Contacts of the helix formed by residues 163 - 176 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D VAL* 3.8 29.2 - - + +
72D LEU* 4.2 17.7 - - + -
136D MET* 4.5 1.1 - - - -
139D ILE* 4.8 2.2 - - + -
156D VAL* 3.6 26.9 - - + -
158D GLY* 3.5 31.6 - - - -
160D ASP 3.4 17.3 - - - +
161D HIS 2.9 1.2 + - - -
162D SER* 1.3 83.3 - - - +
164D SER* 1.3 68.9 + - - +
165D TYR 3.1 0.6 + - - -
166D PRO* 3.2 12.9 - - + +
167D VAL* 3.0 29.9 + - + +
310D ASP* 5.2 1.3 - - + +
312D VAL* 3.8 13.7 - - + -
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D HIS* 3.1 34.4 + - - -
163D ILE* 1.3 79.4 - - - +
165D TYR* 1.3 54.1 + - - +
167D VAL* 4.4 2.2 - - - -
168D VAL* 2.8 40.8 + - - +
204D SER* 4.5 1.1 - - - -
205D PHE* 4.2 17.9 - - - -
208D ILE* 3.9 6.1 - - - -
268D SER* 3.4 1.1 + - - -
310D ASP* 2.7 31.8 + - - -
312D VAL* 4.3 2.1 - - - +
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Residues in contact with TYR 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D SER 3.4 7.9 + - - +
163D ILE 3.1 1.2 - - - -
164D SER* 1.3 77.9 - - - +
166D PRO* 1.4 68.1 - - + +
168D VAL* 3.9 0.5 - - - +
169D ARG* 2.8 57.7 + - + +
198D LYS* 6.3 0.4 - - - -
199D TYR* 3.8 32.7 + + - -
204D SER* 3.8 19.6 - - - +
207D ARG* 3.5 44.9 - - + -
208D ILE* 3.7 18.1 - - + +
213D TYR* 3.9 21.0 + + - -
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Residues in contact with PRO 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D MET* 3.4 36.8 - - + +
139D ILE* 3.9 15.5 - - + -
140D SER* 2.7 33.1 + - - +
162D SER 3.4 9.0 - - - +
163D ILE* 3.2 20.0 - - - +
165D TYR* 1.4 102.8 - - + +
167D VAL* 1.3 60.0 + - - +
169D ARG* 3.9 12.6 - - + +
170D ALA* 3.1 15.4 + - - +
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Residues in contact with VAL 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ILE* 4.2 11.9 - - + -
143D VAL* 4.1 23.9 - - + +
154D PRO* 5.7 1.8 - - + -
156D VAL* 3.9 39.7 - - + -
163D ILE* 3.0 22.7 + - + +
164D SER* 3.8 3.4 - - - +
166D PRO* 1.3 79.8 - - - +
168D VAL* 1.3 62.5 + - - +
170D ALA* 3.2 2.6 + - - +
171D VAL* 3.0 23.0 + - + +
266D TYR* 3.2 34.1 - - + +
309D ALA 5.2 0.2 - - - +
310D ASP* 5.4 0.4 - - - +
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Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D SER* 2.8 25.9 + - - +
165D TYR 4.1 0.2 - - - +
167D VAL* 1.3 69.0 - - - +
169D ARG* 1.3 67.4 + - - +
171D VAL* 3.8 6.6 - - - +
172D SER* 3.0 22.9 + - - -
179D VAL* 4.6 10.8 - - + -
181D ILE* 4.1 12.6 - - + -
205D PHE* 5.8 0.4 - - + -
208D ILE* 3.8 30.7 - - + -
213D TYR* 3.8 22.9 - - + -
266D TYR* 3.6 38.4 - - + -
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Residues in contact with ARG 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D MET* 3.6 17.8 + - - +
137D ASN* 3.1 26.5 + - - -
140D SER* 2.9 27.4 + - - +
165D TYR* 2.8 48.2 + - + +
166D PRO* 3.8 9.4 - - - +
168D VAL* 1.3 77.3 - - - +
170D ALA* 1.3 56.2 + - - +
172D SER* 3.5 1.7 + - - -
173D GLU* 2.9 48.2 + - - +
199D TYR* 5.3 4.6 + - - -
213D TYR* 3.5 45.4 - - + +
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Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D SER* 3.3 32.1 - - - +
143D VAL* 3.9 10.1 - - + -
144D LYS* 3.8 21.1 - - + +
147D MET* 4.5 1.3 - - - -
166D PRO 3.1 15.7 + - - +
167D VAL 3.5 3.8 - - - +
169D ARG* 1.3 75.4 - - - +
171D VAL* 1.3 60.5 + - - +
173D GLU* 3.9 1.9 - - - +
174D LYS* 2.8 33.2 + - - +
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Residues in contact with VAL 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D VAL* 4.1 10.1 - - + -
147D MET* 3.8 22.0 - - + -
154D PRO* 4.3 11.7 - - + -
167D VAL* 3.0 19.9 + - + +
168D VAL* 3.9 7.0 - - + +
170D ALA* 1.3 75.4 - - - +
172D SER* 1.3 53.2 + - - +
174D LYS* 3.3 1.2 + - - +
175D LEU* 2.8 49.2 + - + +
179D VAL* 4.4 8.5 - - + -
266D TYR* 4.5 21.8 - - + -
307D VAL* 3.7 33.7 - - + +
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Residues in contact with SER 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D VAL* 3.0 18.5 + - - -
171D VAL* 1.3 73.7 - - - +
173D GLU* 1.3 59.5 + - - +
175D LEU* 3.4 2.3 + - - +
176D GLY 3.0 24.3 + - - -
177D GLY 2.8 36.9 + - - +
179D VAL* 5.0 5.2 - - - -
212D GLY 4.8 0.3 + - - -
213D TYR* 3.5 45.2 + - - -
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Residues in contact with GLU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D SER* 5.5 1.6 - - - -
144D LYS* 2.9 33.5 + - - +
169D ARG* 2.9 47.5 + - + +
170D ALA* 3.9 1.9 - - - +
172D SER* 1.3 73.3 - - - +
174D LYS* 1.3 65.2 + - - +
176D GLY* 3.3 12.6 + - - -
213D TYR* 4.1 13.4 + - + -
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Residues in contact with LYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LYS* 4.6 15.7 - - + +
147D MET* 3.6 38.1 - - + -
148D GLU* 2.9 46.0 + - - +
170D ALA 2.8 20.0 + - - +
171D VAL 3.6 3.4 - - - +
173D GLU* 1.3 78.5 - - - +
175D LEU* 1.3 63.4 + - + +
176D GLY* 3.3 1.0 + - - -
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D MET* 4.0 16.4 - - + -
171D VAL* 2.8 29.2 + - + +
172D SER* 4.3 3.1 - - - +
174D LYS* 1.3 74.6 - - + +
176D GLY* 1.3 57.6 + - - +
179D VAL* 4.7 1.8 - - + -
263D LYS* 3.3 47.4 - - + +
307D VAL* 3.7 44.0 - - + -
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Residues in contact with GLY 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D SER 3.0 6.4 + - - -
173D GLU* 3.3 7.6 + - - -
174D LYS 3.2 4.8 + - - -
175D LEU* 1.3 78.4 - - - +
177D GLY* 1.3 57.1 + - - +
263D LYS* 3.5 9.9 - - - -
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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