Contacts of the helix formed by residues 192 - 207 (chain C) in PDB entry 1TLF
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 VAL 192 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C PRO* 3.8 5.4 - - + -
128C LEU 3.4 46.4 - - - +
129C ASP* 4.3 4.9 - - - +
130C ASP 5.6 1.3 - - - +
149C ASP* 3.4 13.0 - - - +
150C VAL 3.9 24.0 - - - +
151C SER* 4.2 9.4 - - - +
190C SER 3.7 2.2 + - - +
191C SER* 1.3 74.2 + - - +
193C SER* 1.3 66.5 + - - +
195C ARG* 3.0 26.2 + - - +
196C LEU* 2.9 32.6 + - + +
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Residues in contact with SER 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASP* 2.7 27.7 + - - -
150C VAL 4.7 4.7 + - - -
191C SER* 3.7 5.6 + - - -
192C VAL* 1.3 76.6 - - - +
194C ALA* 1.3 64.0 + - - +
196C LEU* 3.1 14.5 + - - +
197C ARG* 2.8 47.4 + - - +
220C TRP* 5.0 3.8 - - - -
998C IPT 3.4 19.4 - - - +
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Residues in contact with ALA 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ALA* 4.9 2.6 - - - +
187C GLY* 3.8 28.4 + - - +
188C PRO 3.3 26.2 - - - +
189C LEU* 4.8 2.7 - - + -
191C SER* 3.5 11.3 + - - +
192C VAL 3.3 0.6 - - - -
193C SER* 1.3 76.9 - - - +
195C ARG* 1.3 52.6 + - + +
197C ARG* 3.0 8.8 + - - +
198C LEU* 2.8 35.3 + - - +
201C TRP* 5.8 0.2 - - - -
220C TRP* 4.0 13.0 - - + -
245C ALA* 5.7 0.8 - - - +
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Residues in contact with ARG 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ASP* 2.7 33.2 + - - +
189C LEU* 2.9 42.4 - - + +
190C SER 4.0 3.2 + - - -
191C SER 2.9 13.4 + - - +
192C VAL* 3.0 33.0 + - - +
194C ALA* 1.3 74.3 - - - +
196C LEU* 1.3 58.4 + - - +
198C LEU* 3.3 9.4 + - - +
199C ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 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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150C VAL 3.5 25.6 - - - +
151C SER* 4.2 20.4 - - - +
152C ASP* 4.7 0.4 - - - +
160C ILE* 5.2 2.7 - - + -
163C HIS* 3.7 57.0 + - + +
192C VAL* 2.9 19.8 + - + +
193C SER* 3.3 21.5 - - - +
195C ARG* 1.3 77.4 - - - +
197C ARG* 1.3 57.1 + - - +
199C ALA* 3.5 8.8 - - + +
200C GLY* 3.3 18.5 + - - -
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Residues in contact with ARG 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C HIS* 5.1 6.9 - - + +
167C THR* 3.2 16.4 - - + +
193C SER* 2.8 35.3 + - - +
194C ALA* 3.4 9.4 - - - +
196C LEU* 1.3 75.4 - - + +
198C LEU* 1.3 66.8 + - - +
199C ALA 3.0 1.8 - - - -
200C GLY 3.2 0.5 + - - -
201C TRP* 3.0 39.0 + - + -
220C TRP* 3.6 13.7 - - - -
245C ALA* 3.0 27.7 + - + +
273C TYR* 3.4 39.0 + - + +
291C GLN* 3.6 21.8 + - - +
998C IPT 2.8 41.6 + - - +
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Residues in contact with LEU 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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184C LEU* 3.3 34.8 - - + -
186C ALA* 3.9 19.5 - - + -
189C LEU* 4.9 6.3 - - + -
194C ALA 2.8 19.3 + - - +
195C ARG* 3.3 10.1 + - - +
197C ARG* 1.3 73.4 - - - +
199C ALA* 1.3 60.3 + - - +
201C TRP* 3.6 16.0 + - + +
202C HIS* 3.0 38.7 + - + +
215C GLU* 3.1 28.3 - - + +
217C GLU* 4.3 9.4 - - - +
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Residues in contact with ALA 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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195C ARG 2.9 17.5 + - - +
196C LEU* 3.5 10.3 - - + +
198C LEU* 1.3 74.7 - - - +
200C GLY* 1.3 67.1 + - - +
202C HIS* 2.8 10.3 + - - +
203C LYS* 2.8 24.0 + - - +
