Contacts of the helix formed by residues 197 - 212 (chain C) in PDB entry 4UQJ
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 GLU 197 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ASP* 4.7 4.4 + - - +
140C ASP* 5.6 4.7 - - + +
141C ARG* 3.5 15.9 - - - +
196C CYS* 1.3 75.9 - - - +
198C ARG* 1.3 66.1 + - - +
199C ASP* 3.0 14.1 + - + +
200C LYS* 4.3 8.4 - - + +
201C VAL* 3.0 24.8 + - - +
224C ASN* 4.7 0.9 - - - +
280C TYR* 6.1 1.8 - - - -
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Residues in contact with ARG 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C GLU* 1.3 73.7 - - - +
199C ASP* 1.3 65.1 + - - +
201C VAL* 4.1 4.5 - - - +
202C ASN* 3.7 27.0 + - - +
224C ASN* 4.5 14.2 - - - +
226C GLY 5.8 0.4 - - - +
229C ASP* 5.1 19.7 - - + +
230C GLY* 5.3 5.6 - - - +
280C TYR* 6.0 7.2 - - + -
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Residues in contact with ASP 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C GLU* 3.0 6.6 - - + +
198C ARG* 1.3 84.3 - - - +
200C LYS* 1.3 64.3 + - - +
201C VAL 3.0 5.3 + - - -
202C ASN* 3.1 16.2 + - - +
203C ASP* 3.2 20.2 + - - +
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Residues in contact with LYS 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ASP* 4.1 15.3 - - - +
165C VAL* 5.9 4.0 - - + +
177C TYR* 5.0 0.7 + - - -
196C CYS* 3.6 25.1 - - + -
197C GLU* 3.3 7.7 + - + +
199C ASP* 1.3 78.5 - - - +
201C VAL* 1.3 60.5 + - - +
203C ASP* 3.7 12.2 + - - +
204C ILE* 3.2 29.0 + - + +
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Residues in contact with VAL 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 4.6 9.6 - - + -
196C CYS* 3.8 24.5 - - + +
197C GLU 3.0 22.4 + - - +
198C ARG* 4.1 6.1 - - - +
199C ASP 3.0 0.2 - - - -
200C LYS* 1.3 76.8 - - - +
202C ASN* 1.3 66.2 + - - +
204C ILE* 3.2 7.8 + - - +
205C VAL* 2.8 43.2 + - + +
222C ILE* 4.0 36.3 - - + -
224C ASN* 4.6 2.7 - - - +
230C GLY* 6.4 1.1 - - - -
232C LEU* 6.5 0.9 - - + -
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Residues in contact with ASN 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ARG 3.7 14.7 + - - +
199C ASP* 3.1 10.2 + - - +
201C VAL* 1.3 85.0 - - - +
203C ASP* 1.3 61.2 + - - +
205C VAL* 3.8 4.1 - - - +
206C ASP* 2.9 39.1 + - - +
230C GLY* 4.2 7.0 - - - -
231C ASP* 3.8 26.0 + - - +
234C LYS* 3.7 24.4 + - - +
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Residues in contact with ASP 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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170C ASN* 4.8 13.5 + - - +
177C TYR* 4.3 13.5 - - + +
199C ASP* 3.2 14.4 + - - +
200C LYS* 3.7 13.7 - - - +
201C VAL 3.2 0.4 - - - -
202C ASN* 1.3 80.7 - - - +
204C ILE* 1.3 61.7 + - - +
206C ASP* 3.4 7.7 + - - +
207C GLN* 3.1 28.8 + - - +
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Residues in contact with ILE 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU* 4.5 5.6 - - + -
165C VAL* 4.1 20.0 - - + -
177C TYR* 3.9 22.7 - - + +
181C PHE* 4.8 11.2 - - + -
194C LEU* 3.6 43.1 - - + -
196C CYS* 4.0 17.9 - - - -
200C LYS* 3.2 15.7 + - + +
201C VAL* 3.2 7.2 + - - +
203C ASP* 1.3 74.6 - - - +
205C VAL* 1.3 55.6 + - - +
207C GLN* 3.1 7.5 + - - +
208C VAL* 2.8 51.4 + - + +
220C TYR* 5.8 0.4 - - + -
