Contacts of the helix formed by residues 189 - 207 (chain X) in PDB entry 3FEW
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 ASP 189 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187X ASN 3.3 0.6 - - - -
188X LYS* 1.3 89.6 - - - +
190X GLU* 1.3 60.5 + - - +
191X SER 3.5 2.0 - - - -
192X GLN* 3.8 14.9 + - + +
193X ARG* 3.3 45.2 + - + +
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Residues in contact with GLU 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X TYR* 2.9 34.2 + - - -
152X ARG* 2.9 32.9 + - - +
187X ASN* 3.2 25.9 + - + +
188X LYS 3.5 1.6 + - - -
189X ASP* 1.3 74.8 - - - +
191X SER* 1.3 66.7 + - - +
193X ARG* 3.0 14.9 + - - +
194X GLN* 2.9 46.3 + - - +
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Residues in contact with SER 191 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189X ASP 3.5 0.4 - - - -
190X GLU* 1.3 76.9 - - - +
192X GLN* 1.3 64.1 + - - +
194X GLN* 3.2 10.3 + - - +
195X GLU* 3.0 23.3 + - - +
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Residues in contact with GLN 192 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189X ASP* 3.8 21.6 + - + +
190X GLU 3.4 0.4 - - - -
191X SER* 1.3 78.1 - - - +
193X ARG* 1.3 61.7 + - + +
195X GLU* 3.3 8.2 + - - +
196X LYS* 3.1 36.8 + - + +
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Residues in contact with ARG 193 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132X ILE* 3.8 31.0 - - + +
133X ASP* 4.0 13.3 + - - +
135X PHE* 3.3 43.7 - - - -
137X TYR* 2.9 30.5 + - + +
156X ARG* 5.7 0.8 - - - +
186X PHE 2.6 29.7 + - - -
189X ASP* 3.3 36.7 + - + +
190X GLU* 3.0 31.0 + - - +
191X SER 3.2 0.4 - - - -
192X GLN* 1.3 79.4 - - + +
194X GLN* 1.3 57.3 + - - +
196X LYS* 3.4 5.1 + - + +
197X ALA* 2.9 29.2 + - - +
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Residues in contact with GLN 194 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X TYR* 4.2 6.2 - - + -
150X ILE* 3.4 44.1 - - + +
152X ARG* 6.1 0.4 - - - +
190X GLU* 2.9 47.4 + - - +
191X SER* 3.2 11.3 + - - +
193X ARG* 1.3 75.2 - - - +
195X GLU* 1.3 60.6 + - - +
197X ALA* 3.3 1.4 + - - +
198X LYS* 3.0 48.0 + - - +
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Residues in contact with GLU 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191X SER 3.0 12.5 + - - +
192X GLN* 3.6 11.0 - - - +
193X ARG 3.3 0.2 - - - -
194X GLN* 1.3 78.7 - - - +
196X LYS* 1.3 61.9 + - - +
198X LYS* 3.6 14.7 + - - +
199X GLN* 3.2 27.9 + - - +
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Residues in contact with LYS 196 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132X ILE* 4.0 27.1 - - + +
133X ASP* 5.0 8.7 + - - +
192X GLN* 3.1 32.2 + - + +
193X ARG* 3.6 10.1 - - + +
195X GLU* 1.3 73.2 - - - +
197X ALA* 1.3 65.9 + - - +
199X GLN* 3.2 7.9 + - - +
200X GLN* 2.9 23.9 + - - +
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Residues in contact with ALA 197 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X VAL* 3.6 27.5 - - + +
132X ILE* 3.9 11.4 - - + +
137X TYR* 4.0 7.2 - - + -
139X VAL* 4.0 2.7 - - + -
150X ILE* 3.8 19.7 - - + -
193X ARG 2.9 18.2 + - - +
194X GLN 3.3 5.6 + - - +
196X LYS* 1.3 75.0 - - - +
198X LYS* 1.3 57.8 + - - +
200X GLN* 3.2 3.9 + - - +
201X ALA* 2.9 28.9 + - - +
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Residues in contact with LYS 198 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X VAL* 4.2 15.9 - - + -
147X ALA* 3.6 27.6 + - + +
148X ILE 5.9 1.0 - - - -
149X GLY* 4.8 8.5 - - - +
150X ILE* 4.3 29.1 - - + +
194X GLN* 3.0 32.1 + - - +
195X GLU* 3.9 17.3 + - - +
197X ALA* 1.3 72.1 - - - +
199X GLN* 1.3 65.8 + - - +
201X ALA* 3.3 2.4 + - - +
