Contacts of the helix formed by residues 166 - 184 (chain A) in PDB entry 1W5B
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 GLY 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PRO* 5.5 0.3 - - - +
162A PHE 5.0 1.4 - - - +
163A VAL* 3.0 12.9 + - - +
164A MET 3.3 0.6 - - - -
165A GLU* 1.3 83.7 - - - +
167A LYS* 1.3 65.8 + - - -
168A VAL* 3.4 2.7 - - - -
169A ARG* 3.6 2.1 + - - +
170A MET* 3.4 18.2 + - - +
313B PRO* 3.1 10.6 + - - -
314B ASN* 3.0 22.0 - - - -
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Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY* 1.3 71.4 - - - -
168A VAL* 1.3 61.2 + - + +
170A MET* 3.3 7.6 + - + +
171A LYS* 2.9 31.1 + - - +
348A ASP 4.6 2.3 - - - +
349A THR* 4.3 23.3 + - - +
314B ASN* 3.1 17.3 - - - +
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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
----------------------------------------------------------
166A GLY* 3.4 1.2 - - - -
167A LYS* 1.3 78.0 - - + +
169A ARG* 1.3 64.4 + - - +
171A LYS* 3.3 6.7 + - - +
172A ASN* 3.0 39.4 + - - +
314B ASN* 4.9 14.9 - - + +
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Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY* 4.0 17.4 - - - +
132A GLY* 3.3 34.7 + - - +
133A GLY* 3.4 22.8 - - - -
161A PRO* 4.1 7.9 - - + -
165A GLU* 3.3 38.3 + - + +
166A GLY 3.6 3.6 + - - +
167A LYS 3.3 0.4 - - - -
168A VAL* 1.3 82.4 - - - +
170A MET* 1.3 55.7 + - - +
172A ASN* 3.7 1.9 + - - +
173A ALA* 3.1 27.4 + - - +
500A GTP 3.0 38.8 + - - +
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Residues in contact with MET 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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160A LEU* 3.6 22.4 - - + -
161A PRO* 3.8 25.5 - - + +
162A PHE 6.1 0.4 - - - +
166A GLY 3.4 10.1 + - - +
167A LYS* 3.3 10.0 + - + +
168A VAL 3.2 0.4 - - - -
169A ARG* 1.3 75.8 - - - +
171A LYS* 1.3 61.8 + - - +
173A ALA* 3.2 11.4 + - + -
174A MET* 2.8 54.3 + - + +
348A ASP 3.8 3.8 - - - +
349A THR* 3.5 35.0 - - - +
350A GLY* 4.1 4.3 - - - -
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Residues in contact with LYS 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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167A LYS 2.9 16.8 + - - +
168A VAL* 3.7 6.7 - - - +
170A MET* 1.3 78.0 - - - +
172A ASN* 1.3 73.2 + - - +
174A MET* 3.1 3.5 + - - +
175A GLU* 2.9 42.1 + - + +
348A ASP* 3.5 35.1 + - + +
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Residues in contact with ASN 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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99A GLY 3.7 8.0 - - - +
101A PRO* 3.7 35.7 - - + +
132A GLY 4.3 11.3 - - - +
137A THR* 3.2 12.4 - - + +
168A VAL* 3.0 32.6 + - - +
169A ARG* 3.9 4.4 - - - +
171A LYS* 1.3 88.2 - - - +
173A ALA* 1.3 57.5 + - - +
175A GLU* 3.5 11.1 + - - +
176A GLY 3.0 23.0 + - - -
179A ARG* 4.7 0.9 + - - -
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Residues in contact with ALA 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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131A LEU* 3.6 27.7 - - + +
132A GLY* 3.9 8.3 - - - +
137A THR* 4.5 0.7 - - - -
160A LEU* 4.6 1.6 - - + -
161A PRO* 3.6 24.5 - - + -
169A ARG 3.1 19.5 + - - +
170A MET* 3.5 10.1 - - + +
172A ASN* 1.3 77.6 - - - +
174A MET* 1.3 57.5 + - - +
176A GLY* 3.2 2.6 + - - -
177A LEU* 2.8 28.5 + - - +
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Residues in contact with MET 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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160A LEU* 4.2 7.9 - - - -
170A MET* 2.8 42.4 + - + +
171A LYS 3.7 3.4 - - - +
173A ALA* 1.3 69.8 - - - +
175A GLU* 1.3 65.3 + - - +
177A LEU* 3.4 18.4 - - + +
178A GLU* 3.1 21.7 + - - +
346A PHE* 3.8 17.3 - - + +
347A THR 3.0 38.4 - - - +
348A ASP* 4.3 7.9 - - - -
350A GLY* 3.7 27.4 - - - +
351A LEU* 3.8 17.7 - - + -
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Residues in contact with GLU 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 LYS* 2.9 34.2 + - + +
172A ASN* 3.8 11.2 + - - +
174A MET* 1.3 75.4 - - - +
176A GLY* 1.3 64.3 + - - +
178A GLU* 3.2 8.3 + - + +
