Contacts of the helix formed by residues 170 - 187 (chain B) in PDB entry 6TD2
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 ASN 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLY 4.1 4.4 + - - -
158B PHE* 4.1 16.8 + - - +
169B GLY* 1.3 73.7 - - - +
171B VAL* 1.3 60.6 + - - +
172B GLY 3.1 2.9 - - - -
173B LEU* 2.8 34.3 + - + +
174B LEU* 3.0 13.6 + - + +
300B VAL 4.7 0.2 - - - +
301B PRO* 3.3 9.5 - - - +
302B VAL* 2.7 46.9 + - - +
304B ASP* 3.1 28.7 + - - +
307B PHE* 3.6 18.7 - - + +
308B LEU* 4.9 1.4 - - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 3.2 26.2 - - - +
48B MET 3.5 22.9 - - - +
49B PRO* 3.6 12.1 - - + -
152B ARG* 3.6 18.2 - - - +
156B PHE 3.6 19.7 - - - +
157B GLY* 3.1 16.7 + - - +
159B LEU 6.2 0.2 - - - +
168B PRO* 4.3 3.6 - - + -
169B GLY 4.0 12.8 - - - +
170B ASN* 1.3 76.8 - - - +
172B GLY* 1.3 56.4 + - - +
174B LEU* 3.1 10.7 + - + +
175B ASP* 2.7 35.0 + - - +
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TYR* 3.5 4.8 - - - +
152B ARG 3.7 21.1 - - - -
157B GLY* 2.8 18.0 + - - -
158B PHE* 3.8 11.7 - - - -
170B ASN 3.1 0.4 - - - -
171B VAL* 1.3 77.9 - - - +
173B LEU* 1.3 59.7 + - - +
175B ASP* 3.3 23.2 - - - +
176B GLN* 3.3 13.3 - - - +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PHE* 4.7 0.9 - - + -
158B PHE* 3.9 11.5 - - + -
170B ASN* 2.8 24.9 + - + +
172B GLY* 1.3 67.9 - - - +
174B LEU* 1.3 59.9 + - - +
175B ASP 3.0 2.0 - - - -
176B GLN* 3.1 21.4 + - - +
177B ARG* 2.8 27.7 + - - +
208B SER* 3.7 33.7 - - - +
211B MET* 4.2 14.1 - - + -
212B HIS* 3.9 7.6 - - - +
301B PRO* 3.7 31.4 - - + -
307B PHE* 3.7 35.0 - - + -
308B LEU* 5.8 0.7 - - + -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PRO* 4.0 27.8 - - + -
50B PRO* 3.4 23.7 - - + +
168B PRO* 6.1 0.7 - - + -
169B GLY 4.9 5.4 - - - +
170B ASN* 3.0 16.9 + - + +
171B VAL* 3.1 13.0 + - - +
173B LEU* 1.3 75.8 - - - +
175B ASP* 1.3 60.0 + - - +
177B ARG* 3.5 32.7 - - - +
178B LEU* 3.2 17.7 + - - +
307B PHE* 3.9 16.4 - - + -
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Residues in contact with ASP 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.3 18.3 - - + -
50B PRO* 3.1 18.0 - - - +
97B LEU* 3.5 15.7 - - + +
151B TYR* 3.9 13.0 - - + -
152B ARG* 2.8 65.0 + - - +
171B VAL 2.7 16.8 + - - +
172B GLY* 3.3 9.1 - - - +
173B LEU 3.0 0.2 - - - -
174B LEU* 1.3 71.1 - - - +
176B GLN* 1.3 65.4 + - - +
178B LEU 3.2 2.6 + - - -
179B ALA* 3.1 17.7 + - - +
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Residues in contact with GLN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 3.6 12.4 - - + +
123B PHE* 5.0 0.2 - - - -
149B MET* 4.3 20.4 - - + -
151B TYR* 3.5 45.4 - - + +
158B PHE* 5.3 0.2 - - - -
172B GLY 3.3 11.1 + - - +
173B LEU* 3.1 14.6 + - - +
175B ASP* 1.3 73.7 - - - +
177B ARG* 1.3 64.9 + - - +
179B ALA* 3.0 4.8 + - - +
180B LEU* 2.9 28.3 + - + +
208B SER* 3.1 35.8 + - - -
212B HIS* 2.9 26.5 + - - +
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Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU 2.8 19.1 + - - +
174B LEU* 3.5 25.9 - - - +
175B ASP 3.2 0.2 - - - -
176B GLN* 1.3 71.9 - - - +
178B LEU* 1.3 58.1 + - - +
180B LEU* 3.0 9.9 + - - +
181B GLN* 2.9 48.1 + - - +
212B HIS* 3.9 8.0 - - + -
215B SER* 2.9 23.2 + - - -
217B PRO* 3.2 22.9 - - - +
218B SER* 2.6 56.8 + - - +
221B LEU* 4.2 10.1 - - + -
307B PHE* 3.1 24.7 - - - +
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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
----------------------------------------------------------
37B PHE* 3.6 28.9 - - + +
38B ALA* 3.6 20.0 - - + -
50B PRO* 3.8 20.2 - - + +
51B GLU 4.1 11.2 - - - +
52B PRO* 4.5 19.1 - - + -
174B LEU 3.2 15.1 + - - +
175B ASP 3.2 3.8 + - - +
177B ARG* 1.3 75.1 - - - +
179B ALA* 1.3 60.7 + - - +
181B GLN* 3.1 24.3 + - + +
182B TRP* 2.8 29.6 + - + +
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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
----------------------------------------------------------
37B PHE* 3.8 13.9 - - + -
99B LEU* 4.2 9.3 - - + +
116B ILE* 6.2 0.2 - - - -
