Contacts of the strand formed by residues 201 - 210 (chain B) in PDB entry 1U5Y
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 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ARG 4.5 0.7 - - - -
187A CYS* 3.6 12.3 - - - -
188A ILE* 2.8 38.3 + - - -
189A ARG* 3.0 23.6 + - - -
159B GLN* 3.6 30.6 + - - -
160B VAL 3.5 6.5 - - - -
161B LEU* 4.0 12.6 - - - +
189B ARG* 3.4 7.5 + - - -
200B ASN* 1.3 71.9 - - - +
202B CYS* 1.3 60.8 + - - +
203B TYR* 4.0 1.2 + - - -
233B GLY 4.8 0.2 - - - -
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Residues in contact with CYS 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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159B GLN* 3.0 5.8 - - - -
160B VAL 2.9 33.4 + - - +
162B PHE* 3.8 10.8 - - + -
169B MET 4.6 0.2 - - - -
170B GLY* 4.3 5.4 - - - -
171B GLN* 3.1 18.0 + - - +
187B CYS* 2.0 47.3 - - - -
188B ILE* 3.7 7.6 - - - -
189B ARG* 3.6 27.6 - - + +
200B ASN 4.9 0.2 - - - +
201B SER* 1.3 72.9 - - - +
203B TYR* 1.3 60.0 + - - +
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Residues in contact with TYR 203 (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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155A LEU* 5.7 1.2 - - - +
189A ARG* 6.0 0.2 - - - +
203A TYR* 3.5 45.3 + + + +
205A ALA* 3.2 47.9 - - + +
155B LEU* 6.2 0.2 - - - +
157B TYR* 3.1 33.5 - + + +
158B SER 3.3 11.2 - - - -
159B GLN* 3.8 24.7 - - + +
187B CYS* 3.6 10.1 - - - -
189B ARG* 3.6 9.8 + - - +
201B SER 4.0 1.3 - - - +
202B CYS* 1.3 73.2 - - - +
204B SER* 1.3 67.5 + - - +
205B ALA* 3.8 14.6 - - + +
235B PHE* 4.2 4.5 - + - -
159D GLN* 4.4 0.3 - - - +
201D SER* 5.4 0.2 + - - -
203D TYR* 3.6 31.3 - + + +
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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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157B TYR* 3.9 0.5 - - - +
158B SER 2.8 32.5 + - - -
171B GLN* 5.3 0.4 - - - -
185B PHE* 3.2 28.0 - - - -
186B ARG 3.8 9.3 + - - -
187B CYS* 4.1 9.8 - - - +
203B TYR* 1.3 83.5 - - - +
205B ALA* 1.3 64.2 + - - +
159D GLN* 2.6 27.3 + - - -
203D TYR* 4.1 4.4 - - - -
235D PHE* 3.6 6.2 - - - -
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Residues in contact with ALA 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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155B LEU* 4.5 9.2 - - + -
156B LEU 3.1 15.7 - - - +
157B TYR* 3.5 15.7 - - + -
185B PHE* 4.0 6.3 - - - -
203B TYR* 3.8 8.7 - - + +
204B SER* 1.3 79.8 + - - +
206B GLY* 1.3 59.6 + - - +
157D TYR* 3.8 1.4 - - - -
203D TYR* 3.3 28.0 + - - +
235D PHE* 3.3 24.2 - - - -
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Residues in contact with GLY 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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155B LEU* 3.5 4.4 - - - +
156B LEU 2.9 30.8 + - - +
185B PHE* 4.3 0.2 - - - -
205B ALA* 1.3 75.9 - - - +
207B VAL* 1.3 63.1 + - - -
208B PHE* 3.3 27.0 - - - -
110D HIS* 4.8 0.2 - - - -
157D TYR* 3.8 15.7 - - - -
235D PHE* 4.7 1.3 - - - -
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Residues in contact with VAL 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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153B ILE* 3.3 29.4 - - + -
154B TYR 3.3 3.8 - - - +
155B LEU* 3.9 13.9 - - + -
206B GLY* 1.3 75.0 - - - -
208B PHE* 1.3 69.3 + - - +
241B LEU* 3.7 15.3 - - + -
108D VAL* 4.2 11.7 - - + -
109D LEU 6.0 0.4 - - - +
110D HIS* 3.5 24.0 - - + -
133D LEU* 3.6 12.5 - - + +
155D LEU* 5.5 0.2 - - + -
157D TYR* 3.0 23.7 + - + +
238D PHE 5.7 0.7 - - - +
239D VAL* 3.7 25.6 - - + -
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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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153B ILE* 4.4 1.1 - - - -
154B TYR* 2.9 33.7 + - - +
156B LEU* 4.4 11.4 - - + -
182B GLU* 5.9 0.7 - - - -
184B LEU* 3.2 57.4 - - + -
185B PHE* 3.4 25.1 - + + -
206B GLY* 3.3 28.0 - - - -
207B VAL* 1.3 77.4 - - - +
209B HIS* 1.3 63.0 - - - +
210B LEU* 3.4 19.5 + - + +
110D HIS* 3.6 30.5 - + - -
133D LEU* 3.9 7.4 - - - -
235D PHE* 5.7 0.7 - + - -
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Residues in contact with HIS 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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151B THR* 3.7 27.3 - - + +
152B GLY* 3.5 9.3 + - - -
153B ILE* 3.9 24.0 - - + +
175B ARG* 3.8 20.4 + - - +
208B PHE* 1.3 71.4 - - - +
210B LEU* 1.3 65.9 + - - +
211B HIS* 3.1 41.2 + + - +
133D LEU* 3.9 22.9 - - + +
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Residues in contact with LEU 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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148B VAL* 4.0 24.0 - - + -
151B THR* 3.4 6.9 - - - +
152B GLY 2.8 34.7 + - - +
154B TYR* 4.0 32.3 - - + -
156B LEU* 4.5 6.5 - - + -
175B ARG* 4.1 15.5 - - - +
184B LEU* 4.2 12.6 - - + -
208B PHE* 3.4 14.1 + - + +
209B HIS* 1.3 82.0 + - - +
211B HIS* 1.3 61.7 + - - +
214B ASP* 3.8 1.3 - - - +
216B ILE* 3.8 33.9 - - + -
238B PHE* 4.2 13.9 - - + -
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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