Contacts of the helix formed by residues 184 - 201 (chain A) in PDB entry 3CTP
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 PHE 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASP* 3.5 26.5 - - + -
124A ARG* 3.4 54.7 - - + -
126A GLN* 5.0 2.0 - - + -
142A GLU* 5.8 0.2 - - - -
143A ASN* 4.1 4.0 - - - +
181A PRO* 3.1 40.2 + - + +
182A GLU 4.2 1.6 - - - -
183A VAL* 1.3 97.2 - - + +
185A GLU* 1.3 63.7 + - - +
186A ALA 3.1 1.4 + - - +
187A THR* 3.1 27.9 + - + +
188A GLU* 3.1 20.8 + - - +
212A HIS* 5.3 0.9 - - - -
213A ASP* 4.1 15.9 - - + -
238A PHE* 5.0 1.6 - + - -
401A XLF 4.1 8.1 - - - +
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Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU 3.8 7.9 - - - +
143A ASN* 3.0 24.3 + - - +
144A HIS* 2.7 61.2 + - - +
182A GLU 5.2 0.7 - - - +
183A VAL 3.6 3.2 + - - +
184A PHE* 1.3 72.3 - - - +
186A ALA* 1.3 62.2 + - - +
188A GLU* 3.3 9.3 + - - +
189A LEU* 3.0 33.8 + - + +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 3.4 35.0 + - + +
143A ASN* 4.5 1.4 + - - -
153A SER* 5.0 0.4 - - - +
156A ASN* 3.3 34.8 - - - +
184A PHE 3.1 1.0 - - - -
185A GLU* 1.3 79.4 - - - +
187A THR* 1.3 58.7 + - - +
189A LEU* 3.3 3.6 + - - -
190A ARG* 3.0 31.3 + - - +
401A XLF 3.9 10.1 - - - +
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Residues in contact with THR 187 (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 HIS* 4.9 2.3 + - - -
179A LYS* 5.9 0.2 - - - -
180A GLY* 3.7 18.8 + - - -
181A PRO 3.2 12.0 + - - -
184A PHE* 3.1 26.0 + - + +
186A ALA* 1.3 74.5 - - - +
188A GLU* 1.3 62.4 + - - +
190A ARG* 3.7 15.2 - - - +
191A TYR* 2.9 29.5 + - - +
238A PHE* 3.8 23.5 - - + +
401A XLF 3.5 32.1 - - - -
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 2.7 35.3 + - - -
180A GLY 4.3 1.2 - - - +
181A PRO 4.7 0.2 - - - +
182A GLU* 3.4 45.7 - - + +
184A PHE 3.1 12.1 + - - +
185A GLU* 3.6 10.3 - - - +
186A ALA 3.2 0.2 - - - -
187A THR* 1.3 78.6 + - - +
189A LEU* 1.3 59.0 + - + +
191A TYR* 3.3 16.2 + - - +
192A LYS* 2.9 27.8 + - - +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A SER* 6.0 0.9 - - - +
154A SER 6.1 0.2 - - - +
156A ASN* 4.0 14.4 - - + +
157A TYR* 3.5 42.1 - - + +
185A GLU* 3.0 24.8 + - + +
186A ALA* 3.7 8.1 - - - +
187A THR 3.2 0.2 - - - -
188A GLU* 1.3 75.9 - - + +
190A ARG* 1.3 58.6 + - - +
192A LYS* 3.2 6.9 + - + +
193A GLY 2.9 25.6 + - - -
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Residues in contact with ARG 190 (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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142A GLU* 4.0 1.2 + - - -
156A ASN* 2.8 48.4 + - + +
160A GLY* 3.5 6.4 - - - -
177A HIS* 5.1 2.7 - - + +
186A ALA* 3.0 17.7 + - - +
187A THR* 3.3 14.0 + - - +
189A LEU* 1.3 76.2 - - - +
191A TYR* 1.3 62.6 + - - +
193A GLY 3.4 0.2 + - - -
194A PHE* 3.0 25.5 + - - +
236A PHE* 4.1 18.0 - - + -
238A PHE* 2.7 34.4 + - - +
266A PHE* 3.2 33.4 - - + -
284A GLN* 3.3 12.5 - - - +
401A XLF 2.8 54.4 + - - -
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Residues in contact with TYR 191 (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 HIS* 3.8 18.3 + + - +
179A LYS* 3.8 32.8 - - + -
187A THR 2.9 17.9 + - - +
188A GLU* 3.4 18.2 - - - +
190A ARG* 1.3 76.1 - - - +
192A LYS* 1.3 68.7 + - + +
194A PHE* 3.3 2.9 + - - +
195A LEU* 2.9 52.4 + - + +
207A PHE* 3.5 49.0 - + - -
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Residues in contact with LYS 192 (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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157A TYR* 4.0 11.0 - - + -
188A GLU 2.9 17.0 + - - +
189A LEU* 3.2 11.0 + - + +