147B VAL* 6.3 0.7 - - + -
149B MET* 3.7 38.1 - - + -
175B ASP 3.1 11.6 + - - +
176B GLN 3.0 9.5 + - - +
178B LEU* 1.3 76.8 - - - +
180B LEU* 1.3 57.4 + - - +
182B TRP* 3.1 7.4 + - - +
183B VAL* 2.9 33.8 + - + +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 4.1 16.3 - - + +
118B ILE* 5.3 2.5 - - + -
149B MET* 3.8 21.5 - - + -
176B GLN* 2.9 22.5 + - + +
177B ARG* 3.0 9.8 + - - +
179B ALA* 1.3 76.7 - - - +
181B GLN* 1.3 58.1 + - - +
183B VAL* 3.4 9.0 + - - +
184B GLN* 3.1 29.1 + - - +
199B LEU* 4.0 31.6 - - + -
212B HIS* 4.1 28.5 - - + +
218B SER* 4.8 1.3 - - - +
221B LEU* 3.7 30.2 - - + +
222B PHE* 4.9 2.7 - - + -
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Residues in contact with GLN 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 2.9 38.7 + - - +
178B LEU* 3.1 27.1 + - + +
180B LEU* 1.3 74.8 - - - +
182B TRP* 1.3 58.6 + - - +
184B GLN* 3.1 8.8 + - - +
185B GLU* 2.9 44.1 + - + +
217B PRO* 5.3 2.6 + - - +
221B LEU* 3.6 23.7 - - + +
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Residues in contact with TRP 182 (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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12B VAL* 3.9 22.1 - - + +
35B ILE* 3.7 28.4 - - + +
36B PRO 4.4 3.4 + - - -
37B PHE* 4.1 21.1 - - + -
56B TRP* 5.8 2.0 - - - -
99B LEU* 3.7 37.0 - - + -
101B VAL* 4.2 11.0 - - + -
178B LEU* 2.8 19.4 + - + +
179B ALA* 3.4 11.4 - - - +
181B GLN* 1.3 72.8 - - - +
183B VAL* 1.3 72.9 + - + +
185B GLU* 3.3 7.2 + - - +
186B ASN* 3.0 61.1 + - + +
187B ILE* 4.6 5.6 - - + -
190B PHE* 3.6 30.1 - + - -
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Residues in contact with VAL 183 (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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99B LEU* 5.2 0.2 - - + -
114B VAL* 4.2 9.4 - - + -
116B ILE* 3.8 26.7 - - + -
147B VAL* 3.8 33.4 - - + -
179B ALA* 2.9 17.6 + - + +
180B LEU 3.6 8.3 - - - +
181B GLN 3.3 0.2 - - - -
182B TRP* 1.3 86.6 - - + +
184B GLN* 1.3 60.7 + - + +
187B ILE* 2.8 57.3 + - + +
197B VAL* 4.2 11.4 - - + -
221B LEU 6.0 0.4 - - - +
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Residues in contact with GLN 184 (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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180B LEU 3.1 16.0 + - - +
181B GLN* 3.1 11.9 + - - +
183B VAL* 1.3 80.4 - - + +
185B GLU* 1.3 64.8 + - + +
186B ASN 3.3 0.3 + - - -
187B ILE 4.4 0.9 + - - -
188B ALA* 5.3 1.6 + - - +
194B PRO* 2.9 49.7 - - - +
195B MET* 5.8 0.2 - - - +
197B VAL* 5.1 1.3 - - + +
220B SER 3.8 19.7 + - - +
221B LEU* 3.9 28.6 - - + +
223B HIS* 4.9 3.1 + - - -
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Residues in contact with GLU 185 (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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13B ARG* 3.5 55.2 + - - +
181B GLN* 2.9 30.5 + - + +
182B TRP* 4.0 7.2 - - - +
184B GLN* 1.3 78.8 - - + +
186B ASN* 1.3 70.5 + - - +
188B ALA* 5.6 1.0 - - - +
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Residues in contact with ASN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.8 14.9 - - + +
13B ARG* 3.1 33.8 + - - +
182B TRP* 3.0 66.9 + - + +
185B GLU* 1.3 93.9 + - - +
187B ILE* 1.3 67.1 + - - +
188B ALA* 3.1 3.8 - - - -
189B ALA* 2.9 25.3 + - - +
190B PHE* 3.6 5.3 - - - -
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Residues in contact with ILE 187 (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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101B VAL* 4.3 9.2 - - + -
114B VAL* 3.9 22.9 - - + -
145B VAL* 4.1 11.4 - - + -
147B VAL* 4.0 22.7 - - + -
182B TRP* 4.6 7.0 - - + -
183B VAL* 2.8 39.0 + - + +
184B GLN 4.4 0.4 + - - -
186B ASN* 1.3 72.0 - - - +
188B ALA* 1.3 65.5 + - - +
190B PHE* 2.9 30.7 + - + +
192B GLY* 3.0 25.5 + - - -
194B PRO* 3.7 33.2 - - + -
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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
------------------------------------------------------------
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