Contacts of the helix formed by residues 163 - 176 (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 HIS 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C ASP* 2.8 38.0 + - - -
160C ILE* 4.2 13.9 - - + -
161C PHE 2.9 5.9 + - - +
162C SER* 1.3 72.0 - - - +
164C GLU* 1.3 78.6 + - + +
166C GLY 4.2 1.6 - - - -
167C THR* 2.6 37.3 + - - +
196C LEU* 3.7 54.6 + - + +
197C ARG* 5.1 7.0 - - + +
200C GLY* 4.7 0.6 - - - -
273C TYR* 4.2 9.4 - - - +
318C LEU* 4.7 3.1 - - + -
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Residues in contact with GLU 164 (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 ASP* 5.9 0.4 - - - +
162C SER* 3.3 5.3 - - - +
163C HIS* 1.3 103.0 + - + +
165C ASP* 1.3 63.8 + - - +
167C THR* 3.2 5.7 + - - -
168C ARG* 2.9 31.0 + - - +
196C LEU 5.7 0.2 - - - +
200C GLY* 5.1 5.5 - - - -
203C LYS* 3.2 27.8 + - - +
204C TYR* 2.7 34.0 + - - +
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Residues in contact with ASP 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C SER* 2.6 27.6 + - - +
164C GLU* 1.3 76.9 - - - +
166C GLY* 1.3 52.8 + - - +
168C ARG* 2.7 49.6 + - - +
169C LEU* 2.7 31.0 + - + +
320C PRO 4.2 7.6 - - - +
321C VAL* 4.4 7.9 - - + -
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Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C SER 3.4 7.7 + - - -
164C GLU 3.4 0.6 - - - -
165C ASP* 1.3 80.4 - - - +
167C THR* 1.3 61.0 + - - +
169C LEU* 4.8 0.2 - - - -
170C GLY* 3.3 16.6 + - - -
201C TRP* 5.2 0.3 + - - -
273C TYR* 3.6 23.9 - - - -
289C ILE* 3.5 31.6 - - - +
321C VAL* 3.7 5.8 - - - +
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Residues in contact with THR 167 (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 2.6 25.7 + - - +
164C GLU* 3.2 9.9 + - - -
166C GLY* 1.3 74.2 - - - +
168C ARG* 1.3 60.0 + - - +
170C GLY* 4.1 0.4 - - - -
171C VAL* 3.3 29.1 + - - +
197C ARG* 3.2 44.2 - - + +
200C GLY* 3.0 29.7 - - - -
201C TRP* 3.5 19.3 - - - +
204C TYR* 3.9 4.6 - - - +
273C TYR* 4.6 2.7 - - + -
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Residues in contact with ARG 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C GLU 2.9 16.8 + - - +
165C ASP* 2.7 36.5 + - - +
167C THR* 1.3 69.2 - - - +
169C LEU* 1.3 91.4 + - - +
170C GLY 3.1 1.9 + - - -
171C VAL 3.3 0.5 + - - -
172C GLU* 2.8 74.6 + - + +
204C TYR* 3.3 41.9 + - + -
207C ARG* 5.6 0.7 - - - +
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Residues in contact with LEU 169 (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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165C ASP* 2.7 32.7 + - + +
166C GLY* 4.8 0.2 - - - -
168C ARG* 1.3 95.8 - - - +
170C GLY* 1.3 61.6 + - - +
172C GLU* 4.3 3.0 - - - +
173C HIS* 3.0 26.2 + - - +
289C ILE* 3.9 15.0 - - + -
321C VAL* 4.5 9.4 - - + +
322C SER* 4.2 11.9 - - - -
323C LEU* 4.0 35.2 - - + +
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Residues in contact with GLY 170 (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 3.3 12.4 + - - -
167C THR* 3.9 1.3 + - - -
168C ARG 3.1 1.2 - - - -
169C LEU* 1.3 77.7 - - - +
171C VAL* 1.3 65.7 + - - +
173C HIS* 3.3 4.4 + - - +
174C LEU* 3.0 26.0 + - - +
201C TRP* 5.8 0.4 - - - -
243C LEU* 3.9 19.3 - - - -
271C VAL* 4.5 9.6 - - - -
289C ILE* 4.0 9.3 - - - +
323C LEU* 5.0 0.7 - - - -
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Residues in contact with VAL 171 (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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167C THR 3.3 18.2 + - - +
168C ARG 3.3 2.5 + - - +
170C GLY* 1.3 71.0 - - - +
172C GLU* 1.3 66.7 + - - +
174C LEU* 2.9 7.5 + - - +
175C VAL* 2.7 37.0 + - + +
182C ILE* 5.9 0.2 - - - -
201C TRP* 4.1 10.3 - - + +
204C TYR* 3.9 22.4 - - + +
205C LEU* 3.6 48.2 - - + -
208C ASN* 4.4 4.7 - - - +
243C LEU* 4.0 18.9 - - + +
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Residues in contact with GLU 172 (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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168C ARG* 2.8 64.1 + - + +
169C LEU* 4.3 4.0 - - + +
171C VAL* 1.3 73.7 - - + +
173C HIS* 1.3 52.5 + - - +
175C VAL* 2.9 9.5 - - + +
176C ALA* 2.7 37.6 + - - +
204C TYR* 5.0 3.8 - - + -
208C ASN* 4.4 18.2 + - - +
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Residues in contact with HIS 173 (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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169C LEU 3.0 21.8 + - - +
170C GLY 3.3 3.1 - - - +
171C VAL 3.0 0.6 - - - -
172C GLU* 1.3 77.5 - - - +
174C LEU* 1.3 71.7 + - + +
176C ALA* 3.3 5.4 + - + +
177C LEU* 3.1 37.5 + - + +
271C VAL* 4.3 6.2 - - + +
287C THR* 4.2 11.2 - - + -
323C LEU* 4.2 17.9 - - + +
325C LYS* 4.1 33.0 + - - +
329C THR* 3.0 45.5 + - + +
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Residues in contact with LEU 174 (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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170C GLY 3.0 8.6 + - - +
171C VAL 2.9 7.2 + - - +
173C HIS* 1.3 81.0 - - - +
175C VAL* 1.3 61.3 + - - +
177C LEU* 3.4 1.4 + - - -
178C GLY 3.3 3.1 + - - -
179C HIS* 3.1 49.5 + - + +
182C ILE* 4.2 16.6 - - + -
241C ALA* 4.0 20.9 - - + -
242C MET 4.4 3.4 - - - +
243C LEU* 3.5 38.6 - - + -
269C SER* 4.4 4.9 - - - -
271C VAL* 3.5 24.2 - - + -
329C THR* 3.9 18.2 - - - +
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Residues in contact with VAL 175 (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* 2.7 35.8 + - + +
172C GLU* 2.9 34.1 - - + +
174C LEU* 1.3 71.6 - - - +
176C ALA* 1.3 54.0 + - + +
177C LEU 2.7 4.6 + - - -
178C GLY* 2.7 27.0 + - - -
179C HIS 4.4 6.3 - - - +
182C ILE* 4.8 4.0 - - + -
208C ASN* 3.4 24.7 - - + +
210C ILE* 3.8 26.9 - - + -
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Residues in contact with ALA 176 (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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172C GLU 2.7 23.2 + - - +
173C HIS* 3.8 6.3 - - + +
175C VAL* 1.3 73.5 - - + +
177C LEU* 1.3 60.4 + - + +
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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