Contacts of the helix formed by residues 194 - 208 (chain B) in PDB entry 5U03
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 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A UTP 2.7 15.0 + - - +
183B VAL* 5.2 3.6 - - + -
192B GLN 4.5 4.9 - - - +
193B LYS* 1.3 75.0 - - - +
195B LYS* 1.3 60.8 + - - +
196B PRO* 3.3 3.6 - - - -
197B THR* 2.8 28.4 + - - +
198B GLN* 2.9 33.0 + - - +
226B VAL* 3.6 33.0 - - + +
229B LYS* 5.3 6.6 - - + +
230B ILE* 3.7 26.9 - - + +
233B PHE* 4.4 6.8 - - - -
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Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL 4.6 3.8 - - - +
11A ILE* 3.8 18.4 - - + -
12A SER* 4.8 1.8 - - - +
150A THR* 2.9 37.7 - - + -
153A ASP* 2.7 30.5 + - - -
602A UTP 3.2 36.3 + - - +
194B THR* 1.3 77.4 + - - +
196B PRO* 1.3 70.0 - - + +
198B GLN* 2.9 21.4 + - - +
199B ASN* 2.8 47.7 + - - +
202B ARG* 5.7 0.6 - - - +
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Residues in contact with PRO 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.1 14.1 - - + +
11A ILE* 3.6 19.3 - - + -
10B VAL* 3.9 25.9 - - + +
182B LEU 4.4 6.5 - - - +
184B PRO* 3.8 22.9 - - + -
193B LYS 4.0 4.0 - - - +
194B THR 3.3 9.4 - - - +
195B LYS* 1.3 95.1 - - + +
197B THR* 1.3 55.4 + - - +
199B ASN* 3.2 13.2 + - - +
200B SER* 3.0 26.3 + - - -
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Residues in contact with THR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B SER* 2.7 37.3 + - - +
182B LEU 2.9 17.5 + - - -
183B VAL* 4.6 7.2 - - - +
194B THR* 2.8 13.6 + - - -
196B PRO* 1.3 73.2 - - - +
198B GLN* 1.3 62.8 + - - +
200B SER* 3.0 2.0 + - - +
201B VAL* 2.8 43.7 + - + +
214B VAL* 4.5 9.9 - - + -
216B CYS* 5.3 4.3 - - - -
230B ILE* 5.3 10.3 - - + -
234B CYS* 4.8 7.9 - - - -
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Residues in contact with GLN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A UTP 2.8 29.6 + - - -
194B THR* 2.9 34.6 + - - +
195B LYS* 2.9 19.4 + - + +
197B THR* 1.3 76.6 - - - +
199B ASN* 1.3 59.0 + - - +
201B VAL* 4.2 3.5 - - - +
202B ARG* 2.9 42.1 + - - +
205B ARG* 5.6 0.9 + - - -
230B ILE* 6.2 0.4 - - + -
233B PHE* 3.4 46.8 - - + -
234B CYS* 5.3 5.8 - - - -
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Residues in contact with ASN 199 (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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10A VAL* 4.5 9.7 + - - +
150A THR* 5.2 2.0 + - - -
151A VAL 5.8 1.6 + - - -
153A ASP* 5.0 0.9 - - - +
195B LYS* 2.8 48.7 + - - +
196B PRO* 3.4 11.0 - - - +
197B THR 3.0 0.2 - - - -
198B GLN* 1.3 76.3 - - - +
200B SER* 1.3 65.5 + - - +
202B ARG* 2.9 36.3 + - - +
203B GLU* 2.9 25.1 + - - +
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 3.6 12.4 - - - -
10B VAL* 4.3 15.9 - - - -
151B VAL* 4.2 8.9 - - - +
179B HIS* 2.9 28.7 + - - -
181B SER* 4.5 1.3 - - - -
196B PRO 3.0 12.9 + - - -
197B THR* 3.7 8.1 - - - -
199B ASN* 1.3 76.4 - - - +
201B VAL* 1.3 57.5 + - - +
203B GLU* 3.2 7.5 + - - +
204B LEU* 2.8 27.2 + - - +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B HIS* 3.8 21.5 - - + +
197B THR* 2.8 39.9 + - + +
198B GLN* 4.2 2.0 - - - +
200B SER* 1.3 68.3 - - - +
202B ARG* 1.3 55.9 + - - +
204B LEU* 3.0 8.1 + - - +
205B ARG* 2.7 61.0 + - + +
211B PRO* 4.6 13.0 - - + -
214B VAL* 4.7 9.0 - - + -
234B CYS* 4.1 26.5 - - + -
