Contacts of the helix formed by residues 185 - 200 (chain C) in PDB entry 3KHU
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 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C GLN* 5.3 0.3 + - - -
183C ASP* 3.1 19.3 + - + +
184C GLU* 1.3 82.7 - - + +
186C PRO* 1.3 76.8 - - + +
187C GLU* 3.7 6.4 + - - +
188C GLY* 3.0 20.4 + - - -
189C GLN* 2.9 23.5 + - - +
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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 GLU 4.7 1.3 - - - +
185C THR* 1.3 87.9 - - + +
187C GLU* 1.3 57.7 + - - +
189C GLN* 3.3 6.0 + - + +
190C ARG* 3.0 29.2 + - - +
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Residues in contact with GLU 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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123C TYR* 3.6 9.7 + - - -
153C ASN* 3.4 22.4 + - - +
155C GLN* 2.8 46.6 + - - +
185C THR* 3.3 6.6 + - - +
186C PRO* 1.3 79.5 - - - +
188C GLY* 1.3 62.0 + - - +
190C ARG* 3.4 19.8 + - - +
191C ALA* 3.2 21.8 + - - +
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Residues in contact with GLY 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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155C GLN* 4.0 7.8 + - - -
157C LEU* 4.2 2.9 - - - +
183C ASP* 3.7 24.9 - - - -
185C THR* 3.0 17.8 + - - -
187C GLU* 1.3 77.7 - - - +
189C GLN* 1.3 55.9 + - - +
191C ALA* 3.2 6.7 + - - +
192C VAL* 3.0 31.1 + - - +
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Residues in contact with GLN 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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182C GLY 4.4 5.1 + - - -
183C ASP 3.0 24.4 + - - +
184C GLU* 4.1 11.8 - - - +
185C THR 2.9 20.0 + - - +
186C PRO* 3.9 6.3 - - + +
188C GLY* 1.3 74.0 - - - +
190C ARG* 1.3 65.4 + - - +
192C VAL* 3.8 18.8 - - - +
193C GLN* 3.0 44.6 + - - +
210C THR* 5.2 5.2 + - - -
211C THR 5.3 3.2 + - - -
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Residues in contact with ARG 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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0C SER 5.6 0.8 - - - +
1C MET* 3.5 32.7 - - - +
2C PHE* 3.6 42.0 - - + +
123C TYR* 4.6 14.1 + - - +
186C PRO 3.0 13.3 + - - +
187C GLU* 3.4 26.4 + - - +
189C GLN* 1.3 78.8 - - - +
191C ALA* 1.3 61.5 + - - +
193C GLN* 3.5 6.2 + - - +
194C ALA* 3.2 21.8 + - - +
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Residues in contact with ALA 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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123C TYR* 4.0 7.6 - - - +
125C ILE* 3.9 19.6 - - + +
155C GLN* 3.9 22.9 - - + -
157C LEU* 3.7 24.7 - - + +
187C GLU 3.2 9.6 + - - +
188C GLY* 3.2 8.3 + - - +
190C ARG* 1.3 77.4 - - - +
192C VAL* 1.3 65.1 + - - +
194C ALA* 3.2 4.9 + - - +
195C LEU 3.1 17.2 + - - -
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Residues in contact with VAL 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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157C LEU* 3.6 23.6 - - + -
180C ILE* 3.9 14.6 - - + +
182C GLY* 3.9 19.7 - - - +
188C GLY 3.0 20.1 + - - +
189C GLN* 3.8 21.1 - - - +
190C ARG 3.4 0.2 - - - -
191C ALA* 1.3 75.6 - - - +
193C GLN* 1.3 60.9 + - + +
195C LEU* 3.2 4.2 + - - +
196C CYS* 2.9 27.7 + - - -
210C THR* 3.6 37.0 - - + -
211C THR 5.4 0.9 - - - +
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Residues in contact with GLN 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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0C SER* 4.0 31.1 + - - -
189C GLN* 3.0 37.1 + - - +
190C ARG* 3.9 6.3 - - - +
192C VAL* 1.3 77.1 - - + +
