Contacts of the helix formed by residues 185 - 198 (chain C) in PDB entry 1TU8
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 ARG 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C ASP* 3.0 41.8 + - - +
24C GLN* 4.6 4.2 - - - +
141C LEU* 4.5 12.6 - - - +
147C ILE* 3.5 29.2 - - - +
152C TYR* 4.5 0.2 + - - -
181C ARG* 3.5 11.6 + - + +
182C MET* 3.1 40.7 + - - +
184C ASP* 1.3 73.9 - - - +
186C PRO* 1.3 64.2 - - + +
187C LYS 3.3 1.1 - - - -
188C LEU* 2.9 10.6 + - + -
189C LYS 2.7 31.9 + - - -
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Residues in contact with PRO 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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184C ASP 3.2 7.8 - - - +
185C ARG* 1.3 85.3 - - + +
187C LYS* 1.3 67.1 + - + +
189C LYS* 3.7 6.5 - - + +
190C GLU* 3.1 24.9 + - - +
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Residues in contact with LYS 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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22C VAL* 3.7 33.1 - - + +
23C ASP* 4.0 27.1 + - - +
25C ASP* 4.3 27.7 + - + +
185C ARG 3.2 0.8 + - - -
186C PRO* 1.3 81.5 - - + +
188C LEU* 1.3 58.5 + - - +
190C GLU* 3.8 14.5 + - - +
191C TYR* 3.1 27.5 + - - +
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Residues in contact with LEU 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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19C LEU* 3.7 42.6 - - + +
22C VAL* 4.5 5.4 - - + -
23C ASP* 3.6 29.4 - - + +
152C TYR* 4.2 5.2 - - + -
155C PHE* 4.1 14.8 - - + -
182C MET* 3.6 44.6 - - + +
183C LYS 4.0 2.2 - - - +
185C ARG* 2.9 10.9 + - + +
187C LYS* 1.3 77.7 - - - +
189C LYS* 1.3 59.2 + - - +
190C GLU 3.2 0.2 - - - -
191C TYR* 4.2 2.2 - - + -
192C CYS* 2.8 42.7 + - - -
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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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183C LYS* 3.2 41.1 + - + +
184C ASP* 4.0 21.8 + - - +
185C ARG 2.7 17.6 + - - +
186C PRO* 3.7 9.9 - - + +
188C LEU* 1.3 71.0 - - - +
190C GLU* 1.3 63.4 + - - +
192C CYS* 4.0 2.7 - - - +
193C GLU* 3.1 50.0 + - + +
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Residues in contact with GLU 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 PRO 3.1 16.8 + - - +
187C LYS* 3.8 14.3 - - - +
189C LYS* 1.3 78.6 - - - +
191C TYR* 1.3 62.7 + - - +
193C GLU* 3.4 8.7 + - - +
194C LYS* 3.1 27.6 + - + +
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Residues in contact with TYR 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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15C GLU* 2.6 37.2 + - - -
18C ARG* 3.6 20.2 - - + +
19C LEU* 3.6 28.0 - - + -
22C VAL* 3.8 32.1 - - + -
28C PHE* 6.2 1.1 - + - -
30C ASP* 5.8 2.5 - - - -
32C ARG* 5.0 3.5 + - - -
187C LYS 3.1 16.8 + - - +
188C LEU* 3.3 4.0 + - + +
190C GLU* 1.3 79.2 - - - +
192C CYS* 1.3 64.6 + - - +
194C LYS* 3.4 17.8 + - + +
195C ARG* 3.0 41.9 + - + +
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Residues in contact with CYS 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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19C LEU* 4.9 0.4 - - - -
155C PHE* 4.0 28.7 - - - -
159C ASP* 5.8 0.2 - - - -
183C LYS* 4.3 24.9 - - - +
188C LEU* 2.8 30.4 + - - +
189C LYS* 4.0 4.0 - - - +
191C TYR* 1.3 77.9 - - - +
193C GLU* 1.3 59.8 + - - +
195C ARG* 3.3 35.5 + - - +
196C ASP* 2.9 34.5 + - - +
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Residues in contact with GLU 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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183C LYS* 6.3 2.5 - - - -
189C LYS* 3.1 48.1 + - + +
190C GLU* 3.8 7.0 - - - +
191C TYR 3.4 0.2 - - - -
192C CYS* 1.3 75.8 - - - +
194C LYS* 1.3 57.3 + - - +
196C ASP* 3.3 9.6 + - - +
197C ALA* 3.0 29.1 + - - +
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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 GLU* 3.1 17.4 + - + +
191C TYR* 3.5 21.5 - - + +
193C GLU* 1.3 76.1 - - - +
195C ARG* 1.3 62.1 + - - +
197C ALA* 3.6 7.2 + - - +
198C ALA* 3.2 25.0 + - + +
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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
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11C ARG* 3.4 42.0 - - - +
15C GLU* 2.9 31.0 + - - +
19C LEU* 4.2 5.7 - - - +
155C PHE* 5.2 1.8 - - - -
156C GLU* 3.3 19.8 + - - -
159C ASP* 3.5 13.9 + - - +
183C LYS* 5.4 2.0 - - - +
191C TYR* 3.0 32.2 + - + +
192C CYS* 3.5 33.9 + - - +
194C LYS* 1.3 77.3 - - - +
196C ASP* 1.3 64.7 + - - +
198C ALA* 3.5 1.3 + - - -
199C LYS* 3.2 16.8 + - - -
200C VAL* 3.3 40.1 + - + +
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Residues in contact with ASP 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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11C ARG* 5.4 5.0 + - - -
163C ILE* 6.1 0.9 - - - +
183C LYS* 4.2 17.0 + - - -
192C CYS 2.9 21.4 + - - +
193C GLU* 3.3 9.9 + - - +
195C ARG* 1.3 80.2 + - - +
197C ALA* 1.3 65.9 + - - +
199C LYS* 3.1 27.3 + - - +
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Residues in contact with ALA 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 GLU 3.0 17.1 + - - +
194C LYS* 3.8 7.4 - - - +
196C ASP* 1.3 77.7 - - - +
198C ALA* 1.3 60.3 + - - +
199C LYS* 3.4 7.8 + - - +
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Residues in contact with ALA 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* 3.2 17.4 + - + +
195C ARG 3.5 4.0 + - - +
196C ASP 3.2 0.2 - - - -
197C ALA* 1.3 76.5 - - - +
199C LYS* 1.3 70.6 + - - +
200C VAL* 3.2 15.7 + - + +
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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