Contacts of the helix formed by residues 165 - 180 (chain D) in PDB entry 3C6Q
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 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D ASP* 2.9 19.8 + - - +
163D CYS 4.7 1.1 - - - +
164D GLU* 1.3 77.1 - - - +
166D GLY* 1.3 69.1 + - - +
167D ALA* 3.6 8.1 + - - +
168D ARG* 2.8 51.3 + - + +
169D ALA* 3.0 22.9 + - - +
192D TYR* 4.2 3.1 - - - -
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Residues in contact with GLY 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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165D ASP* 1.3 74.3 + - - +
167D ALA* 1.3 60.7 + - - +
169D ALA* 3.2 6.0 + - - +
170D VAL* 2.9 29.7 + - - +
192D TYR* 3.7 26.4 - - - -
196D ALA* 4.8 1.4 - - - +
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Residues in contact with ALA 167 (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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165D ASP* 3.5 8.0 + - - +
166D GLY* 1.3 74.1 - - - +
168D ARG* 1.3 61.7 + - - +
170D VAL* 3.4 11.7 + - - +
171D SER* 3.2 22.2 + - - -
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Residues in contact with ARG 168 (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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40D LYS* 6.3 1.8 - - - +
161D ASN 5.4 1.3 + - - -
162D ASP* 3.9 22.2 + - + +
163D CYS* 4.1 26.1 + - - +
165D ASP* 2.8 39.0 + - + +
166D GLY 3.2 0.2 - - - -
167D ALA* 1.3 73.9 - - - +
169D ALA* 1.3 65.0 + - - +
171D SER* 3.0 17.3 + - - +
172D LEU* 3.2 26.5 - - + +
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Residues in contact with ALA 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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162D ASP* 3.2 29.5 - - - +
165D ASP 3.0 11.2 + - - +
166D GLY* 3.3 10.3 - - - +
168D ARG* 1.3 74.9 - - - +
170D VAL* 1.3 68.0 + - - +
172D LEU* 2.9 17.9 + - - +
173D ALA* 3.0 13.4 + - - +
192D TYR* 5.0 6.1 - - + -
193D ASN* 4.7 5.6 - - - +
196D ALA* 3.9 17.9 - - + -
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Residues in contact with VAL 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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166D GLY 2.9 23.3 + - - +
167D ALA* 3.7 10.3 - - - +
168D ARG 3.4 0.4 - - - -
169D ALA* 1.3 74.8 - - - +
171D SER* 1.3 57.6 + - - +
173D ALA* 4.8 0.2 - - - -
174D GLU* 3.1 33.2 + - - +
196D ALA* 4.2 18.6 - - + +
199D LEU* 4.1 25.8 - - + -
200D VAL* 3.2 26.8 - - + +
203D ASN* 6.0 1.6 - - - +
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Residues in contact with SER 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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167D ALA 3.2 10.6 + - - -
168D ARG* 3.0 19.2 + - - +
170D VAL* 1.3 74.5 - - - +
172D LEU* 1.3 61.0 + - - +
173D ALA 3.1 1.3 - - - -
174D GLU* 3.2 19.0 - - - +
175D ALA* 2.9 32.1 + - - +
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Residues in contact with LEU 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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160D LEU* 3.7 45.2 - - + +
161D ASN 4.0 13.0 - - - +
162D ASP* 3.8 24.0 - - + +
168D ARG* 3.2 24.0 - - + +
169D ALA* 2.9 9.3 + - - +
171D SER* 1.3 81.7 + - - +
173D ALA* 1.3 57.3 + - - +
175D ALA* 3.6 6.7 - - + +
176D ALA* 2.8 29.1 + - - +
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Residues in contact with ALA 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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160D LEU* 4.8 1.5 - - - +
169D ALA 3.0 10.2 + - - +
170D VAL* 3.8 3.1 - - - +
172D LEU* 1.3 75.6 - - - +
174D GLU* 1.3 58.3 + - - +
175D ALA 3.2 0.9 - - - -
176D ALA* 3.8 6.7 - - - +
177D LEU* 2.8 35.5 + - - +
186D PHE* 3.9 17.8 - - + -
196D ALA* 5.6 0.4 - - + -
197D GLN* 4.6 15.9 - - + +
200D VAL* 3.5 25.4 - - + +
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Residues in contact with GLU 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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170D VAL* 3.1 27.5 + - - +
171D SER* 3.2 24.7 - - - +
173D ALA* 1.3 76.1 - - - +
175D ALA* 1.3 59.1 + - - +
177D LEU* 3.3 3.5 + - - +
178D ASN* 2.9 39.4 + - - +
200D VAL* 3.6 21.2 - - + +
203D ASN* 5.0 10.2 + - - +
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Residues in contact with ALA 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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171D SER 2.9 18.5 + - - +
172D LEU* 3.6 8.7 - - + +
174D GLU* 1.3 73.3 - - - +
176D ALA* 1.3 54.2 + - - +
178D ASN* 2.7 32.2 + - - +
179D ALA* 2.7 20.4 + - - +
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Residues in contact with ALA 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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127D VAL* 4.0 22.6 - - + +
158D ASP* 5.5 2.9 - - - +
160D LEU* 3.8 20.2 - - + -
172D LEU 2.8 21.9 + - - +
173D ALA* 3.8 7.2 - - - +
175D ALA* 1.3 72.0 - - - +
177D LEU* 1.3 57.7 + - - +
179D ALA* 4.6 2.5 - - - +
180D HIS* 3.0 43.0 + - + +
186D PHE* 4.3 3.6 - - + -
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Residues in contact with LEU 177 (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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173D ALA 2.8 23.5 + - - +
174D GLU 3.4 4.9 - - - +
176D ALA* 1.3 72.4 - - - +
178D ASN* 1.3 64.4 + - - +
180D HIS 3.3 20.7 - - - +
181D PRO* 3.6 9.5 - - + +
183D LEU* 4.5 11.7 - - + +
186D PHE* 4.5 10.2 - - + -
200D VAL* 3.7 24.5 - - + +
201D VAL* 4.8 5.2 - - + -
204D ALA* 3.6 31.0 - - + -
206D LYS* 5.0 11.4 - - + +
210D VAL* 4.5 19.7 - - + -
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Residues in contact with ASN 178 (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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174D GLU* 2.9 33.3 + - - +
175D ALA* 2.7 12.7 + - - +
177D LEU* 1.3 76.6 - - - +
179D ALA* 1.3 63.7 + - - +
180D HIS 3.0 5.3 + - - -
181D PRO* 3.0 21.5 - - - +
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Residues in contact with ALA 179 (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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158D ASP* 6.0 0.2 - - - +
175D ALA 2.7 18.0 + - - +
176D ALA* 4.7 1.1 - - - -
178D ASN* 1.3 73.8 - - - +
180D HIS* 1.3 80.3 + - + +
181D PRO* 3.3 6.5 - - - +
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Residues in contact with HIS 180 (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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125D LYS* 4.3 16.3 + - + +
127D VAL* 5.0 3.6 - - + -
157D VAL* 3.8 36.6 + - + +
158D ASP* 3.7 21.2 + - - -
176D ALA* 3.0 23.1 + - - +
177D LEU* 3.3 9.9 - - - +
179D ALA* 1.3 96.2 + - + +
181D PRO* 1.3 56.4 - - - +
182D ASP* 3.1 11.7 - - - +
183D LEU* 3.1 38.6 + - + +
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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