Contacts of the strand formed by residues 199 - 209 (chain B) in PDB entry 5I73
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 199 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LYS 5.4 0.4 - - - +
142B THR* 3.4 41.1 - - + +
168B LYS* 6.3 1.8 - - - -
169B GLY* 3.8 24.7 - - - -
170B TYR 3.5 6.1 - - - +
171B PHE* 4.3 2.2 - - + -
195B LEU* 3.6 4.2 - - - +
196B GLN* 2.8 38.6 + - + +
197B SER* 4.1 12.8 - - - +
198B GLY* 1.3 90.6 - - - +
200B TYR* 1.3 61.6 + - - +
201B THR* 4.3 1.0 + - - +
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Residues in contact with TYR 200 (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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135B THR* 5.4 3.5 - - - +
169B GLY* 2.9 19.2 + - - -
170B TYR* 2.7 53.3 + + + +
171B PHE* 3.5 23.4 - + - -
172B PRO* 3.5 15.3 - - + +
173B GLU* 3.4 42.5 + - + +
193B ALA* 4.1 19.1 - - + -
194B LEU 3.4 4.9 - - - -
195B LEU* 3.6 42.9 - - + +
199B LEU* 1.3 69.9 - - - +
201B THR* 1.3 68.6 + - - +
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Residues in contact with THR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.6 8.7 - - + -
167B VAL 3.3 16.6 - - - +
168B LYS* 3.9 16.8 - - + +
169B GLY* 3.4 10.0 + - - -
170B TYR* 4.2 1.1 - - - -
192B PRO 4.2 0.3 - - - +
193B ALA* 3.7 0.4 - - - -
194B LEU* 2.9 40.7 + - - +
196B GLN* 3.4 27.7 + - - +
199B LEU 4.3 1.9 + - - -
200B TYR* 1.3 83.4 + - - +
202B MET* 1.3 63.0 + - - +
180C LEU* 5.9 2.0 - - + -
198C THR* 6.0 5.4 - - + -
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Residues in contact with MET 202 (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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165B CYS 5.8 0.2 - - - +
166B LEU* 3.3 6.9 - - - +
167B VAL* 2.9 55.3 + - + +
170B TYR* 3.3 27.4 - - + +
175B VAL* 4.3 9.9 - - + -
177B VAL* 4.1 18.6 - - + -
190B THR* 3.7 18.6 - - + -
191B PHE* 3.5 20.2 - - - +
192B PRO 4.4 2.0 - - - -
193B ALA* 3.7 13.5 - - + +
201B THR* 1.3 74.2 - - - +
203B SER* 1.3 83.5 + - - +
204B SER* 4.7 1.6 - - - +
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Residues in contact with SER 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 4.8 1.6 - - - -
165B CYS 3.6 9.0 - - - -
166B LEU* 3.8 17.0 - - - -
191B PHE* 2.9 51.2 + - - +
202B MET* 1.3 86.7 - - - +
204B SER* 1.3 63.5 + - - +
153C VAL* 5.6 2.0 - - - -
155C PHE* 3.8 19.3 - - - -
196C SER* 3.9 5.5 + - - -
198C THR* 5.1 4.9 + - - -
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Residues in contact with SER 204 (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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164B GLY* 2.9 4.2 - - - -
165B CYS 2.9 32.2 + - - +
177B VAL* 4.4 20.4 + - - +
179B TRP* 3.4 27.3 + - - -
188B VAL* 3.9 1.0 - - - +
189B HIS 3.6 9.7 + - - -
190B THR* 3.8 14.3 + - - -
191B PHE* 4.3 0.7 - - - -
202B MET* 4.8 4.0 - - - -
203B SER* 1.3 77.1 - - - +
205B SER* 1.3 66.7 + - - +
155C PHE* 4.1 7.9 - - - -
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Residues in contact with SER 205 (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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162B THR* 4.2 7.4 - - - -
163B LEU 3.0 14.8 - - - -
164B GLY* 3.7 1.3 - - - -
179B TRP* 4.8 0.9 - - - -
188B VAL* 2.4 35.8 - - - +
189B HIS* 2.9 37.6 + - - +
191B PHE* 3.7 8.5 - - - -
204B SER* 1.3 77.3 + - - +
206B VAL* 1.3 56.8 + - - +
155C PHE* 3.6 22.2 - - - -
157C ASN* 4.2 6.3 + - - -
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Residues in contact with VAL 206 (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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162B THR* 3.4 2.5 - - - -
163B LEU* 2.7 61.9 + - + +
179B TRP* 3.9 32.3 - - + -
184B LEU* 5.0 11.0 - - + +
185B SER* 5.4 2.0 - - - -
187B SER* 3.8 10.3 - - - +
188B VAL* 3.8 20.9 - - + +
189B HIS* 5.8 0.2 - - - -
205B SER* 1.3 77.7 - - - +
207B THR* 1.3 65.3 + - - +
208B VAL* 3.6 21.1 + - + -
218B VAL* 5.3 1.3 - - + -
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Residues in contact with THR 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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160B SER* 4.0 27.4 - - - +
161B VAL 3.7 4.0 - - - +
162B THR* 3.5 22.9 + - - +
184B LEU* 6.1 0.3 - - - +
186B SER* 5.1 0.7 + - - -
187B SER* 2.8 44.7 + - - -
189B HIS* 4.7 6.1 + - - -
206B VAL* 1.3 71.9 - - - +
208B VAL* 1.3 64.3 + - - +
209B PRO* 4.5 1.9 - - - +
157C ASN* 4.6 7.4 + - - +
158C ASN* 5.4 3.1 + - - -
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Residues in contact with VAL 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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160B SER* 4.4 3.1 - - - -
161B VAL* 2.8 36.1 + - + +
163B LEU* 3.8 30.1 - - + -
184B LEU* 4.7 18.4 - - + +
206B VAL* 4.0 20.2 - - + +
207B THR* 1.3 79.3 - - - +
209B PRO* 1.3 77.7 - - + +
212B THR* 3.9 14.8 - - + -
213B TRP* 4.7 6.7 - - + -
218B VAL* 5.7 7.6 - - + -
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Residues in contact with PRO 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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159B SER 3.7 14.1 - - - +
160B SER* 4.0 4.7 - - - -
161B VAL* 4.4 0.6 - - - +
184B LEU* 6.0 3.8 - - + -
207B THR 4.5 2.5 - - - +
208B VAL* 1.3 95.8 - - + +
210B SER* 1.3 59.4 + - - +
211B SER* 3.0 23.9 + - - +
212B THR* 3.2 27.4 + - + +
213B TRP* 4.1 4.7 + - - +
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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