Contacts of the helix formed by residues 161 - 185 (chain A) in PDB entry 3W8I
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 161 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PHE* 3.9 17.4 - - + -
160A LEU* 1.3 78.3 - - + +
162A HIS* 1.3 59.9 + - - +
164A LYS* 3.7 28.2 + - - +
165A LYS* 2.9 31.0 + - - +
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Residues in contact with HIS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU 3.1 6.7 + - - +
161A GLU* 1.3 79.4 - - - +
163A GLN* 1.3 74.9 + - - +
165A LYS* 3.2 10.8 + - + +
166A GLU* 2.9 62.3 + - + +
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Residues in contact with GLN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU 3.5 11.1 + - - +
162A HIS* 1.3 96.6 + - - +
164A LYS* 1.3 60.7 + - - +
166A GLU* 3.3 10.4 + - - +
167A PHE* 2.9 23.9 + - - +
200A GLN* 4.1 8.2 + - - +
203A LEU* 3.5 43.5 - - - +
204A ILE* 3.4 22.6 + - + +
207A THR* 3.3 38.9 + - + +
208A PHE* 4.9 1.6 - - + -
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 4.3 20.4 - - + -
145A VAL* 4.4 12.3 - - + -
146A ASN* 3.0 29.8 + - - +
149A PHE* 3.9 24.8 - - + -
160A LEU 3.2 12.5 + - - +
161A GLU* 3.7 26.6 + - - +
163A GLN* 1.3 77.7 - - - +
165A LYS* 1.3 59.6 + - - +
167A PHE* 3.2 4.1 + - - +
168A VAL* 2.9 42.7 + - + +
204A ILE* 4.0 9.5 - - - +
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Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLU* 2.9 20.5 + - - +
162A HIS* 3.2 11.4 + - + +
164A LYS* 1.3 75.7 - - - +
166A GLU* 1.3 65.1 + - - +
168A VAL* 3.4 8.5 + - + +
169A LYS* 2.9 32.8 + - + +
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Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A HIS* 2.9 49.0 + - + +
163A GLN* 3.6 15.3 - - - +
164A LYS 3.3 0.2 - - - -
165A LYS* 1.3 82.3 - - - +
167A PHE* 1.3 57.5 + - - +
169A LYS* 3.1 32.8 + - - +
170A TYR* 2.9 46.1 + - + -
200A GLN* 3.8 16.7 + - - +
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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
----------------------------------------------------------
110A LEU* 3.7 15.7 - - + -
138A ILE* 4.0 10.8 - - + -
141A LEU* 3.5 29.4 - - + -
142A LEU* 4.0 31.0 - - + -
145A VAL* 6.1 0.4 - - + -
163A GLN 2.9 17.2 + - - +
164A LYS* 3.5 4.7 - - + +
166A GLU* 1.3 78.0 - - - +
168A VAL* 1.3 57.7 + - - +
170A TYR* 3.4 1.4 + - - +
171A SER* 2.8 47.8 + - - -
197A LEU* 3.7 16.8 - - + -
200A GLN* 4.4 16.1 + - + -
201A THR* 3.6 24.7 - - - -
204A ILE* 4.1 24.9 - - + -
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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
----------------------------------------------------------
142A LEU* 3.8 29.6 - - + -
164A LYS* 2.9 31.3 + - + +
165A LYS* 3.7 9.0 - - + +
167A PHE* 1.3 76.8 - - - +
169A LYS* 1.3 58.3 + - - +
171A SER* 3.3 7.9 + - - -
172A LYS* 2.9 31.8 + - + +
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Residues in contact with LYS 169 (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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165A LYS* 2.9 22.4 + - + +
166A GLU* 3.1 30.0 + - - +
168A VAL* 1.3 78.8 - - - +
170A TYR* 1.3 87.2 + - + +
172A LYS* 3.5 6.9 + - + +
173A SER* 2.9 27.1 + - - -
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Residues in contact with TYR 170 (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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166A GLU* 2.9 37.9 + - - +
167A PHE 4.1 0.7 - - - +
169A LYS* 1.3 102.5 + - + +
171A SER* 1.3 59.6 + - - +
173A SER* 3.6 13.9 - - - -
174A PHE* 2.9 27.0 + - - +
193A SER* 5.2 1.4 - - - +
196A ARG* 4.2 41.2 + - + -
197A LEU* 4.0 17.8 - - + +
200A GLN* 3.5 42.4 + - + -
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Residues in contact with SER 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 3.7 24.8 - - - +
142A LEU* 5.9 1.1 - - - -
167A PHE* 2.8 43.7 + - - -
168A VAL* 3.5 8.3 - - - -
170A TYR* 1.3 77.6 - - - +
172A LYS* 1.3 58.5 + - - +
174A PHE* 3.1 6.6 + - - +
175A SER* 2.9 26.6 + - - -
197A LEU* 3.7 16.8 - - - +
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Residues in contact with LYS 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* 2.9 20.0 + - + +
169A LYS* 3.6 7.4 - - - +
171A SER* 1.3 76.6 - - - +
173A SER* 1.3 57.4 + - - +
175A SER* 3.2 14.8 + - - -
176A ASP* 2.9 53.8 + - - +
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LYS* 2.9 19.5 + - - -
170A TYR* 3.6 19.9 - - - -
172A LYS* 1.3 77.5 - - - +
174A PHE* 1.3 58.2 + - - +
176A ASP* 3.5 8.6 + - - +
177A THR* 2.9 34.2 + - - -
193A SER* 4.2 8.5 + - - -
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Residues in contact with PHE 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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114A LEU* 4.3 2.9 - - + -
