Contacts of the strand formed by residues 192 - 205 (chain O) in PDB entry 4IL6
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 192 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124O ASN* 6.0 0.2 - - - +
147O ASN* 4.1 28.7 - - + +
148O VAL 3.5 2.2 - - - +
149O PRO* 3.8 28.7 - - + -
190O PHE 3.8 2.7 + - - +
191O SER* 1.3 74.8 + - - +
193O THR* 1.3 65.7 - - - +
194O LYS* 5.9 2.9 - - - +
89U THR* 3.8 35.0 - - + +
93U GLU* 4.3 6.7 - - - +
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Residues in contact with THR 193 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147O ASN* 3.7 5.5 + - - +
148O VAL* 2.7 49.9 + - - +
191O SER* 3.6 17.2 + - - +
192O LEU* 1.3 80.6 - - - +
194O LYS* 1.3 67.7 + - - +
220O LEU* 3.8 36.8 - - + +
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Residues in contact with LYS 194 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145O GLU* 3.7 30.7 - - + +
146O PHE 3.5 8.7 - - - +
147O ASN* 3.2 28.1 - - - +
148O VAL* 4.3 3.6 - - - +
192O LEU* 5.9 3.8 - - - +
193O THR* 1.3 82.0 + - - +
195O GLY* 1.3 58.0 + - - +
196O GLN* 3.9 17.3 + - - +
219O GLN* 4.8 5.9 - - - -
220O LEU* 5.1 3.8 + - - +
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Residues in contact with GLY 195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145O GLU* 3.2 11.8 - - - +
146O PHE* 2.9 51.4 + - - -
148O VAL* 4.0 6.3 - - - +
194O LYS* 1.3 73.4 - - - +
196O GLN* 1.3 64.1 + - - -
218O GLU 3.2 13.5 - - - -
219O GLN* 4.3 1.1 - - - -
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Residues in contact with GLN 196 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144O GLY 3.5 5.2 - - - +
145O GLU* 2.8 33.8 + - + +
146O PHE* 3.5 1.8 - - - -
194O LYS* 3.9 16.6 + - - +
195O GLY* 1.3 83.6 - - - +
197O ILE* 1.3 61.6 + - - +
216O GLU 4.1 0.2 - - - +
217O SER* 3.2 4.5 + - - -
218O GLU* 2.8 54.2 + - + +
219O GLN* 5.7 0.2 - - - -
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Residues in contact with ILE 197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O LEU* 3.7 30.5 - - + -
120O PHE* 6.0 0.4 - - + -
122O VAL* 4.0 12.6 - - + -
125O LEU* 3.5 37.9 - - + -
127O ALA* 5.2 2.7 - - + -
142O PHE 3.9 0.2 - - - +
143O LYS* 3.3 2.9 - - - +
144O GLY 2.9 41.5 + - - +
146O PHE* 3.8 10.5 - - + -
196O GLN* 1.3 75.8 - - - +
198O SER* 1.3 73.8 + - - +
199O LEU* 3.9 13.5 - - + -
215O PHE* 4.0 4.0 - - + -
216O GLU 3.4 12.3 - - - +
217O SER* 3.9 15.7 - - - +
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Residues in contact with SER 198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141O ASP* 6.3 0.7 - - - -
142O PHE 3.2 4.5 - - - -
143O LYS* 3.3 40.8 - - - +
197O ILE* 1.3 75.1 + - - +
199O LEU* 1.3 63.1 + - - +
200O ASN* 4.1 1.2 + - - -
215O PHE* 3.2 5.4 - - - +
216O GLU* 2.9 40.3 + - - -
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Residues in contact with LEU 199 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O LEU* 5.0 11.9 - - + -
45O LEU* 4.5 10.5 - - + -
95O PHE* 5.9 3.1 - - + -
125O LEU* 5.3 9.2 - - + -
127O ALA* 5.2 6.5 - - + -
141O ASP* 3.2 8.8 - - - +
142O PHE* 2.6 65.2 + - + +
197O ILE* 3.9 21.8 - - + -
198O SER* 1.3 72.9 - - - +
200O ASN* 1.3 61.9 + - - +
201O VAL* 3.6 2.0 + - - +
214O THR 3.7 2.9 - - - -
215O PHE* 3.6 23.6 - - + -
239O PHE* 3.8 33.0 - - + -
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Residues in contact with ASN 200 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138O THR 4.8 1.6 - - - +
140O THR 4.9 0.7 - - - +
141O ASP* 4.2 10.5 + - + -
198O SER* 4.1 1.6 + - - -
199O LEU* 1.3 69.2 - - - +
201O VAL* 1.3 75.3 + - - +
202O ALA* 3.3 5.2 + - - +
213O GLY* 3.3 3.3 - - - -
214O THR* 2.8 47.1 + - - +
239O PHE* 3.8 2.0 - - - -
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Residues in contact with VAL 201 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O ILE* 4.7 2.7 - - + -
137O THR 3.6 8.1 - - - +
138O THR* 3.2 21.0 - - - +
140O THR* 3.3 33.6 + - - +
142O PHE* 4.6 14.1 - - + -
199O LEU 4.6 0.7 - - - +
200O ASN* 1.3 79.0 + - - +
202O ALA* 1.3 60.1 + - - +
203O LYS 3.6 20.0 - - - +
204O VAL* 3.6 20.2 - - + -
211O ILE* 4.2 21.5 - - + -
212O ALA 3.6 6.7 - - - +
239O PHE* 4.0 15.7 - - + -
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Residues in contact with ALA 202 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27O ARG* 3.2 22.6 + - - +
138O THR* 3.4 18.1 - - - +
200O ASN* 3.3 6.8 + - - +
201O VAL* 1.3 74.1 - - - +
203O LYS* 1.3 65.1 + - + +
212O ALA 2.8 5.5 + - - -
213O GLY* 3.8 17.9 - - - -
214O THR* 5.0 3.8 - - + +
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Residues in contact with LYS 203 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O LEU* 2.8 47.7 + - + +
23O ASP* 3.3 13.2 - - - +
24O ASP* 2.9 26.1 + - - -
26O ALA 3.4 10.3 - - - +
27O ARG* 3.5 29.6 - - - +
138O THR* 4.3 1.6 - - - -
201O VAL* 3.6 1.6 - - - +
202O ALA* 1.3 88.4 - - + +
204O VAL* 1.3 68.8 + - - +
211O ILE* 3.4 1.9 - - - -
212O ALA* 3.0 35.9 + - + +
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Residues in contact with VAL 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O ALA* 3.0 18.1 + - - -
28O GLY 2.9 41.5 + - - +
30O TYR* 3.9 17.0 - - + +
136O ILE 3.7 16.6 - - - +
137O THR* 3.7 24.2 - - - +
138O THR* 3.9 5.6 - - + +
201O VAL* 3.6 20.0 - - + -
203O LYS* 1.3 79.5 - - - +
205O ASP* 1.3 63.4 + - - +
206O GLY 4.0 4.9 - - - +
209O GLY 6.3 0.2 - - - -
210O GLU 3.6 4.5 - - - +
211O ILE* 3.9 15.5 - - + -
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Residues in contact with ASP 205 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O LEU* 4.4 9.3 - - + +
26O ALA* 4.3 16.4 - - + +
30O TYR* 4.8 0.2 - - - -
204O VAL* 1.3 73.6 - - - +
206O GLY* 1.3 58.4 + - - +
207O ARG* 3.2 14.8 + - - +
208O THR* 2.9 49.4 + - - +
209O GLY* 2.9 26.2 + - - -
210O GLU* 2.9 21.4 + - + +
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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