Contacts of the helix formed by residues 163 - 177 (chain C) in PDB entry 6Q2J
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 ASP 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C ALA 5.0 3.1 + - - +
161C PRO 3.8 0.8 + - - -
162C CYS* 1.3 73.8 - - - +
164C LEU* 1.3 73.6 + - - +
165C LYS* 4.1 5.6 + - - +
166C GLN* 3.2 48.0 + - + +
167C CYS* 3.3 23.9 + - - +
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Residues in contact with LEU 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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162C CYS 3.5 4.4 + - - +
163C ASP* 1.3 78.5 + - - +
165C LYS* 1.3 67.8 + - + +
167C CYS* 3.2 5.4 + - + +
168C GLN* 2.9 60.6 + - + +
210C CYS 4.1 19.3 - - - +
211C ALA* 5.2 6.3 - - - +
214C MET* 4.0 30.3 - - + -
289C VAL* 6.4 0.4 - - + -
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Residues in contact with LYS 165 (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 ASP* 4.1 5.3 + - - +
164C LEU* 1.3 80.9 - - + +
166C GLN* 1.3 61.3 + - + +
168C GLN* 3.9 14.6 + - - +
169C ALA* 2.9 31.5 + - - +
172C ARG* 5.1 1.2 + - - -
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Residues in contact with GLN 166 (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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154C ALA* 4.5 18.1 - - + +
163C ASP* 3.2 36.8 + - + +
164C LEU 3.3 0.2 - - - -
165C LYS* 1.3 78.6 - - + +
167C CYS* 1.3 56.5 + - - +
169C ALA* 3.5 4.6 + - - +
170C ALA* 2.9 29.0 + - - +
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Residues in contact with CYS 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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154C ALA 4.3 4.0 + - - +
155C CYS* 2.0 53.6 - - + -
162C CYS* 5.0 2.5 - - + -
163C ASP 3.3 16.4 + - - +
164C LEU* 3.2 6.2 + - + +
166C GLN* 1.3 80.3 - - - +
168C GLN* 1.3 58.7 + - + +
170C ALA* 3.2 3.3 + - - +
171C ILE* 2.9 33.4 + - - +
207C SER* 4.4 12.3 - - - -
210C CYS* 4.5 13.7 - - - +
211C ALA* 4.5 13.0 - - - -
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Residues in contact with GLN 168 (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 LEU* 2.9 52.1 + - + +
165C LYS* 3.9 14.0 + - - +
167C CYS* 1.3 75.0 - - + +
169C ALA* 1.3 60.0 + - - +
171C ILE* 3.2 13.2 + - + +
172C ARG* 3.0 39.5 + - - +
211C ALA* 5.7 5.8 + - + +
214C MET* 6.0 0.2 - - - +
284C GLY 3.2 22.4 - - - +
285C THR* 4.4 16.2 + - - +
286C VAL* 4.7 11.2 + - - +
289C VAL* 5.4 5.7 - - - +
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Residues in contact with ALA 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 LYS 2.9 18.7 + - - +
166C GLN* 3.8 5.8 - - - +
168C GLN* 1.3 76.5 - - - +
170C ALA* 1.3 57.4 + - - +
172C ARG* 3.5 24.4 + - - +
173C PHE* 2.9 30.5 + - - +
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Residues in contact with ALA 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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150C SER 4.9 0.7 - - - +
151C TYR* 3.9 14.8 - - + +
154C ALA* 3.8 24.7 - - + -
155C CYS* 4.2 6.3 - - - -
166C GLN 2.9 17.7 + - - +
167C CYS* 3.4 7.6 - - - +
168C GLN 3.2 0.2 - - - -
169C ALA* 1.3 74.0 - - - +
171C ILE* 1.3 60.0 + - - +
173C PHE* 3.7 6.8 - - - +
174C PHE* 2.8 30.7 + - - +
