Contacts of the helix formed by residues 162 - 184 (chain B) in PDB entry 4TVQ
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 HIS 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B GLU* 1.3 79.8 - - - +
163B GLN* 1.3 71.8 + - + +
165B LYS* 3.3 10.6 + - + +
166B GLU* 2.9 61.4 + - + +
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Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU 3.3 1.4 - - - +
162B HIS* 1.3 89.3 + - + +
164B LYS* 1.3 61.0 + - - +
166B GLU* 3.5 6.7 - - - +
167B PHE* 2.9 28.8 + - - +
200B GLN* 3.7 13.3 - - - +
203B LEU* 3.7 29.6 - - - +
204B ILE* 3.8 28.1 - - + +
207B THR* 3.4 34.4 + - + +
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Residues in contact with LYS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 5.4 9.4 - - + -
145B VAL* 4.6 22.7 - - + -
146B ASN* 3.0 29.3 + - - +
161B GLU* 3.2 26.0 + - + +
162B HIS 3.2 0.2 - - - -
163B GLN* 1.3 77.4 - - - +
165B LYS* 1.3 59.2 + - - +
167B PHE* 3.2 6.6 + - + +
168B VAL* 2.9 44.9 + - + +
204B ILE* 5.3 2.4 - - - +
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU 3.1 9.5 + - - +
162B HIS* 3.7 11.0 - - + +
164B LYS* 1.3 79.9 - - - +
166B GLU* 1.3 63.6 + - - +
168B VAL* 3.9 7.8 - - + +
169B LYS* 2.9 57.2 + - + +
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B HIS* 2.9 48.1 + - + +
163B GLN* 3.5 13.0 - - - +
164B LYS 3.2 0.2 - - - -
165B LYS* 1.3 79.1 - - - +
167B PHE* 1.3 59.5 + - - +
169B LYS* 3.1 19.9 + - - +
170B TYR* 2.9 56.7 + - - -
200B GLN* 3.4 23.2 + - - +
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Residues in contact with PHE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.6 23.8 - - + -
138B ILE* 3.8 30.1 - - + -
141B LEU* 3.7 18.2 - - + -
142B LEU* 5.3 10.1 - - + -
145B VAL* 6.2 2.9 - - + -
163B GLN 2.9 18.6 + - - +
164B LYS* 3.5 6.5 - - + +
166B GLU* 1.3 75.9 - - - +
168B VAL* 1.3 64.6 + - + +
170B TYR 3.5 0.7 + - - -
171B SER* 2.9 30.8 + - - -
197B LEU* 3.7 25.3 - - + +
200B GLN* 4.3 13.1 + - + -
201B THR* 3.4 24.7 - - - -
204B ILE* 3.6 24.2 - - + -
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 4.7 19.7 - - + -
164B LYS* 2.9 34.7 + - + +
165B LYS* 3.9 8.7 - - + +
167B PHE* 1.3 78.4 - - + +
169B LYS* 1.3 61.5 + - - +
171B SER* 3.1 7.0 + - - -
172B LYS* 2.9 59.5 + - + +
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Residues in contact with LYS 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 LYS* 2.9 44.1 + - + +
166B GLU* 3.1 20.4 + - - +
168B VAL* 1.3 78.1 - - - +
170B TYR* 1.3 72.7 + - + +
172B LYS* 3.5 4.7 + - - +
173B SER* 2.9 30.7 + - - -
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Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLU* 2.9 45.4 + - - +
167B PHE 4.1 2.9 - - - +
169B LYS* 1.3 89.7 + - + +
171B SER* 1.3 59.4 + - - +
173B SER* 3.6 11.9 - - - -
174B PHE* 2.9 26.9 + - - +
193B SER* 5.0 3.5 - - - +
196B ARG* 3.8 48.3 + - + -
197B LEU* 4.1 18.9 - - + +
200B GLN* 3.2 36.9 + - + -
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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
----------------------------------------------------------
138B ILE* 3.6 33.9 - - - +
167B PHE* 2.9 21.3 + - - -
168B VAL* 3.1 9.8 + - - -
170B TYR* 1.3 74.1 - - - +
172B LYS* 1.3 62.7 + - - +
174B PHE* 3.0 10.3 + - - +
175B SER* 2.9 24.9 + - - -
197B LEU* 4.0 12.8 - - - +
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Residues in contact with LYS 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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168B VAL* 2.9 40.3 + - + +
169B LYS* 4.1 4.5 - - - +
171B SER* 1.3 76.5 - - - +
173B SER* 1.3 57.5 + - - +
175B SER* 3.3 10.1 + - - -
176B ASP* 2.9 28.9 + - - +
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LYS* 2.9 21.6 + - - -
170B TYR* 3.6 15.8 - - - -
172B LYS* 1.3 77.6 - - - +
174B PHE* 1.3 52.3 + - - +
176B ASP* 3.5 6.8 + - - +
177B THR* 2.4 40.3 + - - -
193B SER* 5.1 3.4 - - - -
