Contacts of the helix formed by residues 192 - 214 (chain A) in PDB entry 4UY3
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 192 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLY* 3.3 7.4 - - - -
61A GLU* 2.9 40.4 + - - +
187A LEU* 2.9 21.7 + - + +
188A LYS* 5.2 0.4 - - - -
190A ASP* 3.7 24.5 + - - +
191A GLY* 1.3 75.1 - - - +
193A TYR* 1.3 58.5 + - - +
194A VAL 3.2 3.8 + - - -
195A GLN* 3.4 24.6 + - + +
196A ALA* 2.9 30.1 + - - +
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Residues in contact with TYR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 3.8 12.8 - - + -
62A THR* 3.5 36.6 - - - -
65A LYS* 3.7 18.8 - - + +
130A GLU* 6.3 0.2 - - + -
131A ILE* 3.6 32.4 - - + +
134A LEU* 3.8 32.3 - - + +
135A TYR* 3.5 31.9 - + + -
138A ASN* 3.1 15.8 + - - +
188A LYS* 5.9 1.6 - - - +
191A GLY 3.1 4.4 + - - -
192A ASN* 1.3 75.0 - - - +
194A VAL* 1.3 77.9 + - + +
196A ALA* 4.0 6.1 - - - -
197A HIS* 3.1 23.0 + - - +
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 3.1 20.2 + - + +
134A LEU* 5.3 4.3 - - + -
193A TYR* 1.3 110.6 - - + +
195A GLN* 1.3 61.5 + - + +
197A HIS* 3.3 5.5 + - + +
198A ASN* 2.9 48.1 + - - +
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Residues in contact with GLN 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLU* 3.1 30.2 + - - +
187A LEU* 3.8 27.2 - - + +
192A ASN* 4.0 17.9 + - - +
194A VAL* 1.3 75.0 - - + +
196A ALA* 1.3 60.1 + - - +
198A ASN* 3.3 8.2 + - - +
199A HIS* 2.8 33.1 + - - +
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ASN* 3.7 11.9 - - - +
184A TYR* 3.8 20.0 - - + -
187A LEU* 4.0 20.7 - - + +
188A LYS* 4.4 9.4 - - + +
192A ASN 2.9 20.0 + - - +
193A TYR* 3.7 7.9 - - - +
195A GLN* 1.3 76.9 - - - +
197A HIS* 1.3 57.6 + - - +
199A HIS* 3.2 2.1 + - - +
200A ILE* 3.0 33.0 + - - +
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Residues in contact with HIS 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 3.8 26.1 - - + +
137A ASP* 5.3 7.9 - - + -
138A ASN* 2.8 30.5 + - - +
141A LEU* 4.3 21.7 - - + +
193A TYR 3.1 17.5 + - - +
194A VAL* 3.3 6.3 + - - +
196A ALA* 1.3 76.1 - - - +
198A ASN* 1.3 76.8 + - - +
199A HIS 3.1 0.2 + - - -
200A ILE* 3.5 2.1 - - - +
201A ALA* 2.9 33.9 + - + +
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Residues in contact with ASN 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A VAL* 2.9 40.8 + - - +
195A GLN* 3.9 7.2 - - - +
197A HIS* 1.3 87.5 - - - +
199A HIS* 1.3 61.1 + - - +
201A ALA* 4.2 4.0 - - - +
202A ALA* 3.3 22.9 + - - +
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Residues in contact with HIS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 2.9 46.3 + - + +
183A GLN* 3.4 31.1 - - + +
184A TYR* 4.0 20.6 - - + -
187A LEU* 3.8 15.7 - - + +
195A GLN 2.8 18.3 + - - +
196A ALA 3.5 3.8 - - - +
198A ASN* 1.3 78.0 - - - +
200A ILE* 1.3 64.0 + - + +
202A ALA* 3.5 5.2 + - - +
203A LEU* 3.0 27.9 + - + +
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ASN* 4.3 10.5 - - - +
141A LEU* 3.8 26.8 - - + +
142A TYR* 3.8 39.3 - - + +
145A CYS* 4.1 3.8 - - + -
181A LEU* 4.8 0.4 - - + -
184A TYR* 4.0 28.7 - - + -
196A ALA 3.0 20.0 + - - +
197A HIS* 3.5 10.1 - - - +
199A HIS* 1.3 78.2 - - + +
201A ALA* 1.3 61.8 + - - +
203A LEU* 3.4 25.8 + - + +
204A ASN* 2.9 28.9 + - - +
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 4.4 11.9 - - + -
197A HIS* 2.9 32.6 + - + +
198A ASN* 4.2 4.7 - - - +
200A ILE* 1.3 79.7 - - - +
202A ALA* 1.3 61.8 + - - +
204A ASN* 3.2 5.3 + - - +
205A GLU* 3.0 23.4 + - - +
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 4.2 10.1 - - - +
198A ASN 3.3 18.2 + - - +
199A HIS* 3.7 5.4 - - - +
201A ALA* 1.3 74.6 - - - +
203A LEU* 1.3 66.3 + - - +
205A GLU* 3.3 7.8 + - - +
206A GLN* 3.0 31.9 + - + +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A CYS* 4.0 7.6 - - + -
177A PHE* 3.7 26.0 - - + +
180A ARG* 3.7 49.1 - - + +
181A LEU* 3.8 33.2 - - + -
199A HIS* 3.0 19.2 + - + +
200A ILE* 3.6 21.1 - - + +
201A ALA 3.3 0.2 - - - -
202A ALA* 1.3 77.9 - - - +
204A ASN* 1.3 62.2 + - - +
206A GLN* 3.2 1.8 + - - +
207A MET* 3.0 37.7 + - + +