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Residues in contact with ILE 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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151C TYR* 3.5 27.8 - - + +
167C CYS* 2.9 23.1 + - - +
168C GLN* 3.2 14.6 + - + +
170C ALA* 1.3 76.3 - - - +
172C ARG* 1.3 56.9 + - - +
174C PHE* 3.1 1.5 + - - +
175C TYR* 3.0 57.5 + - + -
207C SER* 4.4 4.7 - - - +
211C ALA* 3.9 22.2 - - + -
283C LEU 3.9 0.9 - - - +
284C GLY* 3.7 21.8 - - - +
288C GLN* 3.4 25.6 - - - +
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Residues in contact with ARG 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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165C LYS 5.1 1.2 + - - -
168C GLN* 3.0 22.3 + - - +
169C ALA* 3.8 28.1 - - - +
171C ILE* 1.3 76.8 - - - +
173C PHE* 1.3 61.1 + - - +
175C TYR* 4.6 2.1 - - - +
176C GLN* 3.3 38.6 + - - +
230C ASP* 5.5 1.8 + - - -
232C LEU* 3.4 47.2 - - - +
281C ASP 5.7 3.1 - - - +
283C LEU 4.3 6.5 - - - +
284C GLY* 4.0 21.7 + - - -
285C THR* 4.5 9.6 - - + +
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Residues in contact with PHE 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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147C GLN* 3.3 27.1 - - - +
150C SER* 5.8 8.3 - - - -
169C ALA 2.9 20.3 + - - +
170C ALA* 3.9 5.6 - - - +
172C ARG* 1.3 76.2 - - - +
174C PHE* 1.3 62.3 + - - +
176C GLN* 4.2 6.3 - - - -
177C ASN* 2.8 50.9 + - - +
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Residues in contact with PHE 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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138C CYS* 4.6 0.2 - - - -
144C CYS* 4.0 17.0 - - - -
147C GLN* 3.6 32.3 - - + +
148C LEU* 3.6 36.8 - - + -
151C TYR* 3.9 24.2 - + + -
170C ALA 2.8 18.7 + - - +
171C ILE 3.1 3.3 + - - +
173C PHE* 1.3 77.2 - - - +
175C TYR* 1.3 79.5 + + - +
176C GLN 3.2 0.7 + - - -
177C ASN* 3.5 4.5 + - - +
178C ILE* 3.3 48.3 - - + +
186C LEU* 4.4 27.6 - - + -
205C LEU 6.1 0.2 - - - -
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Residues in contact with TYR 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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151C TYR* 5.9 1.8 - + - -
171C ILE* 3.0 46.7 + - + +
172C ARG* 4.8 2.9 - - - +
173C PHE 3.6 0.2 - - - -
174C PHE* 1.3 89.9 - + - +
176C GLN* 1.3 62.8 + - + +
178C ILE* 3.5 19.5 - - + +
183C ALA* 3.8 38.8 - - + +
186C LEU* 3.3 36.6 + - + +
187C ALA* 4.6 0.4 - - - -
205C LEU 5.6 0.2 + - - -
206C HIS* 5.0 7.8 - - - -
280C ILE* 4.1 21.4 - - + +
283C LEU* 3.8 40.1 - - + +
288C GLN* 5.4 4.7 + - - -
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Residues in contact with GLN 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 ARG* 3.3 27.8 + - - +
173C PHE* 4.0 7.6 + - - +
174C PHE 3.2 1.0 - - - -
175C TYR* 1.3 82.6 - - + +
177C ASN* 1.3 65.9 + - - +
178C ILE 3.3 8.4 + - - +
236C HIS* 5.4 8.9 + - - -
281C ASP* 5.4 9.4 + - - +
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Residues in contact with ASN 177 (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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143C VAL* 3.7 19.6 - - - +
147C GLN* 3.9 18.7 - - + +
173C PHE* 2.8 61.0 + - - +
174C PHE 3.5 2.2 + - - +
175C TYR 3.4 0.8 - - - -
176C GLN* 1.3 85.3 + - - +
178C ILE* 1.3 64.0 + - - +
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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