Contacts of the helix formed by residues 163 - 186 (chain A) in PDB entry 4YXH
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 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TYR* 3.3 4.5 + - - +
162A ASN* 1.3 99.5 + - - +
164A GLN* 1.3 62.6 + - - +
165A ASN* 3.1 13.8 + - - +
166A THR* 2.6 47.5 + - - +
167A PHE* 3.3 9.7 + - - +
210A TYR* 3.9 12.3 - - - -
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Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASN* 1.3 75.3 - - - +
165A ASN* 1.3 72.4 + - - +
167A PHE* 3.2 2.8 + - - +
168A VAL* 2.9 39.9 + - + +
207A ILE* 4.2 27.5 - - - +
210A TYR* 3.5 49.6 + - + -
211A GLN* 5.2 5.7 - - - +
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Residues in contact with ASN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASN* 3.1 12.6 + - - +
164A GLN* 1.3 85.6 - - - +
166A THR* 1.3 58.8 + - + +
168A VAL* 3.9 5.5 - - - +
169A HIS* 2.9 31.4 + - - +
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.8 11.7 - - - +
162A ASN* 3.6 19.1 + - + +
163A ASN* 2.6 48.7 + - - +
165A ASN* 1.3 74.0 - - + +
167A PHE* 1.3 65.8 + - - +
169A HIS* 3.2 7.4 + - - +
170A ASP* 2.9 23.9 + - - +
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Residues in contact with PHE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TYR* 3.7 30.7 - + + -
156A ARG 3.3 22.0 - - - -
158A VAL* 4.4 13.9 - - + -
161A TYR* 3.4 41.1 - + + -
163A ASN 3.8 6.5 - - - +
164A GLN 3.2 6.5 + - - +
166A THR* 1.3 80.9 + - - +
168A VAL* 1.3 63.2 - - + +
170A ASP* 3.3 2.8 + - - +
171A CYS* 2.9 40.4 + - + +
206A CYS 3.8 10.5 - - - -
209A GLN* 4.8 4.7 - - + -
210A TYR* 3.5 51.4 - + + -
213A GLU* 5.1 2.0 - - + -
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLN* 2.9 34.3 + - + +
165A ASN* 3.9 5.2 - - - +
167A PHE* 1.3 85.5 - - + +
169A HIS* 1.3 54.7 + - - +
171A CYS* 3.1 5.6 + - - +
172A VAL* 2.8 40.3 + - + +
203A GLU* 3.7 33.7 - - + +
206A CYS* 4.1 14.8 - - + +
207A ILE* 3.8 32.3 - - + +
210A TYR* 4.8 0.4 - - + -
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Residues in contact with HIS 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASN 2.9 19.5 + - - +
166A THR* 3.2 6.9 + - - +
168A VAL* 1.3 75.4 - - - +
170A ASP* 1.3 65.5 + - - +
172A VAL* 3.4 6.1 + - - +
173A ASN* 3.1 58.4 + - - -
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Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A TYR* 4.4 3.5 + - - -
155A TYR* 5.9 0.2 - - - -
156A ARG* 4.5 1.9 + - - +
161A TYR* 2.2 39.1 + - + +
166A THR 2.9 16.2 + - - +
167A PHE 3.6 2.2 - - - +
169A HIS* 1.3 81.7 - - + +
171A CYS* 1.3 62.4 + - - +
173A ASN* 3.2 5.5 + - - +
174A ILE* 3.0 57.1 + - - +
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Residues in contact with CYS 171 (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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153A VAL* 3.6 18.4 - - - -
154A TYR 3.5 24.0 - - - +
155A TYR* 4.4 10.5 - - + +
161A TYR* 5.0 0.6 + - - -
167A PHE* 2.9 27.3 + - + +
168A VAL* 3.4 1.8 - - - +
170A ASP* 1.3 76.1 - - - +
172A VAL* 1.3 61.2 + - - +
174A ILE* 4.9 1.1 - - - -
175A THR* 2.9 30.8 + - - -
206A CYS* 2.1 49.6 - - + -
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Residues in contact with VAL 172 (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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168A VAL* 2.8 24.4 + - + +
169A HIS* 3.7 7.2 - - - +
171A CYS* 1.3 77.2 - - - +
173A ASN* 1.3 72.7 + - - +
175A THR* 3.9 0.2 - - - -
176A VAL* 2.9 33.1 + - + +
199A GLU* 4.3 33.2 - - + +
202A VAL* 4.0 7.2 - - + -
203A GLU* 3.5 38.8 - - + +
206A CYS* 3.8 7.2 - - - -
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Residues in contact with ASN 173 (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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169A HIS* 3.1 49.4 + - - +
170A ASP* 3.8 5.3 + - - +
172A VAL* 1.3 82.6 - - - +
174A ILE* 1.3 66.8 + - + +
176A VAL* 3.4 3.9 + - - +
177A LYS* 2.9 29.5 + - - +
199A GLU* 5.7 2.8 - - - +
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Residues in contact with ILE 174 (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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117A LEU 5.6 0.7 - - - +
120A TYR* 3.1 57.7 - - + +
154A TYR* 4.1 21.5 - - + +
155A TYR* 5.8 0.9 - - - -
156A ARG 5.8 1.1 - - - +
