Contacts of the strand formed by residues 185 - 195 (chain B) in PDB entry 5WJ9
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 ASP 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B TYR* 4.2 8.8 - - - -
171B HIS* 4.5 1.3 + - - +
172B ARG* 3.2 38.2 + - + +
184B ILE* 1.3 80.8 - - - +
186B PRO* 1.3 68.4 - - + +
187B MET* 2.8 36.3 + - - +
289C VAL* 3.8 19.1 - - + +
290C PHE* 5.4 2.2 - - + -
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Residues in contact with PRO 186 (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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170B TYR* 4.3 16.2 - - + -
184B ILE 4.8 0.2 - - - +
185B ASP* 1.3 82.2 - - + +
187B MET* 1.3 59.7 + - - +
188B VAL* 4.0 5.1 + - + -
245C LEU* 4.2 32.7 - - + +
248C ASN* 5.2 6.1 - - - +
250C ILE* 5.9 0.4 - - + -
289C VAL* 5.9 1.1 - - + -
290C PHE* 4.7 27.8 - - + -
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Residues in contact with MET 187 (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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170B TYR* 3.7 2.1 - - - -
171B HIS* 2.8 61.9 + - + +
185B ASP* 2.8 26.1 + - - +
186B PRO* 1.3 72.5 - - - +
188B VAL* 1.3 64.6 + - - +
189B VAL* 5.5 1.3 - - + -
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Residues in contact with VAL 188 (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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168B ARG* 4.5 30.1 - - + +
169B TYR 3.5 6.7 - - - +
170B TYR* 5.2 5.4 - - + -
186B PRO* 4.0 3.8 - - + -
187B MET* 1.3 75.4 - - - +
189B VAL* 1.3 62.5 + - - +
190B THR* 3.8 10.8 + - - +
229B VAL* 4.2 27.4 - - + -
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Residues in contact with VAL 189 (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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167B GLN 2.9 15.6 - - - +
168B ARG* 3.8 1.1 - - - -
169B TYR* 2.8 57.1 + - + +
171B HIS* 3.6 48.2 - - + +
187B MET* 4.1 1.8 - - + +
188B VAL* 1.3 73.0 - - - +
190B THR* 1.3 66.1 + - - +
191B ASP* 4.6 1.1 - - + +
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Residues in contact with THR 190 (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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166B CYS* 4.0 11.7 - - + -
167B GLN 3.5 5.2 - - - +
168B ARG* 5.0 11.1 - - + +
188B VAL* 3.8 14.3 + - - +
189B VAL* 1.3 75.9 - - - +
191B ASP* 1.3 57.5 + - - +
192B CYS* 3.2 32.8 + - - +
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Residues in contact with ASP 191 (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 LEU 3.7 2.1 - - - +
166B CYS* 3.3 1.4 - - - -
167B GLN* 2.8 59.1 + - + +
169B TYR* 3.8 23.7 - - + +
189B VAL* 3.6 3.3 + - + +
190B THR* 1.3 68.4 - - - +
192B CYS* 1.3 58.0 + - - +
193B ILE* 3.5 25.9 + - - +
221B LEU* 4.4 1.9 - - - +
222B THR 5.1 0.7 - - - +
224B LYS* 5.8 0.8 + - - +
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Residues in contact with CYS 192 (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 PRO* 4.6 7.6 - - - -
165B LEU 3.4 3.8 - - - -
166B CYS* 2.0 45.3 - - - -
190B THR* 3.2 25.8 + - - +
191B ASP* 1.3 71.6 - - - +
193B ILE* 1.3 66.5 + - - +
194B GLN* 3.0 31.5 - - - +
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B LEU 3.9 0.3 - - - +
164B ALA* 3.5 2.7 - - - -
165B LEU* 2.8 43.8 + - + +
191B ASP* 3.5 31.2 - - - +
192B CYS* 1.3 74.3 - - - +
194B GLN* 1.3 69.6 + - - +
195B VAL* 3.9 6.1 + - + +
217B SER* 4.6 9.9 - - - +
218B TYR* 4.2 31.4 - - + +
221B LEU* 3.8 25.6 - - + -
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Residues in contact with GLN 194 (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 PRO 3.0 27.7 + - - -
157B TRP* 4.3 1.4 - - - +
158B THR* 3.6 27.3 - - + +
161B SER* 3.3 31.6 - - - +
163B LEU 3.7 2.7 - - - -
164B ALA* 3.8 7.0 - - + +
192B CYS* 3.0 33.4 - - - +
193B ILE* 1.3 79.1 - - - +
195B VAL* 1.3 64.9 + - - +
217B SER* 5.5 5.0 - - - -
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Residues in contact with VAL 195 (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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133B VAL* 4.6 9.2 - - + -
136B TYR* 4.1 1.2 - - - -
137B LEU* 4.3 18.8 - - + -
161B SER* 4.3 1.9 - - - -
162B GLY 4.1 2.0 - - - -
163B LEU* 2.8 74.4 + - + +
165B LEU* 6.2 2.0 - - + -
193B ILE* 4.6 5.6 - - + +
194B GLN* 1.3 77.7 - - - +
196B ASP* 1.3 65.5 + - - +
216B SER* 5.0 9.4 - - - +
217B SER* 6.5 0.9 - - - -
218B TYR* 4.6 23.1 - - + -
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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