Contacts of the helix formed by residues 163 - 176 (chain C) in PDB entry 6VSU
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 ILE 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C VAL* 3.4 31.0 - - + +
72C LEU* 4.2 18.8 - - + -
136C MET* 4.4 1.1 - - - -
139C ILE* 4.7 1.8 - - + -
156C VAL* 3.5 26.0 - - + -
158C GLY* 3.4 32.3 - - - -
160C ASP 3.6 14.1 - - - +
161C HIS 2.8 6.7 + - - -
162C SER* 1.3 75.5 - - - +
164C SER* 1.3 68.8 + - - +
165C TYR 3.1 0.2 - - - -
166C PRO* 3.0 23.6 - - + +
167C VAL* 3.1 16.8 + - + +
310C ASP* 5.0 1.1 - - - +
312C VAL* 3.8 15.7 - - + -
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Residues in contact with SER 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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161C HIS* 2.9 34.4 + - - -
163C ILE* 1.3 77.5 - - - +
165C TYR* 1.3 53.2 + - - +
167C VAL* 3.7 3.8 - - - +
168C VAL* 2.7 45.4 + - - +
204C SER* 3.8 9.0 - - - -
205C PHE* 4.4 9.9 - - - -
208C ILE* 4.3 2.9 - - - -
268C SER* 3.6 4.8 + - - -
310C ASP* 3.1 28.3 + - - -
312C VAL* 4.5 0.3 - - - +
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Residues in contact with TYR 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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162C SER 3.6 7.0 + - - +
163C ILE 3.1 0.2 - - - -
164C SER* 1.3 77.8 - - - +
166C PRO* 1.4 67.0 - - + +
168C VAL* 4.0 1.0 - - - +
169C ARG* 3.0 58.9 + - + +
198C LYS* 6.5 0.2 - - - -
199C TYR* 4.1 27.6 - + + -
204C SER* 3.7 19.9 + - - +
207C ARG* 3.6 52.4 + - + -
208C ILE* 3.7 15.5 - - + -
213C TYR* 3.9 23.7 + + - -
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Residues in contact with PRO 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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136C MET* 3.2 47.3 - - + +
139C ILE* 4.2 9.9 - - + -
140C SER* 2.9 32.8 + - - +
162C SER 3.3 8.7 - - - +
163C ILE* 3.0 16.2 - - - +
165C TYR* 1.4 99.9 - - + +
167C VAL* 1.3 62.0 + - - +
169C ARG* 4.3 8.7 - - + +
170C ALA* 3.2 16.5 + - - +
199C TYR* 5.8 0.2 - - + -
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Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ILE* 4.6 7.2 - - + -
143C VAL* 4.0 22.4 - - + +
154C PRO* 5.4 2.9 - - + +
156C VAL* 3.8 38.8 - - + -
163C ILE* 3.1 25.6 + - + +
164C SER 3.7 1.6 - - - +
166C PRO* 1.3 74.6 - - - +
168C VAL* 1.3 53.7 + - - +
170C ALA* 3.2 4.2 + - - +
171C VAL* 2.8 43.8 + - + +
266C TYR* 3.2 34.8 - - + +
309C ALA 5.7 0.4 - - - +
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Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C SER* 2.7 30.5 + - - +
165C TYR 4.1 2.0 - - - +
167C VAL* 1.3 69.5 - - - +
169C ARG* 1.3 53.4 + - - +
171C VAL* 2.8 12.2 + - - +
172C SER* 2.6 36.5 + - - -
179C VAL* 4.5 7.1 - - + +
181C ILE* 4.1 17.3 - - + -
205C PHE* 5.8 1.1 - - + -
208C ILE* 3.8 33.0 - - + -
213C TYR* 3.9 16.6 - - + +
266C TYR* 3.7 37.7 - - + -
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Residues in contact with ARG 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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136C MET* 3.6 9.5 + - - +
137C ASN* 3.3 41.6 + - - +
140C SER* 3.0 25.6 + - - -
165C TYR* 3.0 48.6 + - + +