170A ASP* 3.0 46.5 + - - +
171A CYS* 4.2 3.4 - - - +
173A ASN* 1.3 78.4 - - + +
175A THR* 1.3 57.9 + - - +
177A LYS* 3.5 4.9 - - - +
178A GLN* 2.9 31.4 + - + +
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Residues in contact with THR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PRO* 4.1 16.6 - - + -
152A GLN 3.8 21.3 - - - +
153A VAL* 3.6 4.5 - - - +
154A TYR* 2.8 38.6 + - + +
171A CYS 2.9 21.9 + - - -
172A VAL 3.9 1.8 - - - -
174A ILE* 1.3 76.5 - - - +
176A VAL* 1.3 59.4 + - - +
178A GLN* 3.5 1.4 + - - +
179A HIS* 2.9 28.1 + - + +
202A VAL* 3.9 19.5 - - + -
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PRO* 5.6 0.2 - - - -
172A VAL* 2.9 30.2 + - + +
173A ASN* 4.0 3.6 - - - +
175A THR* 1.3 77.6 - - - +
177A LYS* 1.3 56.1 + - + +
179A HIS* 3.3 6.4 + - - +
180A THR* 2.8 46.9 + - - +
195A ILE* 5.2 13.7 - - + -
198A MET* 3.8 37.9 - - + +
199A GLU* 4.7 10.5 - - + +
202A VAL* 4.5 12.8 - - + -
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Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASN 2.9 20.1 + - - +
174A ILE* 3.5 6.5 - - - +
176A VAL* 1.3 76.9 - - + +
178A GLN* 1.3 58.0 + - - +
180A THR* 3.1 23.3 + - - +
181A VAL* 3.0 41.0 + - + +
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Residues in contact with GLN 178 (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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117A LEU 6.0 0.3 + - - -
154A TYR* 3.3 42.1 + - + +
174A ILE* 2.9 19.0 + - + +
175A THR 3.9 1.6 - - - +
177A LYS* 1.3 74.3 - - - +
179A HIS* 1.3 64.3 + - - +
181A VAL* 3.2 18.2 - - - +
182A THR* 3.0 49.5 + - + +
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Residues in contact with HIS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG 2.8 24.5 + - - -
149A TYR 4.0 1.6 - - - -
150A PRO* 3.7 45.0 - - + +
154A TYR* 5.7 0.4 - - - -
175A THR* 2.9 18.1 + - + +
176A VAL* 3.8 5.2 - - - +
178A GLN* 1.3 77.8 - - - +
180A THR* 1.3 57.4 + - - +
182A THR* 3.2 11.4 + - - -
183A THR* 2.8 42.9 + - + +
186A LYS* 5.4 3.4 - - - -
190A PHE* 3.3 30.1 - + - -
198A MET* 4.0 3.4 - - - -
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Residues in contact with THR 180 (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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176A VAL* 2.8 33.3 + - - +
177A LYS* 3.1 22.8 + - - +
179A HIS* 1.3 75.9 - - - +
181A VAL* 1.3 63.5 + - + +
183A THR* 3.1 6.5 + - - -
184A THR* 2.8 42.6 + - - +
190A PHE* 3.8 22.5 - - + +
195A ILE* 5.4 5.5 - - + +
198A MET* 4.7 0.5 - - - +
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Residues in contact with VAL 181 (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 LYS* 3.0 22.8 + - + +
178A GLN* 3.2 43.5 - - - +
180A THR* 1.3 78.6 - - + +
182A THR* 1.3 64.1 + - + +
184A THR* 3.3 6.0 + - - -
185A THR* 3.0 27.9 + - - +
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 6.1 0.2 - - - +
178A GLN* 3.0 37.9 + - + +
179A HIS* 3.2 15.9 + - - -
181A VAL* 1.3 78.1 - - + +
183A THR* 1.3 65.3 + - - +
185A THR* 3.7 7.4 + - - -
186A LYS* 3.0 47.2 + - - +
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 4.4 2.9 - - + +
179A HIS* 2.8 41.4 + - + +
180A THR* 3.1 4.5 + - - -
182A THR* 1.3 77.5 + - - +
184A THR* 1.3 65.2 + - - +
186A LYS* 3.1 29.1 + - + +
188A GLU* 3.2 35.2 + - - +
189A ASN* 5.6 0.2 - - - -
190A PHE* 3.0 41.1 - - + -
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A THR* 2.8 34.3 + - - +
181A VAL* 3.3 7.2 + - - +
183A THR* 1.3 78.5 + - - +
185A THR* 1.3 55.6 + - - +
187A GLY* 2.7 26.9 + - - -
188A GLU 3.3 10.7 + - - -
189A ASN* 4.0 16.1 + - - +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 3.0 17.1 + - - +
182A THR* 3.9 8.7 - - - -
183A THR 3.3 0.2 - - - -
184A THR* 1.3 77.3 - - - +
186A LYS* 1.3 58.0 + - + +
187A GLY* 3.1 4.7 + - - -
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Residues in contact with LYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A HIS* 5.4 4.0 - - - -
182A THR* 3.0 42.7 + - - +
183A THR* 3.1 22.4 + - + +
185A THR* 1.3 78.1 - - + +
187A GLY* 1.3 60.4 + - - +
188A GLU* 3.4 25.9 + - - +
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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
------------------------------------------------------------
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