Contacts of the strand formed by residues 164 - 172 (chain B) in PDB entry 5ODS
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 TRP 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B THR* 3.1 8.0 - - - -
159B ASP* 2.8 40.2 + - - +
163B LYS* 1.3 93.3 + - + +
165B LEU* 1.3 62.9 + - - +
183B LEU* 4.0 33.0 - - + -
184B TYR 3.5 9.6 - - - -
185B SER* 3.6 37.7 - - - -
188B ARG* 4.6 13.0 - - - -
201B PHE* 3.7 21.2 - - + -
214B THR* 4.9 2.7 - - + -
233B VAL* 3.5 34.9 + - + +
234B GLY* 3.3 32.4 - - - -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B HIS* 4.0 9.9 - - + -
141B MET* 3.9 18.4 - - + -
142B PHE* 3.6 29.2 - - + -
156B TYR* 3.2 27.4 - - - +
157B ARG 3.5 3.4 - - - -
158B THR* 3.6 20.6 - - + -
162B GLN* 4.2 15.9 - - + +
164B TRP* 1.3 78.4 - - - +
166B LEU* 1.3 61.2 + - - +
182B GLN 3.5 1.7 - - - +
183B LEU* 3.6 5.0 - - - +
184B TYR* 2.9 48.0 + - + +
186B VAL* 4.1 14.1 - - + -
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Residues in contact with LEU 166 (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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156B TYR* 3.2 10.8 - - - -
157B ARG* 2.7 51.6 + - + +
165B LEU* 1.3 75.8 - - - +
167B LEU* 1.3 60.6 + - - +
168B THR* 3.9 18.0 + - - +
181B MET* 4.1 18.4 - - + -
182B GLN 3.5 11.7 - - - +
183B LEU* 3.9 15.9 - - + -
194B ILE* 5.3 0.2 - - + -
199B ALA* 3.5 32.3 - - + -
201B PHE* 3.9 16.4 - - + -
216B PHE* 3.7 26.5 - - + -
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Residues in contact with LEU 167 (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* 3.7 22.4 - - + -
127B VAL* 4.1 8.3 - - + -
142B PHE* 4.3 10.5 - - + -
144B ARG* 3.8 33.0 - - + -
148B LEU* 3.7 23.1 - - + +
153B ILE* 3.7 31.4 - - + -
155B ASN 3.8 6.1 - - - +
156B TYR* 3.9 14.6 - - + -
166B LEU* 1.3 73.6 - - - +
168B THR* 1.3 61.4 + - - +
181B MET* 3.2 5.2 - - - +
182B GLN* 3.0 41.4 + - + +
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Residues in contact with THR 168 (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 LEU* 4.2 2.2 - - - -
153B ILE* 3.5 5.9 - - - +
154B ILE* 3.0 37.2 + - + -
155B ASN* 3.0 24.8 + - - +
166B LEU* 3.9 11.6 + - - +
167B LEU* 1.3 75.7 + - - +
169B GLY* 1.3 64.5 + - - +
170B ILE* 5.2 2.2 - - + -
180B ALA 3.5 2.0 - - - +
181B MET* 3.7 31.0 - - + +
196B GLY 3.9 5.8 - - - +
197B HIS* 3.8 22.7 - - - +
198B ALA* 5.4 0.4 - - - -
199B ALA* 5.3 2.6 + - - +
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Residues in contact with GLY 169 (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 LEU* 3.8 2.9 - - - +
151B CYS* 3.9 17.7 - - - -
152B GLN 3.4 10.5 - - - -
153B ILE* 4.0 7.9 - - - -
154B ILE* 4.4 0.7 - - - -
168B THR* 1.3 75.0 - - - +
170B ILE* 1.3 63.4 + - - +
179B GLY* 3.7 0.2 - - - -
180B ALA* 2.7 44.0 + - - +
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Residues in contact with ILE 170 (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 CYS* 3.9 2.0 - - - +
152B GLN* 2.9 59.9 + - + +
154B ILE* 4.4 20.6 - - + -
168B THR* 5.2 1.3 - - + -
169B GLY* 1.3 79.5 - - - +
171B SER* 1.3 62.4 + - - +
177B VAL* 3.8 28.3 - - + -
178B VAL 3.4 3.1 - - - +
179B GLY* 3.8 17.7 - - - -
197B HIS* 4.2 14.4 - - + +
260B PHE* 5.5 6.5 - - + -
278B LYS* 6.2 1.6 - - - +
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Residues in contact with SER 171 (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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150B GLY 4.7 5.8 - - - -
151B CYS* 3.9 22.1 - - - -
170B ILE* 1.3 78.8 - - - +
172B ALA* 1.3 60.2 + - - +
173B GLN* 3.5 23.6 + - - +
177B VAL* 3.6 4.1 - - - -
178B VAL* 2.7 38.4 + - - +
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Residues in contact with ALA 172 (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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171B SER* 1.3 71.2 - - - +
173B GLN* 1.3 75.1 + - - +
174B GLN 4.1 1.0 + - - -
175B ASN* 5.2 3.6 - - - +
176B ARG 3.6 9.2 - - - +
177B VAL* 4.7 6.7 - - + +
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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