Contacts of the strand formed by residues 202 - 214 (chain B) in PDB entry 3O4O
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 THR 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B THR* 4.0 20.9 - - + -
196B TYR 3.3 7.4 - - - +
197B PRO* 4.6 9.9 - - + -
201B ARG* 1.3 92.5 + - - +
203B PHE* 1.3 62.8 + - - +
204B HIS* 4.0 14.1 + - - -
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Residues in contact with PHE 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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22B PRO* 3.6 30.3 - - + -
82B ARG* 4.1 23.3 - - + -
83B PRO* 3.8 27.1 - - + -
194B VAL 4.0 0.5 - - - +
195B THR* 3.4 6.8 - - - +
196B TYR* 2.8 51.2 + + + -
198B GLU* 3.2 52.3 - - + -
201B ARG* 3.9 29.6 - - + +
202B THR* 1.3 73.1 - - - +
204B HIS* 1.3 62.3 + - - +
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Residues in contact with HIS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASP 5.2 3.4 + - - +
21B GLU* 2.9 38.5 - - + +
22B PRO* 3.3 3.6 - - - +
114B LYS* 5.1 7.4 - - - +
193B VAL* 4.5 15.5 - - + -
194B VAL 3.8 2.0 - - - -
195B THR* 4.2 27.4 + - + +
202B THR* 4.0 14.3 + - - -
203B PHE* 1.3 78.3 - - - +
205B LEU* 1.3 73.9 + - - +
206B THR* 5.1 1.1 - - + +
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Residues in contact with LEU 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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21B GLU* 3.4 3.4 - - - -
22B PRO* 4.1 11.2 - - + +
143B VAL* 4.2 12.8 - - + +
146B TYR* 3.7 39.0 - - + -
147B PHE* 4.8 2.2 - - + -
192B CYS 3.9 1.2 - - - +
193B VAL* 3.4 2.6 - - - +
194B VAL* 2.8 58.0 + - + +
196B TYR* 3.4 31.0 - - + -
204B HIS* 1.3 90.4 - - - +
206B THR* 1.3 60.5 + - - +
207B ARG* 3.5 33.9 + - - +
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Residues in contact with THR 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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18B PHE* 3.3 27.7 - - + -
21B GLU* 3.0 22.2 + - - +
114B LYS* 3.0 43.2 - - + +
118B PHE* 3.9 19.3 - - + -
191B THR* 4.1 3.8 + - - -
192B CYS 3.5 3.6 - - - -
193B VAL* 4.1 22.7 - - + -
204B HIS* 5.2 0.9 - - + -
205B LEU* 1.3 73.6 - - - +
207B ARG* 1.3 67.1 + - - +
208B THR* 4.9 1.2 - - - +
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Residues in contact with ARG 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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18B PHE* 5.0 1.6 - - - -
21B GLU* 4.6 7.7 + - - -
22B PRO 4.3 11.9 + - - -
140B CYS* 4.3 4.3 - - - -
141B PRO* 4.0 14.6 - - + -
142B ASN* 2.6 61.1 + - - +
143B VAL* 4.5 2.5 - - - +
146B TYR* 3.9 11.3 + - - -
191B THR* 3.6 1.3 - - - -
192B CYS* 3.1 52.8 + - - +
205B LEU* 3.5 40.5 - - - +
206B THR* 1.3 81.9 + - - +
208B THR* 1.3 64.6 + - - +
209B LEU* 4.5 3.6 - - - +
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Residues in contact with THR 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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18B PHE* 4.5 20.8 - - + -
118B PHE* 5.0 13.9 - - + +
122B MET* 5.7 4.1 - - + +
124B LEU* 3.3 46.2 - - + +
125B PRO* 3.6 9.7 - - - +
141B PRO* 5.1 1.5 - - - +
189B ASN* 4.5 3.1 - - - +
190B TYR 3.2 18.0 + - - -
191B THR* 3.4 16.8 - - + +
206B THR* 4.9 2.2 - - - +
207B ARG* 1.3 80.1 - - - +
209B LEU* 1.3 64.2 + - - +
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Residues in contact with LEU 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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124B LEU* 4.4 1.6 - - - -
125B PRO* 3.5 27.4 - - + +
127B HIS* 4.6 13.0 - - + -
138B ILE* 4.2 25.8 - - + -
141B PRO* 3.5 36.6 - - + -
157B TRP* 5.0 9.6 - - + -
190B TYR* 2.8 33.8 + - + +
207B ARG 4.5 2.7 - - - +
208B THR* 1.3 80.5 + - - +
210B THR* 1.3 64.9 + - - +
211B VAL* 4.1 21.3 - - + -
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Residues in contact with THR 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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124B LEU* 3.5 34.1 - - + +
125B PRO 3.0 7.2 + - - +
126B VAL* 3.5 21.9 - - + +
127B HIS* 2.9 26.7 + - - -
188B GLY 3.7 6.3 - - - -
189B ASN* 3.5 29.6 - - + +
209B LEU* 1.3 71.9 - - - +
211B VAL* 1.3 64.3 + - - +
212B LYS* 5.6 1.0 - - - +
1E NAG 3.8 10.1 - - - +
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Residues in contact with VAL 211 (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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127B HIS* 3.7 9.6 - - + +
129B LEU* 3.6 33.2 - - + -
138B ILE* 3.3 27.4 - - + -
179B PHE* 3.9 8.5 - - + -
186B ASN 4.4 5.2 - - - +
187B ASN* 3.7 4.3 - - - +
188B GLY 3.1 25.0 + - - +
190B TYR* 3.4 34.5 - - + -
209B LEU* 4.1 7.6 - - + -
210B THR* 1.3 75.9 + - - +
212B LYS* 1.3 66.3 + - - +
213B VAL* 4.9 4.0 - - + +
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Residues in contact with LYS 212 (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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126B VAL* 4.1 23.8 - - + -
127B HIS 3.1 6.3 + - - +
128B LYS* 3.4 6.1 - - + -
129B LEU* 2.7 33.1 + - - -
187B ASN* 3.7 21.9 - - - +
210B THR* 4.7 1.1 - - - +
211B VAL* 1.3 78.3 - - - +
213B VAL* 1.3 75.1 + - - +
214B VAL* 3.7 4.5 + - + +
286B ARG 2.7 30.1 + - - -
288B GLU* 3.5 32.6 - - - +
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Residues in contact with VAL 213 (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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129B LEU* 3.1 11.7 - - + +
131B ILE* 3.7 40.4 - - + -
182B ALA* 4.0 16.8 - - + +
183B LEU 3.3 27.4 - - - +
184B ILE* 4.3 8.2 - - + +
186B ASN* 4.1 12.1 - - + -
187B ASN* 3.3 20.5 + - - +
211B VAL* 5.1 3.6 - - + -
212B LYS* 1.3 89.1 + - - +
214B VAL* 1.3 66.1 + - - +
286B ARG 4.4 0.3 - - - +
287B THR* 4.2 6.6 + - - +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LYS* 3.9 23.6 - - + -
129B LEU 2.7 24.9 + - - +
130B TYR* 3.4 18.7 - - + -
131B ILE* 2.6 38.5 + - - +
212B LYS* 4.0 8.3 - - + +
213B VAL* 1.3 79.6 - - - +
215B GLY* 1.3 56.9 - - - +
252B PHE* 3.6 23.1 - - + -
287B THR* 3.4 21.3 - - - +
288B GLU* 4.1 18.2 - - - -
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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