117A ILE* 3.8 19.3 - - + -
127A PHE* 5.9 0.7 - + - -
134A ILE* 3.8 34.1 - - + -
138A ILE* 5.2 2.5 - - + -
170A TYR 2.9 14.9 + - - +
171A SER 3.1 10.1 + - - +
173A SER* 1.3 74.3 - - - +
175A SER* 1.3 60.7 + - - +
177A THR* 3.3 2.6 + - - -
178A LEU* 2.9 60.1 + - + +
190A VAL* 4.0 17.9 - - + -
193A SER* 3.7 27.3 + - - +
194A ALA* 3.8 26.7 - - + -
197A LEU* 4.3 15.5 - - + -
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Residues in contact with SER 175 (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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171A SER 2.9 11.8 + - - -
172A LYS* 3.4 23.0 + - - -
174A PHE* 1.3 78.1 - - - +
176A ASP* 1.3 59.6 + - - +
178A LEU* 3.1 15.7 + - - +
179A LYS* 3.0 25.5 + - - +
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Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LYS* 2.9 49.4 + - - +
173A SER* 3.8 7.7 - - - +
175A SER* 1.3 77.5 + - - +
177A THR* 1.3 56.7 + - - +
179A LYS* 3.1 18.0 + - + +
180A THR* 2.9 31.8 + - - +
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Residues in contact with THR 177 (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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173A SER* 2.9 20.5 + - - -
174A PHE 3.5 5.4 - - - +
176A ASP* 1.3 76.8 - - - +
178A LEU* 1.3 57.8 + - - +
180A THR* 3.3 8.0 + - - +
181A TYR* 2.9 26.5 + - - +
189A ASN* 3.5 40.7 - - + +
190A VAL* 3.8 13.2 - - + +
193A SER* 2.8 23.3 + - - +
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Residues in contact with LEU 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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127A PHE* 3.8 31.0 - - + -
131A ILE* 3.8 33.0 - - + -
174A PHE* 2.9 43.4 + - + +
175A SER* 3.2 12.1 - - - +
177A THR* 1.3 73.9 - - - +
179A LYS* 1.3 67.0 + - - +
181A TYR* 3.1 4.3 + - + +
182A PHE* 2.9 38.3 + - + -
190A VAL* 4.0 19.3 - - + -
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Residues in contact with LYS 179 (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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175A SER 3.0 11.6 + - - +
176A ASP* 3.1 21.5 + - + +
178A LEU* 1.3 78.2 - - - +
180A THR* 1.3 61.8 + - - +
182A PHE* 3.6 13.7 + - - +
183A LYS* 3.7 10.9 + - - +
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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 ASP 2.9 14.0 + - - -
177A THR* 3.7 10.0 - - - -
179A LYS* 1.3 74.4 - - - +
181A TYR* 1.3 61.8 + - - +
183A LYS* 3.0 11.5 + - + +
184A ASP* 2.9 49.0 + - - +
189A ASN* 5.2 8.5 - - + +
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Residues in contact with TYR 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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121A ILE* 3.7 22.2 + - + +
124A ARG* 3.5 38.0 + - - -
127A PHE* 3.6 29.3 - + - -
177A THR* 2.9 18.7 + - + +
178A LEU* 3.4 6.1 - - + +
180A THR* 1.3 73.1 - - - +
182A PHE* 1.3 71.5 + + - +
183A LYS 3.0 5.6 + - - -
184A ASP* 3.6 7.2 - - - -
185A GLY* 2.7 51.0 + - - -
186A LYS 3.6 21.5 - - - +
187A ALA* 4.0 14.9 - - + +
189A ASN* 6.2 1.1 - - + -
190A VAL* 3.6 20.4 - - + -
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Residues in contact with PHE 182 (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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124A ARG* 3.4 41.6 + - - +
127A PHE* 4.0 8.7 - + - -
128A LEU* 4.2 15.7 - - + -
131A ILE* 3.5 33.2 - - + -
178A LEU* 2.9 36.3 + - + +
179A LYS* 4.1 7.6 - - - +
180A THR 3.3 0.4 - - - -
181A TYR* 1.3 83.9 - + - +
183A LYS* 1.3 59.1 + - - +
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Residues in contact with LYS 183 (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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179A LYS 3.7 9.1 + - - +
180A THR* 3.0 14.4 + - + +
181A TYR 3.0 0.8 - - - -
182A PHE* 1.3 81.6 - - - +
184A ASP* 1.3 70.8 + - + +
185A GLY 3.6 0.4 - - - -
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Residues in contact with ASP 184 (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 THR* 2.9 38.4 + - - +
181A TYR* 3.6 5.7 - - - -
183A LYS* 1.3 85.9 - - + +
185A GLY* 1.3 72.0 + - - +
186A LYS* 3.1 46.8 + - + +
189A ASN* 4.5 5.6 + - - -
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Residues in contact with GLY 185 (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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124A ARG* 5.8 2.5 - - - -
181A TYR* 2.7 39.4 + - - -
182A PHE 4.8 0.2 - - - -
183A LYS 3.6 1.2 + - - -
184A ASP* 1.3 72.6 + - - +
186A LYS* 1.3 59.1 + - - +
187A ALA* 3.4 6.9 + - - +
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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