179A ARG* 3.1 38.5 + - + +
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Residues in contact with GLY 176 (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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131A LEU* 4.9 5.8 - - - +
137A THR* 3.8 10.8 - - - -
141A PRO* 4.1 1.7 - - - +
172A ASN 3.0 13.6 + - - -
173A ALA 3.6 3.8 - - - -
175A GLU* 1.3 77.3 - - - +
177A LEU* 1.3 56.3 + - - +
179A ARG* 3.3 29.3 + - - +
180A LEU* 2.8 31.3 + - - +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 3.7 22.0 - - + +
158A VAL* 4.1 4.9 - - + -
160A LEU* 4.2 8.5 - - + -
173A ALA 2.8 16.8 + - - +
174A MET* 3.4 28.9 - - - +
175A GLU 3.1 0.4 - - - -
176A GLY* 1.3 76.3 - - - +
178A GLU* 1.3 58.6 + - - +
180A LEU* 4.4 2.5 - - + -
181A LYS* 3.0 28.4 + - - +
187A LEU* 3.6 25.5 - - + +
189A VAL* 3.7 21.5 - - + -
346A PHE* 3.6 28.7 - - + -
351A LEU* 3.9 11.4 - - + -
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Residues in contact with GLU 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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174A MET 3.1 11.5 + - - +
175A GLU* 3.5 11.4 - - + +
177A LEU* 1.3 77.5 - - - +
179A ARG* 1.3 64.8 + - + +
181A LYS* 3.4 17.0 - - - +
182A GLN* 3.1 43.9 + - + +
346A PHE* 4.0 27.0 - - + +
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Residues in contact with ARG 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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101A PRO* 3.9 15.6 + - - +
105A GLU* 3.8 23.8 + - - -
137A THR* 3.2 35.0 + - - +
138A GLY* 4.3 4.4 + - - -
141A PRO* 3.2 29.2 - - + +
172A ASN 4.7 1.0 + - - -
175A GLU* 3.1 25.7 + - + +
176A GLY* 3.6 24.2 - - - +
178A GLU* 1.3 77.6 - - + +
180A LEU* 1.3 65.2 + - - +
182A GLN* 3.2 16.7 + - - +
183A HIS* 3.3 19.9 + - + -
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Residues in contact with LEU 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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127A ILE* 5.1 1.6 - - + -
131A LEU* 4.8 8.3 - - + -
140A ALA* 3.7 41.7 - - + +
141A PRO* 3.9 10.5 - - + +
144A ALA* 4.0 4.0 - - + -
156A ALA* 3.9 7.2 - - + -
158A VAL* 3.8 25.1 - - + -
176A GLY 2.8 16.8 + - - +
177A LEU* 3.9 6.5 - - + +
179A ARG* 1.3 75.8 - - - +
181A LYS* 1.3 58.1 + - - +
182A GLN 3.0 0.2 - - - -
183A HIS* 2.9 20.3 + - - -
184A THR* 3.3 41.0 + - + +
187A LEU* 3.8 23.8 - - + -
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Residues in contact with LYS 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 LEU 3.0 18.9 + - - +
178A GLU* 3.4 12.1 - - - +
180A LEU* 1.3 75.4 - - - +
182A GLN* 1.3 72.7 + - - +
183A HIS 3.4 0.6 + - - -
184A THR* 3.9 15.1 + - - +
187A LEU* 3.8 19.0 - - + +
247A GLY* 4.3 5.9 - - - -
248A LEU* 3.8 19.8 - - + +
341A GLN* 3.4 40.8 - - - +
346A PHE* 4.6 15.7 - - + -
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Residues in contact with GLN 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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148A LYS* 5.6 0.9 - - - +
178A GLU* 3.1 41.3 + - + +
179A ARG* 3.4 12.6 - - - +
180A LEU 3.0 0.8 + - - -
181A LYS* 1.3 87.5 - - - +
183A HIS* 1.3 73.0 + - + +
184A THR 3.6 1.7 - - - +
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Residues in contact with HIS 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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141A PRO* 4.0 18.8 + - + -
144A ALA* 3.7 26.6 - - + +
145A GLU* 3.5 41.5 + - + +
148A LYS* 3.0 30.3 - - + +
154A THR* 3.9 0.7 - - - +
179A ARG* 3.3 24.7 - - + +
180A LEU 2.9 4.2 + - - +
182A GLN* 1.3 91.5 + - + +
184A THR* 1.3 61.9 + - - +
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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
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144A ALA* 4.1 7.4 - - + -
148A LYS* 4.6 1.5 - - - +
154A THR* 3.9 9.6 - - + -
156A ALA* 3.9 17.7 - - + +
180A LEU* 3.4 39.4 + - + +
181A LYS* 3.9 12.6 + - - +
182A GLN 3.6 2.4 - - - +
183A HIS* 1.3 82.2 - - - +
185A ASP* 1.3 65.6 + - - +
186A THR 3.8 12.1 - - - -
187A LEU* 3.6 19.5 + - + +
247A GLY* 5.2 0.5 + - - -
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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