Contacts of the helix formed by residues 181 - 199 (chain C) in PDB entry 3T5D
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 THR 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ARG* 3.4 27.8 - - + +
247A GLN* 3.3 31.6 - - + +
248A TYR* 4.1 7.2 - - + -
180C LEU* 1.3 73.9 - - - +
182C PRO* 1.4 64.0 - - - +
183C GLU* 4.0 9.9 + - - +
184C GLU* 2.8 35.1 + - - +
185C CYS* 2.7 31.7 + - - +
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Residues in contact with PRO 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLN 3.7 12.8 - - - +
249A PRO* 3.7 35.4 - - + -
180C LEU 4.5 0.7 - - - +
181C THR* 1.4 87.8 - - - +
183C GLU* 1.3 72.9 + - + +
185C CYS* 4.0 6.5 - - + +
186C GLN* 3.3 27.2 + - - +
259C GLU 6.1 0.7 - - - +
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Residues in contact with GLU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLN 6.1 0.2 - - - +
181C THR* 3.1 10.9 - - - +
182C PRO* 1.3 89.7 - - + +
184C GLU* 1.3 63.2 + - + +
186C GLN* 3.7 5.1 + - - +
187C GLN* 3.3 34.4 + - - +
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Residues in contact with GLU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GDP 2.7 46.3 + - - +
246A ARG* 2.7 28.1 + - - -
180C LEU* 3.7 22.5 - - + +
181C THR* 2.8 27.5 + - - +
183C GLU* 1.3 78.4 - - + +
185C CYS* 1.3 61.1 + - - +
187C GLN* 3.3 9.6 + - - +
188C PHE* 2.8 33.4 + - - +
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Residues in contact with CYS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 4.8 1.6 - - - +
177C ALA* 5.4 4.3 - - - -
180C LEU* 4.0 26.8 - - + +
181C THR 2.7 22.6 + - - +
182C PRO* 4.1 6.7 - - + +
184C GLU* 1.3 74.1 - - - +
186C GLN* 1.3 60.9 + - - +
188C PHE* 3.8 1.7 - - - +
189C LYS* 3.2 40.9 + - - +
228C ALA* 3.7 29.8 - - - -
262C ASP* 5.4 0.2 - - - -
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Residues in contact with GLN 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C PRO 3.3 17.0 + - - +
183C GLU* 4.0 5.8 - - - +
185C CYS* 1.3 79.3 - - - +
187C GLN* 1.3 63.0 + - + +
189C LYS* 3.5 10.3 + - + +
190C LYS* 3.4 26.6 + - - +
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Residues in contact with GLN 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C GLU* 3.3 21.9 + - - +
184C GLU* 3.3 10.3 + - - +
186C GLN* 1.3 77.1 - - + +
188C PHE* 1.3 64.6 + - - +
190C LYS* 3.6 5.2 + - - +
191C GLN* 3.2 24.3 + - - +
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Residues in contact with PHE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ILE* 4.0 17.9 - - + -
147C ALA 4.0 10.5 - - - -
148C PRO* 4.1 11.9 - - + -
149C SER* 5.1 0.4 - - - -
150C GLY* 3.4 30.3 - - - +
151C HIS 3.3 19.7 - - - -
152C GLY 3.7 12.6 - - - -
174C ILE* 3.7 32.3 - - + -
180C LEU* 3.7 21.5 - - + -
184C GLU 2.8 19.1 + - - +
185C CYS* 3.8 6.1 - - - +
187C GLN* 1.3 75.1 - - - +
189C LYS* 1.3 63.8 + - - +
191C GLN* 3.5 2.5 + - - +
192C ILE* 3.1 51.9 + - + +
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Residues in contact with LYS 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 3.7 9.0 - - + -
185C CYS* 3.2 38.8 + - - +
186C GLN* 3.7 9.6 - - + +
187C GLN 3.3 0.2 - - - -
188C PHE* 1.3 76.3 - - - +
190C LYS* 1.3 56.4 - - - +
192C ILE* 3.2 3.8 + - - +
193C MET* 3.0 34.7 + - - +
223C ASP 5.3 1.3 - - - +
224C ARG* 3.1 39.4 + - - +
225C LEU 4.0 4.5 - - - +
226C PRO* 3.3 34.3 - - + +
228C ALA* 4.2 2.5 - - - -
262C ASP* 2.8 27.8 + - - -
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Residues in contact with LYS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C GLN* 3.4 17.4 + - - +
