Contacts of the helix formed by residues 194 - 209 (chain C) in PDB entry 1TTT
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 GLU 194 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ASN* 1.3 75.7 + - - +
195C TRP* 1.3 100.3 + - + +
197C ASP* 3.1 7.0 + - - +
198C LYS* 3.0 33.7 + - + +
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Residues in contact with TRP 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C VAL* 4.6 14.8 - - + -
139C ASP* 4.7 8.5 - - + -
173C GLY* 4.4 7.2 - - - -
174C SER* 3.9 29.4 - - - +
177C LEU* 3.1 44.5 - - + +
178C ALA* 3.5 28.4 - - - +
181C GLU* 5.8 1.1 - - + -
193C ASN* 2.7 20.4 + - - +
194C GLU* 1.3 103.1 + - + +
196C VAL* 1.3 67.1 + - - +
198C LYS* 3.1 31.2 + - + +
199C ILE* 3.6 4.2 + - - +
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Residues in contact with VAL 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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34C VAL* 4.4 6.1 - - + -
178C ALA* 3.6 11.0 - - + +
181C GLU* 3.3 28.7 - - + -
182C MET* 3.1 37.2 - - + -
188C THR* 3.9 17.7 - - + +
189C LYS 4.4 2.2 - - - +
193C ASN* 2.6 22.5 + - + +
195C TRP* 1.3 70.5 - - - +
197C ASP* 1.3 67.5 + - - +
199C ILE* 2.9 24.3 + - - +
200C TRP* 3.3 24.2 + - + +
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Residues in contact with ASP 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C LYS 4.1 0.9 - - - +
190C ARG* 3.2 15.2 + - - +
191C GLY* 2.7 41.6 + - - -
193C ASN 2.6 31.9 + - - +
194C GLU* 3.1 8.7 + - - +
196C VAL* 1.3 73.0 - - - +
198C LYS* 1.3 64.0 + - + +
200C TRP* 3.2 11.5 + - - +
201C GLU* 3.0 23.5 + - + +
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Residues in contact with LYS 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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171C ILE* 4.3 7.3 - - + +
172C ARG* 3.1 29.7 + - - +
173C GLY* 4.2 8.5 - - - -
174C SER 5.3 0.2 - - - +
194C GLU* 3.0 28.4 + - + +
195C TRP* 3.1 28.9 + - + +
196C VAL 3.0 0.2 + - - -
197C ASP* 1.3 76.5 - - + +
199C ILE* 1.3 60.5 + - + +
201C GLU* 2.5 54.1 + - - +
202C LEU* 2.9 9.9 + - - +
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Residues in contact with ILE 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.3 24.5 - - + -
30C ALA* 5.0 7.0 - - + -
31C LEU* 4.1 26.5 - - + -
34C VAL* 3.9 31.2 - - + -
134C PHE* 4.3 12.3 - - + -
174C SER 4.6 5.8 - - - +
175C ALA* 5.0 2.2 - - - -
178C ALA* 3.8 24.2 - - + -
195C TRP 4.1 4.9 - - - +
196C VAL 2.9 12.8 + - - +
198C LYS* 1.3 73.2 - - + +
200C TRP* 1.3 56.6 - - - +
202C LEU* 2.9 7.9 + - + +
203C LEU* 2.7 35.6 + - + +
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Residues in contact with TRP 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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34C VAL* 2.8 46.7 + - + +
35C ALA* 4.1 9.9 - - - -
38C GLU* 3.8 30.4 + - + +
39C ASN* 4.3 6.7 - - - -
72C THR* 4.9 10.3 - - + -
188C THR 5.3 0.6 + - - -
189C LYS* 4.4 1.4 - - - +
190C ARG* 3.6 73.8 - - + +
196C VAL* 3.3 20.0 + - + +
197C ASP* 3.2 12.3 + - - +
198C LYS 3.1 0.4 - - - -
199C ILE* 1.3 80.2 - - - +
201C GLU* 1.3 58.4 + - - +
203C LEU* 3.2 26.5 + - + +
204C ASP* 2.7 37.9 + - - +
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ILE* 4.1 20.7 - - + +
197C ASP* 3.0 20.6 + - + +
198C LYS* 2.5 48.2 + - - +
200C TRP* 1.3 72.5 - - - +
202C LEU* 1.3 63.0 + - - +
204C ASP* 3.3 8.6 + - - +
205C ALA* 2.9 20.6 + - - +
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Residues in contact with LEU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 3.3 39.0 - - + -