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Residues in contact with GLY 200 (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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163C HIS* 4.7 0.4 - - - -
164C GLU* 5.1 6.3 - - - -
167C THR* 3.0 32.5 - - - -
196C LEU 3.3 7.1 + - - -
197C ARG 3.2 3.4 + - - -
199C ALA* 1.3 76.4 - - - +
201C TRP* 1.3 62.0 + - - +
202C HIS 2.9 1.7 + - - -
203C LYS* 2.9 14.5 + - - -
204C TYR* 3.0 22.5 + - - -
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Residues in contact with TRP 201 (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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166C GLY 5.2 0.4 + - - -
167C THR* 3.7 30.7 - - + +
170C GLY* 5.8 1.0 - - - -
171C VAL* 4.1 5.8 - - + -
184C LEU* 3.7 27.6 - - + -
185C LEU 3.8 12.6 - - - -
186C ALA* 4.2 7.6 - - - -
194C ALA 5.7 0.4 - - - -
197C ARG* 3.0 26.9 + - + +
198C LEU* 3.6 35.2 - - + +
200C GLY* 1.3 72.7 - - - +
202C HIS* 1.3 58.5 + - - +
205C LEU* 2.9 37.4 + - - +
243C LEU* 3.9 36.8 - - + +
244C VAL 3.5 19.7 - - - -
245C ALA* 3.5 33.0 - - + -
273C TYR* 4.4 11.5 - + - -
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Residues in contact with HIS 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C LEU* 3.8 12.1 - - + +
198C LEU* 3.0 30.3 + - + +
199C ALA* 2.8 13.2 + - - +
201C TRP* 1.3 78.2 - - - +
203C LYS* 1.3 59.7 - - - +
204C TYR 3.4 0.2 - - - -
205C LEU* 4.5 1.1 - - - -
206C THR* 2.9 37.3 + - + +
211C GLN* 5.0 5.8 - - - -
212C PRO* 3.7 28.3 - - + +
215C GLU* 3.2 31.1 + - - -
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Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C GLU* 3.2 32.6 + - - +
199C ALA 2.8 14.3 + - - +
200C GLY* 3.6 8.5 - - - +
202C HIS* 1.3 72.8 - - - +
204C TYR* 1.3 72.7 + - + +
206C THR* 3.4 4.2 + - - -
207C ARG* 3.1 68.7 + - + +
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Residues in contact with TYR 204 (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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164C GLU* 2.7 56.0 + - - +
167C THR* 3.9 9.4 - - - +
168C ARG* 3.3 41.1 + - + -
171C VAL* 4.0 20.9 - - + -
172C GLU* 5.0 4.9 - - + -
200C GLY* 3.0 21.1 + - - +
203C LYS* 1.3 91.7 + - + +
205C LEU* 1.3 64.5 + - - +
207C ARG* 3.8 32.0 + - + -
208C ASN* 2.6 34.9 + - - +
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Residues in contact with LEU 205 (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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171C VAL* 3.6 26.6 - - + +
182C ILE* 3.9 21.5 - - + -
184C LEU* 4.1 16.2 - - + -
201C TRP 2.9 27.2 + - - +
202C HIS* 4.3 2.7 - - - +
203C LYS 3.5 0.2 - - - -
204C TYR* 1.3 74.7 - - - +
206C THR* 1.3 54.4 + - - +
208C ASN* 2.8 17.8 + - - +
210C ILE* 2.7 58.1 + - + +
212C PRO* 3.7 37.7 - - + -
243C LEU* 4.6 4.7 - - + -
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Residues in contact with THR 206 (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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202C HIS* 2.9 28.7 + - + +
203C LYS* 3.4 5.9 + - - -
205C LEU* 1.3 76.3 - - + +
207C ARG* 1.3 57.6 + - - +
209C GLN* 2.6 27.0 + - - +
210C ILE 3.5 9.0 - - - +
211C GLN* 3.1 36.6 - - - +
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Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ARG* 5.6 0.8 - - - +
203C LYS* 3.1 59.8 + - + +
204C TYR* 3.4 32.4 + - - +
206C THR* 1.3 77.9 + - - +
208C ASN* 1.3 65.4 + - - +
209C GLN* 3.1 13.5 + - - +
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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