Contacts of the helix formed by residues 180 - 193 (chain B) in PDB entry 1TVK
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 VAL 180 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASN* 3.5 35.2 - - + +
100B ASN* 5.8 0.2 - - - -
140B GLY 4.6 0.9 - - - -
178B THR* 4.4 2.9 - - + -
179B VAL* 1.3 73.5 - - + +
181B GLU* 1.3 67.3 + - - +
182B PRO* 3.5 4.3 - - - -
183B TYR* 3.2 35.8 + - + -
184B ASN* 3.3 14.7 + - - +
388B MET* 4.7 2.7 - - - -
394B PHE* 3.4 39.3 - - + -
398B TYR* 3.3 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU 4.1 2.1 - - - +
140B GLY* 3.0 23.8 - - - +
171B PRO* 3.1 42.2 - - + +
176B SER* 3.1 43.2 + - - +
178B THR* 3.0 11.8 + - - -
179B VAL 2.8 9.5 + - - +
180B VAL* 1.3 78.0 - - - +
182B PRO* 1.3 75.0 - - + +
183B TYR 3.0 0.3 + - - -
184B ASN* 3.3 3.3 + - - +
185B ALA* 3.1 19.2 + - - +
384B GLN* 4.5 3.8 - - - +
1500B GDP 3.6 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL 4.1 4.3 - - - +
180B VAL 3.8 0.2 - - - -
181B GLU* 1.3 95.3 - - + +
183B TYR* 1.3 63.9 + - - +
185B ALA* 3.2 4.4 - - + +
186B THR* 3.2 15.1 + - - -
381B ILE* 3.7 15.1 - - + +
384B GLN* 3.6 38.8 - - + +
385B PHE* 3.0 28.8 - - + +
388B MET* 3.3 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B VAL* 3.2 25.3 + - + +
181B GLU 3.0 1.4 + - - -
182B PRO* 1.3 80.4 - - - +
184B ASN* 1.3 63.1 + - - +
185B ALA 2.8 1.6 + - - -
187B LEU* 3.3 26.4 + - - +
385B PHE* 3.2 24.2 - + - -
388B MET* 2.4 55.2 + - + -
389B PHE* 3.5 17.4 - + + -
392B LYS 4.3 2.1 - - - -
393B ALA 3.8 5.0 + - - -
394B PHE* 4.0 20.9 - - + -
395B LEU* 4.4 6.7 - - + +
398B TYR* 2.8 29.4 - + + +
408B PHE* 3.3 29.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASN* 2.6 14.2 + - - +
101B TRP* 2.6 52.2 + - - +
139B LEU 3.4 2.2 - - - +
140B GLY* 3.0 29.7 + - - -
141B GLY 2.5 26.4 + - - +
145B SER* 3.8 8.7 - - - +
180B VAL* 3.3 13.9 + - - +
181B GLU 3.3 2.4 + - - +
183B TYR* 1.3 78.9 - - - +
185B ALA* 1.3 66.0 + - - +
188B SER* 2.9 22.0 + - - -
398B TYR* 3.6 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 2.9 25.2 + - + +
171B PRO* 4.5 3.6 - - + -
181B GLU 3.1 7.1 + - - +
182B PRO 3.2 9.6 - - - +
183B TYR 2.8 1.2 + - - -
184B ASN* 1.3 70.7 - - - +
186B THR* 1.3 58.2 + - - +
187B LEU 3.0 1.3 - - - -
188B SER* 2.3 39.3 + - - -
189B VAL* 3.3 8.9 + - + -
381B ILE* 3.3 33.4 - - + +
415B MET* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO 3.2 2.4 + - - -
185B ALA* 1.3 76.3 - - - +
187B LEU* 1.3 65.1 + - - +
189B VAL* 3.7 7.7 + - - +
190B HIS* 3.1 22.3 + - - +
381B ILE 4.2 8.6 + - - -
382B SER* 4.5 4.0 - - - -
385B PHE* 3.5 41.0 - - + +
411B ALA* 3.5 8.1 - - + +
412B GLU* 3.2 38.2 - - - +
