Contacts of the strand formed by residues 206 - 215 (chain B) in PDB entry 1HB0
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 GLN 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B VAL* 3.6 35.6 - - + +
201B CYS 3.5 0.9 - - - +
202B LEU* 3.8 3.1 - - - +
203B VAL* 2.9 35.0 + - - +
204B ASN* 3.2 4.6 - - + +
205B GLY* 1.3 79.4 - - - +
207B TYR* 1.3 72.0 + - - +
208B ALA* 3.7 4.7 + - - +
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Residues in contact with TYR 207 (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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27B TRP* 4.2 16.8 - + + -
122B VAL* 3.6 12.1 - - - +
135B PRO* 4.8 4.8 - - - +
137B TYR* 3.6 34.2 - + - -
200B HIS* 3.8 29.4 - - + +
201B CYS 3.3 18.2 - - - -
202B LEU* 3.8 38.8 - - + +
205B GLY 5.4 1.3 - - - -
206B GLN* 1.3 86.3 - - - +
208B ALA* 1.3 58.0 + - - +
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Residues in contact with ALA 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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122B VAL* 3.2 23.1 - - + +
123B LEU 4.4 0.4 - - - -
124B PRO* 4.3 12.3 - - + -
200B HIS* 3.6 2.9 - - - -
201B CYS 2.9 29.0 + - - +
203B VAL* 5.8 2.0 - - + -
206B GLN* 4.7 5.2 - - - +
207B TYR* 1.3 76.9 - - - +
209B VAL* 1.3 62.6 + - - +
210B HIS* 3.1 26.9 + - + +
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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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29B SER* 4.3 4.5 - - - +
45B THR* 3.9 16.6 - - + +
53B MET* 3.8 22.4 - - + -
121B GLY* 4.7 4.7 - - - -
122B VAL 2.7 17.8 + - - +
123B LEU* 4.0 6.9 - - + +
124B PRO* 3.2 17.3 - - - +
198B PRO* 3.6 28.0 - - + -
199B LEU 3.5 4.7 - - - +
200B HIS* 3.9 16.4 - - + +
208B ALA* 1.3 70.0 - - - +
210B HIS* 1.3 56.1 + - - +
211B GLY 3.5 21.8 - - - +
231B VAL* 3.4 11.8 - - + +
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Residues in contact with HIS 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* 3.5 30.7 - - + +
128B THR* 4.0 24.2 + - + -
130B LEU* 3.5 34.5 - - + +
181B VAL* 4.0 12.4 - - + +
199B LEU* 3.0 6.7 + - + -
201B CYS* 3.7 28.7 - - + -
203B VAL* 3.7 17.2 - - + +
208B ALA* 3.1 37.1 + - + +
209B VAL* 1.3 74.1 - - - +
211B GLY* 1.3 58.1 + - - +
230B ARG* 3.7 8.1 - - - +
231B VAL* 3.0 25.4 + - - +
232B SER* 4.6 1.0 + - - -
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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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181B VAL* 5.2 0.7 - - - -
198B PRO* 3.4 7.4 - - - +
199B LEU* 3.0 34.9 + - - +
209B VAL* 3.4 8.5 - - - +
210B HIS* 1.3 82.2 - - - +
212B VAL* 1.3 65.0 + - - +
228B PHE* 3.8 14.6 - - - -
229B THR 3.3 8.1 - - - -
231B VAL* 3.8 1.3 - - - -
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Residues in contact with VAL 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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53B MET* 3.9 38.8 - - + -
54B THR 3.6 7.4 - - - +
55B ALA* 3.6 34.3 - - + +
102B ASP 4.2 4.9 - - - +
103B ILE* 4.6 7.2 - - + -
196B GLY* 3.7 13.5 - - - +
197B GLY 3.3 4.5 - - - +
211B GLY* 1.3 73.9 - - - -
213B THR* 1.3 68.9 + - - +
214B SER 3.1 0.3 + - - -
228B PHE* 3.2 2.7 - - - +
229B THR* 2.8 45.4 + - - +
231B VAL* 3.9 6.7 - - + -
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Residues in contact with THR 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* 3.7 7.6 - - - +
138B ILE* 3.8 10.7 - - + +
139B THR 5.3 0.2 + - - -
190B GLY* 5.2 2.0 - - - -
191B CYS 5.4 1.8 - - - +
194B ASP* 3.4 30.1 + - + +
195B SER* 3.5 18.3 - - - +
196B GLY 2.8 24.0 + - - +
197B GLY 2.9 17.8 + - - -
212B VAL* 1.3 70.2 - - - +
214B SER* 1.3 63.3 + - - +
215B PHE* 5.8 0.7 - - - -
216B VAL* 6.0 1.3 - - + -
226B THR* 4.2 22.2 - - + -
228B PHE* 3.4 23.1 - - + -
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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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57B HIS* 3.1 22.6 + - - -
99B VAL* 3.4 15.2 + - - +
102B ASP* 2.5 31.6 + - - +
180B MET* 6.5 0.7 - - - -
195B SER* 4.3 3.3 + - - -
212B VAL 3.1 6.9 + - - -
213B THR* 1.3 77.8 - - - +
215B PHE* 1.3 70.6 + - - +
227B VAL 2.9 17.2 + - - -
228B PHE 4.5 0.7 - - - -
229B THR* 4.0 14.4 - - - -
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Residues in contact with PHE 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 VAL* 3.8 39.7 - - + -
172B TRP* 3.7 31.2 - + - -
175B THR* 4.3 18.2 - - + -
176B VAL* 4.7 1.8 - - + -
180B MET* 4.0 16.4 - - + -
213B THR* 5.0 1.3 - - - +
214B SER* 1.3 95.5 - - - +
216B VAL* 1.3 72.6 + - - +
226B THR* 4.0 1.2 - - - +
227B VAL* 2.9 69.7 + - + +
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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