166C PRO* 4.0 8.3 - - - +
168C VAL* 1.3 74.5 - - - +
170C ALA* 1.3 57.2 + - - +
172C SER* 3.8 0.5 - - - -
173C GLU* 2.9 63.2 + - - +
199C TYR* 4.7 7.1 + - - -
213C TYR* 3.6 39.4 - - + -
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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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140C SER* 3.2 33.9 - - - +
143C VAL* 4.0 9.4 - - + -
144C LYS* 3.7 20.5 - - + +
147C MET* 3.9 3.1 - - - +
166C PRO 3.2 18.2 + - - +
167C VAL 3.4 4.3 - - - +
169C ARG* 1.3 76.0 - - - +
171C VAL* 1.3 66.3 + - - +
173C GLU* 4.4 0.9 - - - -
174C LYS* 3.0 26.3 + - - +
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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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143C VAL* 4.1 10.3 - - + -
147C MET* 3.7 16.0 - - + +
154C PRO* 4.6 8.7 - - + -
167C VAL* 2.8 33.9 + - + +
168C VAL* 2.8 9.7 + - + +
170C ALA* 1.3 75.5 - - - +
172C SER* 1.3 57.7 + - - +
175C LEU* 3.0 56.3 + - + +
179C VAL* 4.6 7.2 - - + -
266C TYR* 4.2 15.5 - - + -
307C VAL* 3.6 21.3 - - + +
308C GLY* 5.0 1.6 - - - -
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Residues in contact with SER 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 VAL* 2.6 20.0 + - - -
171C VAL* 1.3 70.6 - - - +
173C GLU* 1.3 55.6 - - - +
175C LEU* 3.6 1.5 + - - -
176C GLY 3.0 11.8 + - - -
177C GLY* 2.8 55.3 + - - +
178C PRO* 3.8 0.2 - - - +
179C VAL* 5.0 4.0 - - - -
212C GLY 4.5 0.9 + - - -
213C TYR* 3.4 49.2 - - - -
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Residues in contact with GLU 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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140C SER* 5.5 1.0 - - - -
144C LYS* 2.8 39.3 + - - +
169C ARG* 2.9 45.5 + - - +
170C ALA 4.1 0.9 - - - +
172C SER* 1.3 72.5 - - - +
174C LYS* 1.3 66.7 + - - +
175C LEU 3.2 1.0 + - - -
176C GLY* 3.2 13.2 + - - -
213C TYR* 4.0 16.2 + - + -
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Residues in contact with LYS 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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144C LYS* 4.4 16.6 - - + +
147C MET* 3.3 55.7 + - + -
148C GLU* 3.7 33.7 + - - +
150C GLU* 5.5 5.5 + - - -
170C ALA 3.0 19.1 + - - +
173C GLU* 1.3 76.0 - - - +
175C LEU* 1.3 64.9 + - - +
176C GLY* 3.7 0.3 + - - -
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Residues in contact with LEU 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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147C MET* 3.6 17.5 - - + -
171C VAL* 3.0 44.5 + - + +
172C SER* 4.1 2.5 - - - +
173C GLU 3.2 0.2 - - - -
174C LYS* 1.3 82.6 - - + +
176C GLY* 1.3 59.3 + - - +
177C GLY 3.8 0.2 - - - -
179C VAL* 4.4 3.6 - - + -
263C LYS* 3.2 48.0 + - + +
307C VAL* 3.6 31.6 - - + -
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Residues in contact with GLY 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 SER 3.0 5.4 + - - -
173C GLU* 3.2 10.4 + - - -
174C LYS 4.6 0.4 - - - -
175C LEU* 1.3 79.2 - - - +
177C GLY* 1.3 58.3 + - - +
263C LYS* 3.6 13.4 - - - -
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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