202X GLU* 2.9 32.4 + - - +
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Residues in contact with GLN 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195X GLU* 3.2 18.7 + - - +
196X LYS* 3.2 10.5 + - - +
198X LYS* 1.3 78.8 - - - +
200X GLN* 1.3 57.9 + - - +
202X GLU* 3.3 22.4 + - - +
203X ASP* 3.1 62.3 + - - +
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Residues in contact with GLN 200 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X VAL* 3.6 31.3 - - + +
131X SER 4.1 9.1 + - - +
132X ILE* 3.5 19.4 - - - +
196X LYS 2.9 16.3 + - - +
197X ALA* 3.6 6.7 - - - +
199X GLN* 1.3 74.7 - - - +
201X ALA* 1.3 59.1 + - - +
203X ASP* 3.3 10.4 + - + +
204X ALA* 3.0 25.5 + - - +
207X ARG* 4.1 10.6 + - - +
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Residues in contact with ALA 201 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X ILE* 3.9 23.7 - - + +
130X VAL* 4.0 9.1 - - + +
139X VAL* 3.7 30.5 - - + -
141X LEU* 3.7 14.7 - - + +
197X ALA 2.9 16.7 + - - +
198X LYS 3.3 4.5 + - - +
200X GLN* 1.3 73.4 - - - +
202X GLU* 1.3 64.7 + - - +
204X ALA* 3.3 3.6 + - - +
205X TRP 3.2 17.5 + - - -
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Residues in contact with GLU 202 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141X LEU* 4.1 2.7 - - + -
145X GLY 3.4 24.1 - - - +
146X ARG* 4.1 9.5 - - - +
147X ALA* 3.1 31.6 + - - +
198X LYS* 2.9 21.7 + - - +
199X GLN* 3.5 26.4 + - - +
200X GLN 3.2 0.2 - - - -
201X ALA* 1.3 76.5 - - - +
203X ASP* 1.3 65.4 + - - +
205X TRP* 3.4 5.8 - - - +
206X ASP* 3.0 29.0 + - - +
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Residues in contact with ASP 203 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199X GLN* 3.1 38.6 + - - +
200X GLN* 3.7 10.1 - - + +
201X ALA 3.3 0.2 - - - -
202X GLU* 1.3 77.5 - - - +
204X ALA* 1.3 64.4 + - - +
206X ASP* 3.2 14.1 + - - +
207X ARG* 3.1 46.1 + - - +
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Residues in contact with ALA 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X ILE* 4.0 25.4 - - + -
130X VAL* 6.0 0.7 - - + -
200X GLN 3.0 13.3 + - - +
201X ALA 3.3 9.4 + - - +
203X ASP* 1.3 74.8 - - - +
205X TRP* 1.3 57.5 + - - +
207X ARG* 2.9 39.1 + - - +
208X LEU* 3.2 17.0 + - + +
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Residues in contact with TRP 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X LYS* 5.0 1.6 - - + -
124X LEU* 3.9 19.3 - - + -
125X PRO 3.6 22.4 - - - -
126X ARG* 3.8 35.4 - - - -
128X ILE* 5.0 2.1 - - + +
141X LEU* 3.7 24.9 - - + +
142X ASN 4.6 0.4 - - - -
143X ASP 3.6 20.6 - - - -
144X ASN 3.8 8.4 + - - -
145X GLY* 3.5 27.1 - - - +
201X ALA 3.2 3.8 + - - +
202X GLU 3.4 9.2 - - - +
203X ASP 3.3 0.4 - - - -
204X ALA* 1.3 76.9 - - - +
206X ASP* 1.3 70.7 + - - +
208X LEU* 3.2 31.0 + - + +
211X ASN* 2.7 45.4 + - - +
297X MET* 3.8 20.0 - - + +
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Residues in contact with ASP 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202X GLU* 3.0 19.3 + - - +
203X ASP* 3.2 15.5 + - - +
205X TRP* 1.3 89.9 - - - +
207X ARG* 1.3 61.5 + - + +
208X LEU 3.3 1.1 - - - -
211X ASN* 3.3 31.3 + - - +
212X VAL* 4.1 3.5 + - - +
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Residues in contact with ARG 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71X VAL* 3.3 34.0 - - + +
72X ASP 5.6 0.7 - - - -
73X ASP 5.1 5.8 - - - -
75X GLY* 4.5 22.9 - - - +
200X GLN* 4.1 14.8 + - - +
203X ASP* 3.1 35.0 + - - +
204X ALA* 2.9 32.7 + - - +
206X ASP* 1.3 76.9 - - + +
208X LEU* 1.3 63.8 + - - +
212X VAL* 3.4 8.1 - - - +
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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