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Residues in contact with ASN 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 3.5 28.6 - - + +
144A LYS* 3.3 28.1 + - - +
145A CYS* 3.8 19.2 - - - -
148A ASP* 4.1 3.8 - - - +
200A ILE 2.9 17.6 + - - +
201A ALA* 3.5 4.9 - - - +
203A LEU* 1.3 78.9 - - - +
205A GLU* 1.3 58.4 + - - +
207A MET* 3.7 3.2 - - - +
208A LYS* 2.8 53.7 + - - +
211A ARG* 5.2 0.2 + - - -
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Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ALA 3.0 14.1 + - - +
202A ALA* 3.4 12.6 - - - +
204A ASN* 1.3 76.9 - - - +
206A GLN* 1.3 60.4 + - + +
208A LYS* 3.2 20.1 + - - +
209A GLN* 3.1 57.6 + - - +
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Residues in contact with GLN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PHE* 4.4 9.2 - - + -
180A ARG* 2.7 41.6 + - - +
202A ALA* 3.0 19.2 + - + +
203A LEU 3.9 3.1 - - - +
204A ASN 3.2 0.2 - - - -
205A GLU* 1.3 76.8 - - + +
207A MET* 1.3 67.9 + - - +
209A GLN* 3.4 7.4 + - - +
210A LEU* 3.0 24.4 + - - +
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Residues in contact with MET 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A CYS* 3.3 35.9 - - - +
148A ASP* 3.7 11.9 - - + +
149A TYR* 3.1 44.2 - - + +
152A MET* 4.3 4.7 - - - +
177A PHE* 3.8 40.6 - - + -
181A LEU* 5.7 0.4 - - - -
203A LEU* 3.0 30.3 + - + +
204A ASN* 3.7 4.7 - - - +
206A GLN* 1.3 77.4 - - - +
208A LYS* 1.3 63.3 + - - +
210A LEU* 3.1 4.7 + - - +
211A ARG* 2.9 36.0 + - - +
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Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LYS* 4.3 18.1 - - - +
204A ASN* 2.8 37.2 + - - +
205A GLU* 3.3 28.4 + - - +
207A MET* 1.3 73.5 - - - +
209A GLN* 1.3 58.7 + - + +
211A ARG* 3.0 33.6 + - - +
212A SER* 3.1 16.9 + - - +
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Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLU* 3.1 48.1 + - - +
206A GLN* 3.4 7.3 + - - +
208A LYS* 1.3 77.5 - - + +
210A LEU* 1.3 61.6 + - - +
212A SER* 3.5 9.3 + - - +
213A TYR* 3.2 22.3 + - - +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A MET* 3.6 25.8 - - + -
170A LEU* 4.4 15.0 - - + -
173A GLU* 4.7 15.9 - - + +
174A ILE* 3.9 14.8 - - + -
177A PHE* 3.7 19.5 - - + -
206A GLN 3.0 18.7 + - - +
207A MET* 3.1 4.5 + - - +
209A GLN* 1.3 79.8 - - - +
211A ARG* 1.3 56.6 + - - +
213A TYR* 3.6 21.2 + - + +
214A MET* 3.1 30.7 + - + +
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Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LYS* 3.8 13.9 - - - +
148A ASP* 3.4 37.8 + - - +
151A GLU* 5.9 4.9 - - - -
152A MET* 3.4 33.9 - - + +
204A ASN* 5.2 0.8 + - - -
207A MET* 2.9 33.6 + - - +
208A LYS* 3.0 25.0 + - - +
210A LEU* 1.3 76.9 - - - +
212A SER* 1.3 65.6 + - - +
214A MET* 3.1 18.8 + - + +
215A HIS* 3.5 21.5 + - + -
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Residues in contact with SER 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LYS* 3.1 15.7 + - - +
209A GLN* 3.7 10.4 - - - -
211A ARG* 1.3 72.9 - - - +
213A TYR* 1.3 67.3 + - - +
215A HIS* 3.0 25.4 + - - +
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Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PHE* 6.2 1.8 - + - -
166A ALA* 3.4 25.0 - - + +
170A LEU* 3.8 28.0 - - + -
209A GLN 3.2 12.0 + - - +
210A LEU* 3.6 25.6 - - + +
212A SER* 1.3 80.7 - - - +
214A MET* 1.3 60.8 + - + +
215A HIS 2.9 14.6 + - - +
216A GLY* 3.9 11.0 + - - -
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Residues in contact with MET 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A MET* 4.0 36.6 - - + +
155A ASP* 3.8 29.3 - - + +
156A VAL* 4.1 11.7 - - + -
162A GLN* 5.0 1.6 + - - -
163A PHE* 3.3 43.4 - - + -
170A LEU* 3.8 22.0 - - + -
174A ILE* 4.2 12.3 - - + -
210A LEU* 3.1 22.3 + - + +
211A ARG* 3.1 16.2 + - + +
213A TYR* 1.3 76.9 - - + +
215A HIS* 1.3 61.8 + - - +
216A GLY 3.3 3.3 + - - -
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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
------------------------------------------------------------
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