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Residues in contact with ARG 202 (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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152A GLY* 4.4 19.1 + - - -
153A ASP* 5.3 3.1 + - - -
195B LYS* 5.7 0.8 - - - +
198B GLN* 2.9 42.6 + - - +
199B ASN* 2.9 40.5 + - - +
201B VAL* 1.3 77.3 - - - +
203B GLU* 1.3 56.0 + - - +
205B ARG* 3.2 20.0 + - - +
206B GLY* 2.8 26.2 + - - -
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Residues in contact with GLU 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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151B VAL* 3.7 20.4 - - + +
152B GLY* 5.2 8.6 - - - -
199B ASN 2.9 17.9 + - - +
200B SER* 3.5 5.8 - - - +
202B ARG* 1.3 76.6 - - - +
204B LEU* 1.3 58.5 + - - +
206B GLY* 3.0 5.0 + - - +
207B LEU* 2.8 44.7 + - + +
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Residues in contact with LEU 204 (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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7B THR* 4.1 9.2 - - - +
151B VAL* 4.0 22.2 - - + +
160B ILE* 4.7 3.4 - - + -
177B ASN* 4.3 7.2 - - - +
179B HIS* 3.6 26.5 - - + +
200B SER 2.8 13.8 + - - +
201B VAL* 3.0 8.7 + - - +
203B GLU* 1.3 77.6 - - - +
205B ARG* 1.3 56.1 + - - +
207B LEU* 3.0 19.3 + - + +
208B GLY 2.9 21.8 + - - -
209B LEU* 3.0 41.0 + - + +
211B PRO* 3.7 28.9 - - + -
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Residues in contact with ARG 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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198B GLN 5.6 0.4 + - - -
201B VAL* 2.7 41.0 + - + +
202B ARG* 3.8 16.5 - - - +
204B LEU* 1.3 69.5 - - - +
206B GLY* 1.3 65.7 + - - +
208B GLY* 3.2 11.8 + - - -
209B LEU 3.1 17.3 - - - +
210B SER* 4.3 20.2 - - - -
211B PRO* 4.5 1.6 - - + -
233B PHE 3.1 22.4 + - - -
234B CYS* 2.9 31.1 + - - +
235B HIS* 3.0 20.3 + - - +
164C ARG* 4.1 30.7 - - - +
165C GLN* 4.8 0.2 + - - -
206C GLY 3.8 1.9 - - - +
207C LEU 4.5 0.7 - - - +
208C GLY* 4.4 9.7 - - - -
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Residues in contact with GLY 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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202B ARG 2.8 14.8 + - - -
203B GLU* 3.0 7.5 + - - -
205B ARG* 1.3 77.6 - - - +
207B LEU* 1.3 60.2 + - - +
208B GLY 3.1 0.9 + - - -
205C ARG 3.8 0.2 - - - +
206C GLY* 1.6 42.3 - - - +
207C LEU* 4.6 6.3 - - - -
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Residues in contact with LEU 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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151B VAL* 3.7 30.7 - - + -
152B GLY* 5.1 4.3 - - - +
157B MET* 5.7 13.9 - - + -
160B ILE* 3.8 41.8 - - + +
164B ARG* 4.1 13.3 - - - -
203B GLU* 2.8 28.9 + - + +
204B LEU* 3.2 17.3 - - + +
206B GLY* 1.3 74.4 - - - +
208B GLY* 1.3 57.0 + - - +
209B LEU 3.7 0.7 - - - +
205C ARG 4.5 3.3 - - - +
206C GLY* 4.6 4.6 - - - -
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Residues in contact with GLY 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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164B ARG* 4.0 12.0 - - - +
167B GLN* 4.0 8.7 + - - -
168B PHE* 5.5 2.3 - - - -
204B LEU 2.9 1.8 + - - -
205B ARG 3.2 10.0 + - - -
206B GLY 3.0 5.4 - - - -
207B LEU* 1.3 80.2 - - - +
209B LEU* 1.3 72.6 + - - +
210B SER* 4.3 0.3 + - - -
205C ARG 4.4 8.5 - - - -
208C GLY* 5.7 1.8 - - - -
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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