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Residues in contact with PHE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 4.4 5.4 - - + -
117B ILE* 3.9 19.3 - - + -
127B PHE* 6.1 0.4 - + - -
131B ILE* 6.1 0.9 - - + -
134B ILE* 4.3 23.6 - - + -
138B ILE* 5.1 4.3 - - + -
170B TYR 2.9 15.7 + - - +
171B SER* 3.0 13.0 + - - +
173B SER* 1.3 75.8 - - - +
175B SER* 1.3 61.8 + - - +
177B THR* 3.2 6.9 + - - -
178B LEU* 2.9 59.3 + - + +
190B VAL* 3.8 19.7 - - + -
193B SER* 3.2 33.9 - - - +
194B ALA* 3.8 17.9 - - + -
197B LEU* 4.7 14.8 - - + -
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B SER 2.9 11.6 + - - -
172B LYS* 3.5 13.2 - - - -
174B PHE* 1.3 78.9 - - - +
176B ASP* 1.3 57.4 + - - +
178B LEU* 3.0 18.2 + - - +
179B LYS* 2.9 43.1 + - - +
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Residues in contact with ASP 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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172B LYS 2.9 16.8 + - - +
173B SER* 3.9 7.2 - - - +
175B SER* 1.3 76.2 + - - +
177B THR* 1.3 53.2 + - - +
179B LYS* 3.3 16.1 + - - +
180B THR* 2.8 41.6 + - - -
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B SER* 2.4 27.7 + - - -
174B PHE* 3.3 6.7 - - - -
175B SER 3.1 0.2 - - - -
176B ASP* 1.3 76.6 - - - +
178B LEU* 1.3 59.5 + - - +
180B THR* 3.3 7.8 + - - -
181B TYR* 2.9 26.0 + - - +
189B ASN* 3.4 35.6 - - + +
190B VAL* 3.6 6.3 - - + +
193B SER* 3.4 27.8 - - - +
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Residues in contact with LEU 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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127B PHE* 3.7 33.0 - - + -
131B ILE* 4.2 28.5 - - + -
174B PHE* 2.9 43.7 + - + +
175B SER* 3.2 13.0 - - - +
177B THR* 1.3 75.0 - - - +
179B LYS* 1.3 66.4 + - + +
181B TYR* 2.9 15.9 + - + +
182B PHE* 2.9 30.3 + - + -
190B VAL* 4.0 21.5 - - + -
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Residues in contact with LYS 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 SER* 2.9 31.3 + - - +
176B ASP* 3.4 22.7 - - - +
178B LEU* 1.3 76.9 - - + +
180B THR* 1.3 60.9 + - - +
182B PHE* 3.6 16.1 + - + +
183B LYS* 3.0 35.1 + - - +
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Residues in contact with THR 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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176B ASP* 2.8 27.2 + - - -
177B THR* 3.6 9.4 - - - -
178B LEU 3.2 0.2 - - - -
179B LYS* 1.3 76.5 - - - +
181B TYR* 1.3 58.4 + - - +
183B LYS* 3.3 10.0 + - + +
184B ASP* 2.9 56.6 + - - +
189B ASN* 5.0 9.6 - - - +
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Residues in contact with TYR 181 (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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121B ILE* 3.5 30.0 + - + +
127B PHE* 3.9 29.8 - + - -
177B THR 2.9 15.2 + - - +
178B LEU* 2.9 9.4 + - - +
180B THR* 1.3 73.2 - - - +
182B PHE* 1.3 76.4 + + - +
183B LYS 3.0 5.4 - - - -
184B ASP* 3.5 1.7 - - - -
185B GLY* 2.8 55.5 + - - +
186B LYS 3.3 26.5 - - - +
187B ALA* 3.9 9.7 - - + +
189B ASN* 5.9 2.0 - - + +
190B VAL* 3.7 18.8 - - + -
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Residues in contact with PHE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ARG* 6.4 2.5 - - + -
127B PHE* 3.9 22.7 - + - -
128B LEU* 4.7 11.0 - - + -
131B ILE* 3.7 30.3 - - + -
178B LEU* 2.9 37.4 + - + +
179B LYS* 4.1 13.7 - - + +
180B THR 3.4 0.2 - - - -
181B TYR* 1.3 85.9 - + - +
183B LYS* 1.3 60.8 + - + +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS* 3.0 38.5 + - - +
180B THR* 3.3 10.6 + - + +
181B TYR 3.0 0.2 - - - -
182B PHE* 1.3 80.9 - - + +
184B ASP* 1.3 74.2 + - - +
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Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B THR* 2.9 40.3 + - - +
181B TYR* 3.5 0.9 - - - -
183B LYS* 1.3 85.0 - - - +
185B GLY* 1.3 59.7 + - - +
186B LYS* 3.6 24.5 + - + +
189B ASN* 4.4 9.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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