Contacts of the strand formed by residues 207 - 215 (chain B) in PDB entry 2BQ6
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 TYR 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLY* 2.7 31.0 + - - +
47A GLN* 3.6 34.7 + - + -
29B TRP* 3.4 31.4 - + + -
121B ALA* 4.0 1.0 - - - -
122B CYS* 3.0 24.4 + - - +
137B ILE* 3.9 23.9 - - + +
200B VAL* 4.1 22.9 - - + -
201B THR 3.8 1.1 - - - -
202B ARG* 3.2 61.0 + - + -
205B ASP 4.5 9.0 - - - -
206B THR* 1.3 75.9 - - - +
208B PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLN* 4.1 22.2 - - + -
11A PHE* 3.9 22.0 - + - -
24A ALA* 4.7 0.2 - - + -
122B CYS* 3.1 34.5 - - + +
124B PRO* 3.9 15.5 - - + -
127B TRP* 3.5 23.3 - + - -
131B LEU* 3.6 36.3 - + + -
200B VAL* 3.0 8.5 - - - -
201B THR 2.9 35.6 + - - +
203B PHE* 4.2 8.5 - + + -
206B THR* 3.7 28.9 - - + -
207B TYR* 1.3 75.3 - - - +
209B VAL* 1.3 61.8 + - - +
210B THR* 3.2 1.9 + - + +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B THR* 3.8 23.3 - - + +
47B LEU* 4.4 7.2 - - + -
53B LEU* 4.0 23.3 - - + -
121B ALA* 3.6 21.2 - - + +
122B CYS 2.8 18.9 + - - +
123B LEU* 3.5 22.0 - - + -
124B PRO* 3.6 16.5 - - - +
199B HIS 4.4 2.7 - - - +
200B VAL* 3.7 8.5 - - + +
208B PHE* 1.3 68.1 - - - +
210B THR* 1.3 64.2 + - - +
211B GLY 4.1 10.8 - - - +
231B VAL* 4.0 10.8 - - + +
232B THR* 6.0 0.3 - - - +
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Residues in contact with THR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PRO* 5.3 1.1 - - + -
128B ALA* 5.9 0.9 - - + -
131B MET* 4.0 39.4 + - + -
162B TYR* 3.7 9.9 - - - +
181B PHE* 3.7 9.9 - - - -
199B HIS* 2.7 33.1 + - - -
200B VAL 3.3 3.3 - - - -
201B THR* 2.8 31.8 + - - +
208B PHE 3.5 11.4 - - - +
209B VAL* 1.3 76.9 - - - +
211B GLY* 1.3 58.6 + - - +
230B LYS* 4.4 0.3 - - - -
231B VAL* 3.3 22.6 + - - +
232B THR* 4.6 5.3 + - + +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 4.7 0.3 - - - +
181B PHE* 3.9 8.7 - - - -
197B GLY 4.1 1.6 - - - +
198B PRO* 4.3 0.3 - - - +
199B HIS* 2.8 36.8 + - - +
209B VAL* 4.1 7.3 - - - +
210B THR* 1.3 81.5 + - - +
212B ILE* 1.3 69.4 + - - +
229B THR 3.3 6.3 - - - -
231B VAL* 3.3 9.7 - - - +
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B THR* 5.9 0.2 - - - +
53B LEU* 3.4 39.5 - - + -
54B THR* 3.9 4.7 - - - +
55B ALA* 3.7 26.9 - - + +
102B ASP 4.7 1.1 - - - +
103B ILE* 3.5 25.4 - - + -
196B GLY* 3.8 13.7 - - - +
197B GLY 3.5 7.2 - - - +
211B GLY* 1.3 80.1 - - - +
213B VAL* 1.3 71.4 + - - +
214B SER* 2.9 3.1 + - - -
228B TYR* 3.2 5.5 - - - +
229B THR* 2.7 42.0 + - - +
231B VAL* 3.5 13.7 - - + -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA* 3.9 6.1 - - - +
138B VAL* 3.3 32.1 - - + -
139B SER 4.9 0.2 - - - +
190B ALA* 4.3 2.5 - - + -
194B ASP* 3.2 42.6 - - + +
195B SER* 3.6 4.3 - - - +
196B GLY* 2.8 25.8 + - - -
197B GLY* 3.3 19.0 + - - +
198B PRO 4.7 1.3 - - - +
199B HIS* 5.1 0.2 - - - +
212B ILE* 1.3 69.5 - - - +
214B SER* 1.3 57.5 + - - +
228B TYR* 3.7 13.1 - - + -
1246B IIB 3.5 33.7 - - + -
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA* 5.2 0.2 - - - -
57B HIS* 2.9 25.5 + - - -
99B TYR* 4.3 0.7 + - - -
102B ASP* 2.8 30.9 + - - +
180B MET* 5.5 2.9 - - - +
195B SER* 4.3 2.8 + - - -
212B ILE 2.9 9.2 + - - -
213B VAL* 1.3 75.0 - - - +
215B TRP* 1.3 87.6 + - - +
227B ILE* 3.0 18.6 + - - -
228B TYR* 4.1 4.3 - - - -
229B THR* 4.1 8.0 + - - -
1246B IIB 4.0 6.8 + - - +
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Residues in contact with TRP 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B TYR* 4.1 23.4 - + + +
172B SER* 3.6 12.1 - - - -
174B PHE* 3.6 34.3 - + + -
175B ILE 4.9 2.2 - - - -
176B ILE* 4.0 10.1 - - + -
180B MET* 3.7 18.8 - - - +
214B SER* 1.3 107.2 - - - +
216B GLY* 1.3 79.5 + - - +
217B GLU* 4.0 17.3 - - + -
227B ILE* 2.8 67.2 + - + +
1246B IIB 3.4 69.9 - - + +
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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
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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