194C ALA* 1.3 58.6 + - - +
196C CYS* 3.2 10.6 + - - +
197C ALA* 2.9 29.9 + - - +
200C GLU* 5.1 0.5 - - - +
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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
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2C PHE* 3.8 32.3 - - + +
4C ILE* 3.6 18.6 + - + +
125C ILE* 3.8 19.1 - - + -
190C ARG 3.2 13.7 + - - +
191C ALA* 3.5 9.2 - - - +
193C GLN* 1.3 75.1 - - - +
195C LEU* 1.3 63.8 + - - +
197C ALA* 3.2 14.8 + - - +
198C VAL* 3.4 9.5 + - - +
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Residues in contact with LEU 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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4C ILE* 3.9 6.8 - - + +
84C LEU* 3.8 29.6 - - + -
86C PHE* 4.2 7.4 - - + -
125C ILE* 5.6 0.2 - - + -
127C THR* 4.0 17.7 - - + +
157C LEU* 3.9 22.4 - - + -
159C ASN* 4.0 22.0 - - + +
180C ILE* 3.9 19.7 - - + -
191C ALA 3.1 12.7 + - - +
192C VAL 3.8 6.7 - - - +
194C ALA* 1.3 72.6 - - - +
196C CYS* 1.3 66.7 + - - +
198C VAL* 3.1 23.0 + - + +
199C TYR* 3.3 24.9 + - + -
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Residues in contact with CYS 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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180C ILE* 3.8 15.6 - - - +
192C VAL* 2.9 27.8 + - - -
193C GLN* 3.4 12.8 - - + +
195C LEU* 1.3 77.0 - - - +
197C ALA* 1.3 57.7 + - - +
199C TYR* 3.0 5.7 + - - +
200C GLU* 2.8 41.6 + - - +
205C ARG* 4.6 11.4 - - - +
208C ILE* 3.9 15.4 - - + +
210C THR* 3.7 29.8 - - - -
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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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0C SER* 6.2 3.8 - - - -
2C PHE 5.6 2.9 - - - +
3C GLU* 6.5 1.1 - - + -
193C GLN 2.9 13.3 + - - +
194C ALA* 3.5 13.0 - - - +
195C LEU 3.2 0.4 - - - -
196C CYS* 1.3 75.5 - - - +
198C VAL* 1.3 61.5 + - - +
200C GLU* 3.4 22.2 + - - +
201C HIS* 3.0 21.2 + - + -
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Residues in contact with VAL 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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4C ILE* 3.8 32.1 - - + +
7C ILE* 4.6 6.5 - - + -
23C ILE* 3.9 32.8 - - + -
27C CYS* 3.7 7.7 - - - -
30C ILE* 4.3 12.8 - - + -
194C ALA 3.4 13.2 + - - +
195C LEU* 3.1 17.4 + - + +
196C CYS 3.1 0.6 - - - -
197C ALA* 1.3 76.5 - - + +
199C TYR* 1.3 66.1 + - + +
201C HIS* 3.0 30.2 + - - +
202C TRP* 3.6 7.2 - - + -
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Residues in contact with TYR 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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19C THR* 4.6 8.0 - - + +
23C ILE* 5.1 8.7 - - + -
86C PHE* 4.5 2.6 - + - -
129C LYS* 4.1 12.1 + - - -
159C ASN* 2.6 37.0 + - - -
172C LEU* 6.2 2.9 - - + -
178C VAL* 3.8 35.9 - - + -
180C ILE* 4.2 6.1 - - + -
195C LEU* 3.3 34.4 + - + -
196C CYS 3.0 7.1 + - - +
198C VAL* 1.3 80.3 - - + +
200C GLU* 1.3 58.7 + - - +
201C HIS 3.1 0.2 - - - -
202C TRP* 3.0 40.7 + + - -
203C VAL* 2.9 27.6 + - + +
208C ILE* 3.9 18.4 - - + -
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Residues in contact with GLU 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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193C GLN 5.1 0.2 - - - +
196C CYS* 2.8 24.3 + - - +
197C ALA* 3.8 20.2 + - - +
198C VAL 3.1 0.8 - - - -
199C TYR* 1.3 76.1 - - - +
201C HIS* 1.3 61.0 + - - +
202C TRP* 3.1 1.7 + - - -
203C VAL 3.6 15.0 + - - +
205C ARG* 3.7 33.4 + - - +
208C ILE* 3.6 16.6 - - + -
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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