Contacts of the helix formed by residues 155 - 170 (chain B) in PDB entry 3CTP
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 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B SER* 1.3 68.5 - - - +
156B ASN* 1.3 57.7 + - - +
157B TYR* 3.9 5.0 + - - +
158B ASN* 2.7 45.0 + - - +
159B GLY* 2.9 23.2 + - - -
162B MET* 5.8 0.3 - - - +
312B ILE* 3.5 19.4 - - + +
313B MET 2.8 20.5 + - - +
314B GLU* 4.5 3.8 - - - +
315B VAL* 3.6 21.4 + - + +
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Residues in contact with ASN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU* 4.2 4.8 + - - -
153B SER* 4.4 6.9 - - - -
154B SER* 2.9 35.4 + - - +
155B ASP* 1.3 69.2 - - - +
157B TYR* 1.3 65.9 + - - +
159B GLY 3.8 0.2 - - - -
160B GLY 3.0 18.4 + - - -
186B ALA* 3.3 40.2 - - - +
189B LEU* 4.0 14.8 - - + +
190B ARG* 2.8 47.1 + - + +
266B PHE* 3.4 13.2 - - - -
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Residues in contact with TYR 157 (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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155B ASP* 3.3 5.1 + - - +
156B ASN* 1.3 78.5 - - - +
158B ASN* 1.3 83.1 + - - +
160B GLY 3.2 2.4 + - - -
161B ARG* 3.1 28.6 + - + +
189B LEU* 3.5 34.0 - - + +
192B LYS* 3.7 17.4 + - + -
193B GLY* 3.4 32.5 + - - -
196B ASP* 2.6 38.4 + - - +
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Residues in contact with ASN 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ASP* 2.7 35.5 + - - +
157B TYR* 1.3 98.0 - - - +
159B GLY* 1.3 57.3 + - - +
161B ARG* 3.2 8.5 + - - +
162B MET* 2.8 45.4 + - + +
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Residues in contact with GLY 159 (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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155B ASP 2.9 12.8 + - - -
157B TYR 3.2 0.2 - - - -
158B ASN* 1.3 78.1 - - - +
160B GLY* 1.3 60.2 + - - +
162B MET* 3.3 5.3 + - - +
163B ALA* 3.0 23.2 + - - +
266B PHE* 3.7 20.4 - - - -
282B ILE* 3.8 9.9 - - - +
315B VAL* 3.7 20.1 - - - +
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Residues in contact with GLY 160 (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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156B ASN 3.0 14.1 + - - -
157B TYR 3.2 3.1 + - - -
159B GLY* 1.3 74.8 - - - +
161B ARG* 1.3 62.7 + - - +
163B ALA* 3.3 1.6 + - - +
164B PHE 3.1 17.2 + - - -
190B ARG* 3.4 24.7 - - - -
194B PHE* 3.5 19.3 - - - -
236B PHE* 4.2 11.7 - - - -
266B PHE* 4.1 1.2 - - - -
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Residues in contact with ARG 161 (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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157B TYR* 3.1 21.5 + - + +
158B ASN* 3.6 15.0 - - - +
160B GLY* 1.3 75.2 - - - +
162B MET* 1.3 58.2 + - + +
164B PHE* 3.1 2.0 + - - +
165B ASP* 2.9 55.1 + - - +
193B GLY* 3.5 13.3 - - - +
194B PHE* 4.6 0.4 - - - +
196B ASP* 4.2 9.9 + - - +
197B GLY* 3.4 33.7 - - - +
200B ALA* 3.9 20.2 - - - +
201B LYS* 4.4 10.1 - - - +
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Residues in contact with MET 162 (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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158B ASN* 2.8 26.0 + - + +
159B GLY* 3.6 7.2 - - - +
160B GLY 3.3 0.2 - - - -
161B ARG* 1.3 77.1 - - + +
163B ALA* 1.3 58.8 + - - +
165B ASP* 3.7 8.4 - - - +
166B HIS* 2.9 30.5 + - - +
282B ILE* 4.0 11.9 - - + -
314B GLU* 6.0 0.4 - - + -
315B VAL* 3.5 46.7 - - + +
316B LYS* 4.1 13.7 - - - -
317B LEU* 4.1 14.0 - - + +