31C LEU* 4.2 13.9 - - + -
103C ILE* 4.3 7.9 - - + -
132C VAL* 3.4 32.8 - - + -
134C PHE* 3.9 29.2 - - + -
171C ILE* 4.0 12.2 - - + +
198C LYS 2.9 6.0 + - - +
199C ILE* 2.9 18.0 + - + +
201C GLU* 1.3 75.1 - - - +
203C LEU* 1.3 56.3 + - - +
205C ALA* 2.7 27.5 + - + +
206C ILE* 2.9 25.4 + - + +
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Residues in contact with LEU 203 (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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31C LEU* 3.9 24.0 - - + +
34C VAL* 4.2 5.8 - - + -
35C ALA* 4.3 15.3 - - + -
70C TYR* 4.4 13.5 - - + -
72C THR* 3.6 22.0 - - + -
77C TYR* 4.9 1.8 - - + -
199C ILE* 2.7 27.7 + - + +
200C TRP* 3.3 46.2 - - + +
202C LEU* 1.3 70.9 - - - +
204C ASP* 1.3 66.2 + - - +
206C ILE* 3.2 15.3 - - + +
207C ASP* 2.8 27.2 + - - -
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Residues in contact with ASP 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LYS* 4.3 12.3 + - - +
190C ARG* 2.8 35.7 + - - -
200C TRP* 2.7 22.4 + - - +
201C GLU* 3.6 8.0 - - - +
203C LEU* 1.3 78.9 - - - +
205C ALA* 1.3 52.3 + - - +
207C ASP* 2.8 14.1 + - - +
208C GLU* 2.4 43.1 + - + +
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Residues in contact with ALA 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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132C VAL* 4.3 9.2 - - + -
169C PRO* 4.2 25.1 - - + -
171C ILE* 4.2 11.4 - - + -
201C GLU 2.9 12.2 + - - +
202C LEU* 2.7 15.2 + - - +
204C ASP* 1.3 71.5 - - - +
206C ILE* 1.3 56.0 + - - +
208C GLU* 4.3 2.0 - - - +
209C TYR* 2.4 44.1 + - - +
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Residues in contact with ILE 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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14C VAL* 4.4 5.4 - - + -
31C LEU* 4.6 3.6 - - + -
70C TYR* 4.3 15.5 - - + +
75C ARG* 2.7 21.8 + - - -
77C TYR* 3.1 37.0 - - + +
103C ILE* 4.7 12.3 - - + -
132C VAL* 4.5 8.3 - - + +
202C LEU* 2.9 38.7 + - + +
203C LEU* 3.2 23.1 - - + +
205C ALA* 1.3 74.8 - - - +
207C ASP* 1.3 59.8 + - - +
210C ILE* 3.3 35.9 - - + +
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Residues in contact with ASP 207 (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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72C THR* 2.6 43.4 + - - +
74C LYS* 3.9 36.2 + - + +
75C ARG* 3.6 21.4 + - - +
77C TYR* 2.5 27.9 + - - -
203C LEU 2.8 17.4 + - - +
204C ASP* 3.2 11.1 - - - +
206C ILE* 1.3 80.6 - - - +
208C GLU* 1.3 67.9 + - - +
210C ILE 3.7 1.7 - - - +
211C PRO* 5.5 0.2 - - - +
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Residues in contact with GLU 208 (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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74C LYS* 3.6 33.8 - - - +
204C ASP* 2.4 32.0 + - + +
205C ALA* 4.4 2.2 - - - +
207C ASP* 1.3 76.9 - - + +
209C TYR* 1.3 60.6 + - - +
210C ILE 4.6 1.7 - - - -
211C PRO* 4.9 2.3 - - - +
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Residues in contact with TYR 209 (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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130C TYR* 4.2 24.7 - + - -
131C ILE 2.8 28.2 + - - -
132C VAL* 3.0 13.5 - - + -
164C PRO* 4.3 13.9 - - - +
167C GLU* 4.2 10.9 + - + +
168C VAL* 3.4 21.5 + - - +
169C PRO* 2.9 44.2 - - + -
205C ALA* 2.4 32.8 + - - +
208C GLU* 1.3 67.1 - - - +
210C ILE* 1.3 57.8 + - + +
211C PRO* 3.1 14.7 - - - +
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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