Contacts of the helix formed by residues 165 - 180 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B ASP* 3.1 28.3 + - - +
163B CYS 4.0 2.9 - - - +
164B GLU* 1.3 79.4 - - - +
166B GLY* 1.3 57.4 + - - +
167B ALA* 2.9 20.0 + - - +
168B ARG* 2.7 45.6 + - - +
169B ALA* 2.9 23.4 + - - +
192B TYR* 5.1 2.8 - - - -
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ASP* 1.3 71.1 + - - +
167B ALA* 1.3 67.5 + - - +
169B ALA* 3.3 9.4 - - - +
170B VAL* 2.9 30.5 + - - +
192B TYR* 4.2 27.2 - - - -
196B ALA* 4.7 3.1 - - - +
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ASP* 2.9 12.0 + - - +
166B GLY* 1.3 76.3 - - - +
168B ARG* 1.3 67.7 + - + +
170B VAL* 3.2 8.7 + - - +
171B SER* 3.2 20.6 + - - -
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Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ASN 4.0 9.9 + - - -
162B ASP* 3.5 32.7 + - + +
163B CYS* 4.0 16.1 - - - +
165B ASP* 2.7 34.0 + - - +
167B ALA* 1.3 72.0 - - + +
169B ALA* 1.3 51.1 + - - +
171B SER* 2.7 15.6 + - - -
172B LEU* 2.7 54.2 + - - +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ASP* 3.3 28.4 - - - +
165B ASP 2.9 13.1 + - - +
166B GLY* 3.3 15.3 - - - +
168B ARG* 1.3 74.1 - - - +
170B VAL* 1.3 56.0 + - - +
172B LEU* 3.4 4.5 + - - +
173B ALA* 2.9 31.0 + - - +
192B TYR* 5.3 3.4 - - + +
193B ASN* 4.2 9.2 - - - +
196B ALA* 3.9 18.0 - - + +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY 2.9 23.0 + - - +
167B ALA* 3.4 9.0 - - - +
169B ALA* 1.3 72.0 - - - +
171B SER* 1.3 63.2 + - - +
173B ALA 3.4 0.7 + - - -
174B GLU* 3.1 40.8 + - - +
196B ALA* 4.2 16.8 - - + +
199B LEU* 4.1 27.8 - - + -
200B VAL* 3.4 22.6 - - + +
203B ASN* 6.2 0.9 - - - +
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA 3.2 9.8 + - - -
168B ARG* 2.7 17.5 + - - -
170B VAL* 1.3 74.9 - - - +
172B LEU* 1.3 60.5 - - - -
174B GLU* 3.2 15.4 + - - +
175B ALA* 2.9 28.3 + - - +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 3.3 40.3 - - + +
161B ASN 3.7 8.7 - - - +
162B ASP* 3.5 43.1 - - + +
168B ARG* 2.7 34.0 + - - +
169B ALA* 3.6 5.6 - - - +
171B SER* 1.3 75.5 - - - +
173B ALA* 1.3 62.3 + - - +
175B ALA* 3.1 10.3 + - + +
176B ALA 3.1 18.2 + - - -
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 4.2 3.3 - - - +
169B ALA 2.9 17.6 + - - +
170B VAL* 3.7 4.9 - - - +
171B SER 3.3 0.2 - - - -
172B LEU* 1.3 76.2 - - - +
174B GLU* 1.3 55.9 + - - +
176B ALA* 3.4 4.2 + - - +
177B LEU* 3.0 27.9 + - - +
186B PHE* 3.6 26.2 - - + -
197B GLN* 4.5 16.6 - - + -
200B VAL* 3.7 21.1 - - + -
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL* 3.1 29.5 + - - +
171B SER* 3.2 13.3 + - - +
173B ALA* 1.3 72.9 - - - +
175B ALA* 1.3 62.0 + - - +
177B LEU* 3.1 5.0 + - - +
178B ASN* 2.8 41.8 + - - +
200B VAL* 3.6 22.5 - - + +
203B ASN* 5.4 5.9 + - - +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 5.8 1.1 - - + -
171B SER 2.9 13.8 + - - +
172B LEU* 3.4 15.7 - - + +
174B GLU* 1.3 75.8 - - - +
176B ALA* 1.3 52.1 + - - +
178B ASN* 2.9 9.1 + - - +
179B ALA* 2.7 38.0 + - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 4.0 25.8 - - + -
158B ASP* 5.6 1.8 - - - +
160B LEU* 3.9 18.3 - - + +
172B LEU 3.1 9.3 + - - +
173B ALA 3.6 8.3 - - - +
175B ALA* 1.3 78.9 - - - +
177B LEU* 1.3 55.7 + - - +
179B ALA* 4.4 2.5 - - - -
180B HIS* 2.7 48.5 + - + +
183B LEU* 5.0 1.1 - - - +
186B PHE* 4.3 5.8 - - + -
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ALA 3.0 9.5 + - - +
174B GLU* 3.1 9.8 + - - +
176B ALA* 1.3 76.0 - - - +
178B ASN* 1.3 63.2 + - - +
180B HIS 3.0 20.8 - - - +
181B PRO* 3.9 5.2 - - - +
183B LEU* 3.7 15.0 - - + -
186B PHE* 3.4 35.4 - - + -
200B VAL* 3.4 27.6 - - + +
201B VAL* 4.6 5.2 - - + -
204B ALA* 3.6 28.7 - - + -
206B LYS* 4.6 12.8 - - + +
210B VAL* 4.9 9.4 - - + -
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Residues in contact with ASN 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLU* 2.8 26.2 + - - +
175B ALA* 3.6 8.3 - - - +
177B LEU* 1.3 78.1 - - - +
179B ALA* 1.3 64.1 + - - +
181B PRO* 4.5 8.8 - - - +
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ALA 2.7 19.7 + - - +
176B ALA* 3.9 4.0 - - - +
178B ASN* 1.3 75.0 - - - +
180B HIS* 1.3 78.2 + - + +
181B PRO* 3.3 9.4 - - - +
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Residues in contact with HIS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LYS* 5.6 7.6 + - + -
127B VAL* 4.0 15.7 - - + -
157B VAL* 4.0 21.6 - - + +
158B ASP* 2.7 29.7 + - - -
176B ALA* 2.7 38.8 + - - +
177B LEU* 3.0 14.9 - - - +
179B ALA* 1.3 88.0 + - + +
181B PRO* 1.3 66.3 - - - +
182B ASP* 3.2 10.7 + - - +
183B LEU* 3.5 25.7 + - + +
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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