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Residues in contact with ALA 163 (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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159B GLY 3.0 13.9 + - - +
160B GLY 3.6 7.4 - - - +
161B ARG 3.2 0.2 - - - -
162B MET* 1.3 74.9 - - - +
164B PHE* 1.3 64.7 + - - +
166B HIS* 3.4 2.3 + - - +
167B LEU* 3.1 26.9 + - - +
194B PHE* 3.9 2.5 - - - -
236B PHE* 3.8 38.6 - - + -
264B ILE* 3.9 24.0 - - + +
282B ILE* 4.2 2.7 - - + +
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Residues in contact with PHE 164 (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 GLY 3.1 7.9 + - - +
161B ARG 3.1 6.7 + - - +
163B ALA* 1.3 78.1 - - - +
165B ASP* 1.3 77.8 + - - +
166B HIS 3.2 0.2 + - - -
167B LEU* 3.2 3.4 + - - +
168B TYR* 2.9 53.2 + + + +
175B ILE* 3.9 21.5 - - + -
194B PHE* 3.4 55.7 - + + +
197B GLY* 3.4 24.2 - - - -
198B ALA* 3.5 27.8 - - + -
201B LYS* 3.9 13.5 - - + -
203B LEU* 4.1 7.4 - - + -
205B ILE* 4.2 1.3 - - + -
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Residues in contact with ASP 165 (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 ARG* 2.9 55.4 + - - +
162B MET* 3.7 7.4 - - - +
164B PHE* 1.3 88.1 - - - +
166B HIS* 1.3 58.2 + - - +
168B TYR* 3.8 3.5 - - - +
169B GLU* 2.9 31.6 + - - +
201B LYS* 4.8 6.2 + - - -
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Residues in contact with HIS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B MET 2.9 18.3 + - - +
163B ALA 3.8 3.8 - - - +
165B ASP* 1.3 74.9 - - - +
167B LEU* 1.3 67.4 + - + +
169B GLU* 3.4 10.5 + - - +
170B LYS* 3.1 50.0 + - + +
264B ILE* 4.1 8.5 - - + -
280B THR* 3.7 15.8 - - + +
317B LEU* 3.6 23.0 - - + +
319B GLU* 3.5 35.1 + - + -
323B THR* 2.9 41.0 + - + -
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Residues in contact with LEU 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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163B ALA 3.1 12.1 + - - +
164B PHE* 3.8 5.4 - - - +
166B HIS* 1.3 76.6 - - + +
168B TYR* 1.3 62.0 + - - +
170B LYS* 3.2 9.1 + - + -
171B GLY 3.4 0.3 + - - -
172B CYS* 3.0 47.4 + - + +
175B ILE* 4.3 10.1 - - + -
194B PHE* 4.1 24.9 - - + -
234B GLY* 4.2 7.4 - - - -
235B ILE 4.1 20.0 - - - +
236B PHE 4.2 0.2 - - - +
262B GLN* 4.3 12.3 - - + +
264B ILE* 3.9 27.6 - - + -
323B THR* 4.3 20.4 - - + -
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Residues in contact with TYR 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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164B PHE* 2.9 44.2 + + + +
165B ASP* 3.8 4.7 - - - +
167B LEU* 1.3 76.4 - - - +
169B GLU* 1.3 62.2 + - - +
171B GLY* 3.0 9.9 + - - -
172B CYS 3.9 9.0 - - - -
173B ARG* 2.9 68.4 + - - +
175B ILE* 4.9 0.6 - - - +
201B LYS* 3.7 52.0 + - + +
203B LEU* 4.2 10.1 - - + -
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Residues in contact with GLU 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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165B ASP 2.9 18.4 + - - +
166B HIS* 3.8 11.3 + - - +
168B TYR* 1.3 80.2 - - - +
170B LYS* 1.3 77.9 + - + +
171B GLY* 3.1 4.0 + - - -
319B GLU* 5.7 0.9 - - - +
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Residues in contact with LYS 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 HIS* 3.1 45.4 + - + +
167B LEU* 3.2 6.0 + - - +
169B GLU* 1.3 92.5 - - + +
171B GLY* 1.3 57.5 + - - +
172B CYS 3.4 2.5 - - - -
262B GLN* 3.3 36.6 + - - +
319B GLU* 3.7 10.8 + - - -
323B THR* 4.8 0.7 - - + -
324B ILE* 2.6 46.8 + - + +
325B SER* 3.2 23.4 - - - +
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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