Contacts of the helix formed by residues 200 - 209 (chain C) in PDB entry 1U75
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 ASN 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A PRO* 6.1 2.8 - - - +
199C THR* 1.3 73.8 - - - +
201C GLU* 1.3 64.3 + - - +
202C PHE* 3.1 4.6 + - - -
203C TYR* 3.2 20.4 + - + +
204C LEU* 3.4 24.3 + - - +
251C TYR 3.3 18.8 - - - +
252C ALA* 3.3 23.7 - - - +
255C GLN* 3.0 42.5 + - + +
258C PHE* 3.9 16.2 - - + -
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 5.2 6.5 - - + +
176C ALA* 4.6 8.2 - - + +
192C GLY* 3.5 5.5 - - - -
193C ALA* 3.0 40.0 + - - +
194C ALA* 3.1 24.8 + - + +
199C THR* 3.3 17.6 + - - +
200C ASN* 1.3 76.9 - - - +
202C PHE* 1.3 53.8 + - - +
204C LEU* 3.2 16.4 + - + +
205C ASN* 2.7 62.9 + - - +
229C TYR* 4.1 2.8 + - - -
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Residues in contact with PHE 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C MET* 3.7 24.5 - - + -
173C GLY* 3.9 18.4 - - - +
175C HIS* 3.8 23.8 - - + -
176C ALA* 4.3 12.1 - - + +
191C TRP* 4.2 3.6 - + + -
200C ASN 4.9 0.2 - - - -
201C GLU* 1.3 77.7 - - - +
203C TYR* 1.3 82.8 + + + +
205C ASN* 3.5 6.1 + - - +
206C LEU* 2.9 45.7 + - + +
231C MET* 3.6 32.6 - - + +
235C ASP* 3.8 31.0 - - + -
238C LEU* 3.9 21.5 - - + -
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Residues in contact with TYR 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C VAL* 2.5 43.8 + - + -
170C ALA* 3.4 1.4 + - - -
173C GLY* 3.3 13.3 - - - -
200C ASN* 3.2 20.7 + - + +
202C PHE* 1.3 88.8 - + + +
204C LEU* 1.3 64.7 + - - +
206C LEU* 3.4 6.4 + - - +
207C LEU* 3.1 28.8 + - - +
248C VAL* 3.7 42.2 - - + +
251C TYR* 3.7 16.8 - + + -
252C ALA* 3.7 9.6 - - + -
258C PHE* 3.2 49.9 - + - -
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Residues in contact with LEU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A PRO* 6.0 6.3 - - + -
200C ASN* 3.4 28.0 + - - +
201C GLU* 3.2 19.3 + - + +
203C TYR* 1.3 77.9 - - - +
205C ASN* 1.3 60.1 + - - +
207C LEU* 4.7 1.1 - - - -
208C ASN* 2.8 51.0 + - - +
252C ALA* 3.2 33.9 - - + +
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Residues in contact with ASN 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C TRP 3.5 25.6 + - - +
192C GLY* 3.6 3.0 - - - -
201C GLU* 2.7 57.5 + - - +
202C PHE 3.8 4.0 - - - +
204C LEU* 1.3 74.9 - - - +
206C LEU* 1.3 60.5 + - - +
208C ASN* 5.2 0.4 - - - -
209C GLU* 3.1 39.6 + - + +
211C TRP* 3.2 12.8 - - + -
229C TYR* 3.3 23.3 - - + -
231C MET* 4.5 0.9 - - + -
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Residues in contact with LEU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C PHE* 2.9 39.1 + - + +
203C TYR 3.7 4.0 - - - +
204C LEU 3.3 0.2 - - - -
205C ASN* 1.3 74.8 - - - +
207C LEU* 1.3 60.6 + - - +
209C GLU 4.8 0.3 - - - +
211C TRP* 3.3 22.6 + - - +
231C MET* 3.8 28.0 - - + +
235C ASP 3.7 25.8 - - - +
236C TYR* 3.9 16.2 - - + -
238C LEU* 4.2 6.1 - - + -
239C ILE* 3.7 42.2 - - + +
248C VAL* 4.1 12.1 - - + -
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Residues in contact with LEU 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C TYR 3.1 10.6 + - - +
204C LEU* 3.9 2.7 - - - +
206C LEU* 1.3 79.7 - - - +
208C ASN* 1.3 71.6 + - - +
209C GLU 3.6 4.2 + - - +
239C ILE* 3.9 26.5 - - + -
245C LEU* 3.9 17.3 - - + -
248C VAL* 4.1 9.6 - - + +
249C LYS* 4.0 28.3 - - + +
252C ALA* 3.8 27.1 - - + -
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Residues in contact with ASN 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C LEU* 2.8 40.3 + - - +
205C ASN* 5.2 0.2 - - - -
207C LEU* 1.3 82.2 + - - +
209C GLU* 1.3 65.6 + - + +
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Residues in contact with GLU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C ASN* 3.1 35.2 + - - +
206C LEU 4.8 0.2 - - - +
207C LEU 3.6 5.8 - - - +
208C ASN* 1.3 84.2 - - + +
210C ASP* 1.3 62.5 + - - +
211C TRP* 3.5 29.4 + - + +
225C SER* 3.2 17.6 + - - -
227C SER* 2.8 27.7 + - - -
229C TYR* 3.9 18.1 - - + -
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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