191A TYR* 1.3 87.7 - - + +
193A GLY* 1.3 57.4 + - - +
195A LEU* 4.2 21.0 - - + +
196A ASP* 2.8 66.4 + - - +
199A ARG* 4.8 9.1 - - - +
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Residues in contact with GLY 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 3.4 40.3 - - - -
161A ARG* 3.5 20.3 - - - +
189A LEU 2.9 11.7 + - - -
190A ARG 3.9 0.4 - - - -
192A LYS* 1.3 77.1 - - - +
194A PHE* 1.3 63.2 + - - +
196A ASP* 3.9 1.4 - - - +
197A GLY 3.1 17.3 + - - -
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Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLY 3.5 19.1 - - - +
163A ALA 3.9 3.4 - - - -
164A PHE* 3.4 42.4 - + + +
167A LEU* 4.1 5.4 - - + -
175A ILE* 3.4 34.5 - - + -
176A LEU 4.7 0.2 - - - -
177A HIS* 3.8 25.1 - + + -
190A ARG 3.0 18.2 + - - +
191A TYR* 3.6 5.8 - - - +
193A GLY* 1.3 77.3 - - - +
195A LEU* 1.3 63.1 + - - +
197A GLY* 3.2 4.0 + - - -
198A ALA* 3.0 18.2 + - - +
205A ILE* 4.1 13.0 - - + -
207A PHE* 4.8 2.7 - + - -
236A PHE* 3.2 43.1 - + + -
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TYR* 2.9 46.4 + - + +
192A LYS* 3.9 22.0 - - + +
194A PHE* 1.3 75.4 - - - +
196A ASP* 1.3 61.2 + - - +
198A ALA* 3.0 12.2 + - + +
199A ARG* 2.8 71.1 + - + +
203A LEU 5.9 1.1 - - - +
205A ILE* 5.0 4.5 - - + +
207A PHE* 4.1 25.4 - - + -
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Residues in contact with ASP 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 2.5 38.5 + - - +
161A ARG* 4.3 8.6 + - - +
192A LYS* 2.8 48.2 + - - +
193A GLY 3.9 2.7 - - - +
195A LEU* 1.3 76.7 - - - +
197A GLY* 1.3 62.4 + - - +
199A ARG* 3.3 10.7 + - - +
200A ALA* 3.1 22.2 + - - +
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Residues in contact with GLY 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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161A ARG* 3.4 34.5 + - - +
164A PHE* 3.4 19.6 - - - -
193A GLY 3.1 11.3 + - - -
194A PHE 3.2 3.6 + - - -
195A LEU 3.2 0.2 - - - -
196A ASP* 1.3 77.2 - - - +
198A ALA* 1.3 61.0 + - - +
200A ALA* 3.2 13.2 + - - +
201A LYS* 3.3 9.7 + - - +
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Residues in contact with ALA 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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164A PHE* 3.5 22.2 - - + -
194A PHE 3.0 9.0 + - - +
195A LEU* 3.0 12.7 + - + +
197A GLY* 1.3 75.6 - - - +
199A ARG* 1.3 62.4 + - - +
201A LYS* 3.0 7.8 + - - +
203A LEU* 3.0 35.1 + - + +
205A ILE* 3.3 35.2 - - + -
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Residues in contact with ARG 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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192A LYS* 4.8 9.1 - - - +
195A LEU* 2.8 55.3 + - + +
196A ASP* 3.7 9.8 + - - +
197A GLY 3.3 0.2 - - - -
198A ALA* 1.3 76.7 - - - +
200A ALA* 1.3 62.3 + - - +
202A ASP* 3.1 21.1 + - - +
203A LEU 4.9 2.9 - - - +
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ARG* 4.0 19.7 - - - +
196A ASP 3.1 13.2 + - - +
197A GLY 3.5 10.1 - - - +
198A ALA 3.2 0.2 - - - -
199A ARG* 1.3 78.1 - - - +
201A LYS* 1.3 68.0 + - - +
202A ASP* 3.4 6.7 + - - +
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ARG* 4.4 18.0 - - - +
164A PHE* 3.9 12.1 - - + -
165A ASP* 4.8 7.3 + - - -
168A TYR* 3.8 54.9 + - + +
197A GLY 3.3 10.2 + - - +
198A ALA 3.0 8.2 + - - +
200A ALA* 1.3 84.2 + - - +
202A ASP* 1.3 73.8 + - - +
203A LEU* 3.2 7.1 + - + +
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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
------------------------------------------------------------
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