415B MET* 4.1 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 3.0 31.2 - - + -
183B TYR 3.3 15.3 + - - +
185B ALA 2.7 4.2 + - - -
186B THR* 1.3 78.8 - - + +
188B SER* 1.3 51.1 + - - +
190B HIS* 3.1 6.9 - - - +
191B GLN* 2.6 29.6 - - - +
385B PHE* 4.6 4.9 - - + -
398B TYR* 3.9 13.5 - - + -
403B MET* 3.5 17.7 - - + -
407B GLU* 3.8 16.2 - - + +
408B PHE* 3.4 45.8 - - + -
411B ALA* 3.5 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 3.2 8.0 - - - +
137B HIS* 4.5 0.7 + - - -
139B LEU* 3.6 23.0 - - - +
145B SER* 3.0 35.4 + - - -
149B THR* 2.9 17.8 - - - +
184B ASN 2.9 20.8 + - - -
185B ALA 2.3 22.8 + - - -
187B LEU* 1.3 64.3 - - - +
189B VAL* 1.3 52.1 + - - -
190B HIS 2.9 4.3 - - - -
191B GLN* 2.7 26.2 + - - +
192B LEU* 3.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.6 23.5 - - + +
185B ALA* 3.7 15.0 - - + +
186B THR* 4.1 1.8 - - - +
188B SER* 1.3 67.5 - - - +
190B HIS* 1.3 66.7 + - - +
191B GLN 2.7 7.4 + - - -
192B LEU* 3.3 17.9 - - + +
193B VAL* 2.7 40.2 + - + +
265B PHE* 4.7 7.2 - - + -
378B PHE* 4.9 8.7 - - + -
415B MET* 3.3 42.4 - - + -
418B LEU* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 5.6 0.2 - + - -
186B THR 3.1 12.4 + - - +
187B LEU* 3.1 17.7 - - + +
188B SER 2.9 0.2 - - - -
189B VAL* 1.3 79.9 - - - +
191B GLN* 1.3 81.5 + - - +
193B VAL* 3.5 5.4 - - - +
194B GLU* 4.5 5.0 + - - +
195B ASN* 4.9 0.5 + - - -
407B GLU* 3.6 11.4 - - - -
410B GLU* 2.6 35.8 + - + +
411B ALA* 2.9 32.6 - - + -
414B ASN* 2.7 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 3.0 18.4 - - - -
105B HIS* 4.1 10.9 + - - +
149B THR* 3.1 46.0 - - + +
152B ILE* 4.0 0.7 - - - -
153B SER* 4.4 9.6 - - - +
187B LEU 2.6 29.6 - - - +
188B SER 2.7 4.0 + - - +
190B HIS* 1.3 104.1 + - - +
192B LEU* 1.3 61.0 + - - +
194B GLU 3.4 0.9 - - - -
195B ASN* 2.5 36.8 + - - +
407B GLU* 4.5 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B HIS* 3.8 12.8 - - + +
139B LEU* 3.7 33.0 - - + -
149B THR* 5.0 1.6 - - + -
152B ILE* 3.2 28.9 - - + -
166B THR* 3.4 20.9 - - + +
168B SER* 4.0 9.0 - - - +
188B SER* 3.4 4.0 + - - +
189B VAL* 2.7 25.3 + - + +
191B GLN* 1.3 70.1 - - - +
193B VAL* 1.3 52.9 + - - +
194B GLU 2.4 19.1 + - - -
195B ASN 2.7 10.2 + - - -
196B THR* 2.4 46.2 + - + +
199B THR* 4.6 2.5 - - + -
263B LEU* 2.7 1.2 - - - +
265B PHE* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 2.7 29.6 + - + +
190B HIS 3.5 1.6 - - - +
192B LEU* 1.3 71.8 - - - +
194B GLU* 1.3 72.5 - - + +
262B ARG* 2.8 45.5 + - - +
263B LEU* 3.1 14.5 - - - +
265B PHE* 3.4 13.2 - - + -
414B ASN* 3.2 28.5 - - - +
418B LEU* 3.4 32.1 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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