Contacts of the strand formed by residues 185 - 192 (chain B) in PDB entry 4P22
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 LYS 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B GLN* 3.0 17.5 + - - +
161B VAL* 3.4 7.5 - - + +
162B VAL* 3.0 25.1 + - - -
183B GLY 4.6 3.4 - - - +
184B ILE* 1.3 73.1 - - - +
186B LEU* 1.3 60.2 + - - +
201B ASP 3.5 7.0 - - - +
202B PHE* 3.7 23.1 - - + +
205B GLU* 3.4 23.2 + - - +
206B MET* 3.2 27.1 - - + +
412B ALA* 3.0 50.0 + - + +
413B CYS 5.4 0.6 + - - -
415B GLY 5.4 1.8 + - - +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL* 3.5 29.4 - - + +
164B LEU* 4.1 18.4 - - + -
172B GLN 4.9 1.3 - - - +
175B VAL* 4.5 2.9 - - + -
176B GLY* 3.8 25.8 - - - +
179B CYS* 4.3 18.6 - - + -
184B ILE 3.6 1.2 + - - +
185B LYS* 1.3 73.7 - - - +
187B VAL* 1.3 64.6 + - - +
188B VAL* 4.1 20.4 - - + -
199B PHE* 4.0 5.9 - - + +
200B CYS* 3.5 3.5 - - - +
201B ASP* 2.8 50.6 + - + +
202B PHE* 4.3 1.0 - - - -
306B LEU* 4.3 17.5 - - + +
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B VAL* 5.1 5.8 - - + -
162B VAL 3.0 10.6 + - - +
163B VAL* 3.4 17.2 - - + +
164B LEU* 2.9 25.8 + - - +
186B LEU* 1.3 79.6 - - - +
188B VAL* 1.3 70.2 + - - +
189B ALA 4.8 0.4 - - - +
198B LEU* 4.3 16.4 - - + -
199B PHE 3.3 9.0 - - - +
200B CYS* 3.7 17.5 - - - -
202B PHE* 4.0 11.7 - - + -
405B ALA* 4.5 20.9 - - + +
408B GLU* 4.1 9.4 - - + -
409B VAL* 4.6 12.3 - - + +
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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
----------------------------------------------------------
164B LEU* 3.6 19.3 - - + +
172B GLN* 3.4 37.0 - - + +
186B LEU* 4.1 18.6 - - + -
187B VAL* 1.3 77.7 - - - +
189B ALA* 1.3 64.3 + - - +
190B ASP* 5.8 0.4 - - + -
197B GLN* 3.8 15.6 - - - +
198B LEU* 3.5 4.3 - - - +
199B PHE* 2.8 61.7 + - + +
306B LEU* 4.6 9.2 - - + -
423B TRP* 6.0 1.3 - - + -
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Residues in contact with ALA 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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83B LEU* 3.5 21.0 - - + +
87B ILE* 4.1 21.5 - - + -
163B VAL* 5.3 1.1 - - + -
164B LEU 3.1 18.2 + - - +
165B THR* 3.6 10.8 - - + -
166B ASN 4.6 0.2 + - - -
187B VAL* 4.1 3.3 + - + -
188B VAL* 1.3 77.5 - - - +
190B ASP* 1.3 65.0 + - - +
197B GLN 3.5 3.8 - - - -
198B LEU* 3.7 19.1 - - + -
401B ILE* 4.8 0.9 - - + -
405B ALA* 4.1 4.9 - - + -
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Residues in contact with ASP 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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83B LEU* 3.7 8.2 - - - +
166B ASN* 4.5 12.5 + - - -
172B GLN* 5.8 4.7 - - - +
188B VAL* 5.8 0.7 - - + -
189B ALA* 1.3 76.0 - - - +
191B THR* 1.3 69.4 + - - +
192B ARG* 2.9 37.5 + - - -
196B GLY* 3.4 4.2 - - - -
197B GLN* 2.9 60.7 + - + +
333B PHE* 3.6 12.4 - - + -
337B HIS* 4.8 5.4 + - - -
401B ILE* 4.4 3.8 - - - +
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Residues in contact with THR 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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83B LEU* 4.0 7.9 - - - +
190B ASP* 1.3 80.9 + - - +
192B ARG* 1.3 76.1 + - - +
193B GLY 3.6 24.4 + - - +
195B PHE 3.4 3.7 + - - -
392B GLY 4.4 8.6 - - - +
393B ASP* 4.7 6.1 - - - +
394B LEU 4.9 3.4 - - - +
397B ILE* 3.3 19.2 - - + +
398B ASN* 3.1 30.6 + - - +
401B ILE* 4.3 10.7 - - - +
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Residues in contact with ARG 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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190B ASP* 2.9 27.0 + - - -
191B THR* 1.3 78.5 + - - +
193B GLY* 1.3 64.6 + - - +
194B LEU 3.0 0.9 + - - -
195B PHE* 2.8 23.6 + - - +
333B PHE* 3.6 24.2 - - + -
336B LEU* 3.5 41.1 - - + +
337B HIS* 3.9 24.1 + - - -
340B CYS* 3.9 18.4 - - - -
346B PRO* 5.3 4.0 - - - +
386B LEU* 4.0 17.5 - - + -
389B VAL* 3.2 13.5 - - - +
390B ALA* 4.3 18.7 + - - +
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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