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Residues in contact with VAL 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 4.6 9.2 - - + -
201C VAL* 2.8 39.6 + - + +
202C ASN* 3.8 9.0 - - - +
204C ILE* 1.3 72.4 - - - +
206C ASP* 1.3 62.4 + - - +
208C VAL* 3.3 9.6 + - - +
209C ILE* 3.0 29.0 + - + +
222C ILE* 5.1 5.4 - - + -
231C ASP 4.9 2.2 - - - +
232C LEU* 6.6 0.2 - - + -
234C LYS* 3.7 24.0 - - + -
235C ILE* 3.5 39.7 - - + -
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Residues in contact with ASP 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ASN* 2.9 25.5 + - - +
203C ASP* 3.6 8.2 - - - +
205C VAL* 1.3 76.4 - - - +
207C GLN* 1.3 62.8 + - + +
209C ILE* 3.3 10.4 + - - +
210C THR* 3.0 26.6 + - - -
234C LYS* 3.1 33.2 + - - +
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Residues in contact with GLN 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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173C LYS 4.1 10.5 + - - -
174C ASP* 3.3 26.5 + - - +
177C TYR* 3.9 42.0 - - + +
181C PHE* 5.0 4.7 - - + -
203C ASP 3.1 14.8 + - - +
204C ILE 3.1 7.5 + - - +
206C ASP* 1.3 77.1 - - + +
208C VAL* 1.3 64.4 + - - +
210C THR* 3.1 15.0 + - - +
211C ILE* 3.0 35.0 + - + +
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Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C PHE* 3.9 20.9 - - + -
194C LEU* 5.8 0.2 - - + -
204C ILE* 2.8 31.4 + - + +
205C VAL* 3.5 11.7 - - - +
206C ASP 3.3 0.2 - - - -
207C GLN* 1.3 72.9 - - - +
209C ILE* 1.3 57.3 + - - +
211C ILE* 3.3 8.4 - - - +
212C GLY 3.0 6.8 + - - -
213C LYS* 2.8 57.6 + - + +
214C HIS* 3.7 10.8 - - + -
220C TYR* 3.2 28.5 - - + +
235C ILE* 4.8 3.6 - - + -
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Residues in contact with ILE 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 VAL* 3.0 18.1 + - + +
206C ASP* 3.7 9.2 - - - +
207C GLN 3.2 0.2 - - - -
208C VAL* 1.3 73.7 - - - +
210C THR* 1.3 66.0 + - - +
212C GLY* 3.1 12.3 + - - -
214C HIS* 3.3 30.4 + - + +
234C LYS* 3.4 43.5 - - + +
235C ILE* 3.4 24.5 - - + -
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Residues in contact with THR 210 (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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206C ASP* 3.0 16.1 + - - +
207C GLN* 3.4 18.9 + - - +
209C ILE* 1.3 80.3 - - - +
211C ILE* 1.3 65.7 + - + +
212C GLY* 3.3 1.0 + - - -
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Residues in contact with ILE 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C TYR* 6.3 1.1 - - + -
178C ARG* 5.9 7.6 - - + -
181C PHE* 3.6 47.6 - - + -
207C GLN* 3.0 23.5 + - + +
208C VAL* 3.3 12.1 - - - +
210C THR* 1.3 80.0 - - + +
212C GLY* 1.3 58.4 + - - +
213C LYS* 3.6 25.3 + - + +
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Residues in contact with GLY 212 (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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208C VAL 3.0 4.2 + - - -
209C ILE 3.1 11.6 + - - -
210C THR 3.1 5.1 - - - -
211C ILE* 1.3 79.7 - - - +
213C LYS* 1.3 57.4 + - - +
214C HIS* 3.1 18.7 + - - -
215C VAL* 3.7 23.0 - - - +
218C TYR* 4.7 0.9 - - - -
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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