - - + -
601A SAM 5.8 1.8 - - + -
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Residues in contact with VAL 217 (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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196A PRO* 4.7 9.2 - - + -
215A VAL* 3.5 26.5 - - + +
216A TYR* 1.3 80.9 - - - +
218A VAL* 1.3 57.9 + - - +
219A ASN 3.3 9.4 + - - +
222A GLN* 2.8 47.6 - - + +
223A VAL* 3.8 15.0 - - + +
226A LEU* 4.8 4.5 - - + -
321A ALA* 3.8 2.5 - - - -
322A PHE* 2.5 46.6 + - - +
324A VAL* 4.4 9.6 - - + -
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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