187C GLN* 4.1 6.1 - - - +
189C LYS* 1.3 79.6 - - - +
191C GLN* 1.3 61.5 + - - +
193C MET* 4.0 6.7 - - + +
194C LYS* 3.1 43.1 + - + +
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Residues in contact with GLN 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C HIS 3.4 26.2 - - - +
152C GLY* 3.6 3.9 - - - +
187C GLN 3.2 18.9 + - - +
188C PHE* 3.7 5.2 - - - +
189C LYS 3.2 0.2 - - - -
190C LYS* 1.3 77.2 - - - +
192C ILE* 1.3 61.6 + - - +
194C LYS* 4.2 5.0 - - - +
195C GLU* 2.9 53.5 + - - +
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Residues in contact with ILE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ILE* 4.1 12.8 - - + -
153C LEU* 3.8 32.5 - - + +
174C ILE* 3.9 7.4 - - + -
188C PHE* 3.1 56.7 + - + +
189C LYS 3.2 5.8 + - - +
191C GLN* 1.3 74.3 - - - +
193C MET* 1.3 60.5 + - - +
195C GLU* 3.0 5.4 + - - +
196C ILE* 2.8 46.8 + - + +
226C PRO* 3.8 28.9 - - + -
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Residues in contact with MET 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LYS 3.0 17.5 + - - +
190C LYS* 4.1 7.0 - - + +
192C ILE* 1.3 75.9 - - - +
194C LYS* 1.3 58.2 + - + +
196C ILE* 3.5 21.6 + - + +
197C GLN* 3.2 41.1 + - + +
203C ILE* 4.1 20.9 - - + -
222C LYS* 5.7 2.0 - - + +
225C LEU* 3.3 44.0 - - + +
226C PRO* 3.7 12.3 - - + -
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Residues in contact with LYS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C LYS* 3.1 36.0 + - + +
191C GLN* 4.2 7.9 - - - +
193C MET* 1.3 77.0 - - + +
195C GLU* 1.3 59.1 + - + +
197C GLN* 3.6 17.0 + - + +
198C GLU* 3.0 28.3 + - - +
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Residues in contact with GLU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLY* 3.4 13.9 - - - -
153C LEU* 2.9 45.1 + - + +
158C ILE* 4.1 9.6 - - + +
191C GLN* 2.9 40.8 + - - +
192C ILE 3.0 5.0 + - - +
194C LYS* 1.3 76.6 - - + +
196C ILE* 1.3 63.8 + - - +
198C GLU* 3.9 15.0 - - - +
199C HIS* 3.2 31.9 + - + +
201C ILE* 4.6 0.2 - - - +
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Residues in contact with ILE 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C LEU* 4.2 8.5 - - + -
161C MET* 4.8 10.8 - - - -
172C PRO* 4.6 6.7 - - + -
192C ILE* 2.8 38.8 + - + +
193C MET* 3.6 27.8 - - + +
194C LYS 3.3 0.2 - - - -
195C GLU* 1.3 77.2 - - - +
197C GLN* 1.3 64.6 + - + +
199C HIS 3.5 1.0 + - - -
200C LYS 3.3 3.6 + - - -
201C ILE* 3.0 64.4 + - + +
203C ILE* 4.1 32.3 - - + -
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Residues in contact with GLN 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C MET* 3.2 24.8 + - + +
194C LYS* 3.6 19.0 + - + +
196C ILE* 1.3 79.0 - - + +
198C GLU* 1.3 63.6 + - - +
200C LYS* 3.4 16.9 + - - +
201C ILE 5.4 0.9 - - - -
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Residues in contact with GLU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C LYS 3.0 19.1 + - - +
195C GLU* 4.0 17.4 - - - +
196C ILE 3.3 0.4 - - - -
197C GLN* 1.3 77.9 - - - +
199C HIS* 1.3 73.8 + - + +
200C LYS* 3.3 12.1 + - - +
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Residues in contact with HIS 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C ILE* 3.7 33.2 - - + +
162C LYS* 3.4 48.3 + - - +
195C GLU* 3.2 30.0 + - + +
196C ILE 3.5 0.2 + - - -
197C GLN 3.3 0.2 - - - -
198C GLU* 1.3 92.7 + - + +
200C LYS* 1.3 69.9 + - - +
201C ILE* 3.3 14.5 + - + -
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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