Contacts of the strand formed by residues 213 - 226 (chain N) in PDB entry 5U0A
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 ARG 213 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C MET* 5.3 11.5 - - - +
177C ASP* 5.2 8.3 + - - -
180C GLU* 4.6 17.3 - - - +
183C TRP* 6.0 5.2 - - - -
205N LEU* 3.0 61.0 + - + +
206N SER* 3.5 17.2 + - - +
211N SER* 3.4 19.8 + - - +
212N ARG* 1.3 78.6 - - - +
214N TYR* 1.3 71.4 + - - +
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Residues in contact with TYR 214 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C PRO* 5.8 3.8 - - - +
3K G 2.3 69.3 + + - -
33N SER* 3.0 19.1 - - - -
201N ASN* 3.8 25.2 + - + -
202N ASP 3.1 18.4 - - - -
203N VAL 3.4 5.4 - - - +
204N PRO* 3.3 23.1 - - + -
205N LEU* 3.6 7.4 - - - +
206N SER 4.9 0.9 - - - -
207N PHE* 4.0 9.0 - + - -
212N ARG* 3.3 32.7 + - + -
213N ARG* 1.3 82.7 - - - +
215N SER* 1.3 69.6 + - - +
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Residues in contact with SER 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 6.2 0.2 - - - +
31C ARG* 5.1 10.3 - - - -
39C PRO* 5.2 8.4 - - - +
58C GLU* 5.5 0.9 - - - -
201N ASN* 3.7 9.0 - - - +
202N ASP 2.9 18.5 + - - -
203N VAL* 2.9 30.8 + - - +
205N LEU* 3.4 18.3 - - - +
214N TYR* 1.3 78.9 + - - +
216N THR* 1.3 63.4 + - - +
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Residues in contact with THR 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ARG* 2.7 40.0 + - - +
58C GLU* 3.0 30.1 + - - +
199N VAL* 3.3 28.7 - - + +
200N LEU* 3.1 13.2 - - - +
201N ASN* 3.1 13.7 - - - +
203N VAL* 4.2 5.5 - - - +
215N SER* 1.3 77.5 - - - +
217N ARG* 1.3 60.8 + - - +
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Residues in contact with ARG 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N LEU* 5.6 0.4 - - - +
29N TYR* 5.4 4.6 - - - -
30N PRO 3.4 18.4 + - - -
31N SER* 3.6 0.6 - - - +
32N ARG* 3.4 28.5 - - + +
59N PHE* 5.5 6.7 + - - +
185N ILE* 6.1 1.8 - - - +
187N GLU* 4.3 30.8 - - + +
198N THR 3.6 3.1 - - - +
199N VAL* 4.4 1.6 - - - -
200N LEU* 3.0 35.8 + - - +
202N ASP* 2.8 46.9 + - + -
203N VAL* 5.1 6.7 - - + +
215N SER 5.0 0.7 - - - +
216N THR* 1.3 74.7 - - - +
218N GLN* 1.3 66.1 + - - +
219N ILE* 3.2 27.4 - - - +
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Residues in contact with GLN 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 3.8 26.4 - - - +
373C ARG* 5.0 12.3 - - - +
187N GLU* 3.5 26.4 - - - +
194N THR* 5.5 1.6 - - - +
196N THR* 3.0 40.3 + - + +
198N THR 3.4 4.0 - - - -
199N VAL* 4.2 22.6 - - + +
216N THR 6.1 0.2 - - - -
217N ARG* 1.3 77.0 - - - +
219N ILE* 1.3 61.9 + - - +
220N ARG* 5.4 4.3 + - - +
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Residues in contact with ILE 219 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N TYR* 3.5 40.2 - - + +
185N ILE* 4.6 13.7 - - + -
186N TYR 3.5 9.0 - - - +
187N GLU* 5.6 0.7 - - - -
196N THR* 3.1 1.7 - - - -
197N LEU* 2.2 48.8 + - + -
198N THR* 2.9 34.2 + - + +
200N LEU* 4.8 2.5 - - + -
217N ARG* 3.2 43.5 - - - +
218N GLN* 1.3 71.9 - - - +
220N ARG* 1.3 52.7 - - - +
221N VAL* 4.3 7.4 - - + -
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Residues in contact with ARG 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185N ILE* 3.8 0.2 - - - -
186N TYR* 2.8 61.4 + - + +
187N GLU 3.3 34.7 + - - +
194N THR* 4.9 4.2 + - - -
195N ARG* 2.9 59.8 + - - +
196N THR* 4.1 16.9 - - - +
197N LEU 3.8 0.9 - - - +
218N GLN* 4.3 4.4 + - - +
219N ILE* 1.3 73.3 - - - +
221N VAL* 1.3 63.2 + - - +
222N VAL* 3.8 8.4 + - + -
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Residues in contact with VAL 221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C VAL* 5.6 6.7 - - + +
482C TRP* 6.0 3.8 - - + -
486C TYR* 4.1 11.0 + - - +
29N TYR* 5.2 1.8 - - + -
183N ASP* 3.6 20.9 - - - +
184N LEU 3.5 3.8 - - - -
185N ILE* 3.4 33.7 - - + -
195N ARG 4.9 0.6 + - - -
197N LEU* 3.8 45.4 - - + +
219N ILE* 4.1 5.5 + - + -
220N ARG* 1.3 73.4 - - - +
222N VAL* 1.3 62.2 + - - +
223N PRO* 3.5 9.8 - - + +
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Residues in contact with VAL 222 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N ASP* 3.7 2.5 - - - -
184N LEU 2.9 30.6 + - - +
186N TYR* 4.5 24.9 - - + -
195N ARG* 4.9 22.7 - - + +
220N ARG* 3.8 14.3 + - + +
221N VAL* 1.3 75.0 - - - +
223N PRO* 1.3 76.5 - - + +
224N THR* 3.2 18.8 + - + +
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Residues in contact with PRO 223 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486C TYR* 3.5 36.3 - - + +
488C ARG* 3.7 36.8 - - - +
181N LEU* 4.7 12.6 - - + +
182N VAL 3.8 5.8 - - - +
183N ASP* 3.9 8.9 - - - +
221N VAL* 3.5 11.0 - - + +
222N VAL* 1.3 88.3 - - + +
224N THR* 1.3 61.1 + - - +
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Residues in contact with THR 224 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163N VAL* 5.7 3.6 - - + -
181N LEU* 3.2 8.1 - - - +
182N VAL* 2.8 41.5 + - - +
184N LEU* 3.2 32.4 - - + +
186N TYR* 5.1 4.3 - - + +
222N VAL* 3.3 28.7 - - + +
223N PRO* 1.3 75.7 - - - +
225N GLU* 1.3 63.3 + - - +
226N VAL* 4.1 10.1 - - - +
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Residues in contact with GLU 225 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164N GLU* 4.8 4.7 - - - +
179N THR* 2.5 51.8 + - - +
180N VAL 3.9 1.6 - - - -
181N LEU* 4.0 16.3 - - + +
224N THR* 1.3 76.5 - - - +
226N VAL* 1.3 61.0 + - - +
227N PRO* 4.7 1.0 - - - +
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Residues in contact with VAL 226 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N ARG* 6.3 0.4 - - - +
162N LEU 4.3 4.9 - - - +
163N VAL* 3.0 36.3 - - + +
164N GLU* 5.4 0.4 - - - -
168N LEU* 4.8 13.5 - - + -
179N THR* 2.9 3.1 - - - -
180N VAL* 2.7 54.2 + - + +
182N VAL* 3.8 26.5 - - + -
184N LEU* 5.8 0.9 - - + -
224N THR* 4.3 13.7 - - - +
225N GLU* 1.3 78.1 - - - +
227N PRO* 1.3 64.7 - - + +
230N LEU* 4.9 3.4 - - + -
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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