Contacts of the helix formed by residues 189 - 200 (chain B) in PDB entry 3TQI
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 GLN 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B ILE* 3.2 32.5 - - + -
126B GLU 4.1 10.5 + - - +
127B ASP* 2.8 41.3 + - - +
137B LEU* 4.8 5.2 - - + -
138B ASP 5.1 0.6 + - - +
187B THR 3.0 1.2 + - - -
188B PRO* 1.3 83.8 - - - +
190B GLY* 1.3 63.7 + - - +
191B HIS* 3.3 7.0 + - - -
192B ARG* 3.1 48.7 + - - +
193B ILE* 3.4 14.7 + - + +
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Residues in contact with GLY 190 (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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182B PRO* 3.2 36.3 - - - +
187B THR* 2.7 19.7 + - - -
188B PRO 3.2 1.0 + - - -
189B GLN* 1.3 78.6 - - - +
191B HIS* 1.3 62.3 + - - +
193B ILE* 3.2 11.0 + - - +
194B LEU* 3.1 19.8 + - - +
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Residues in contact with HIS 191 (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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26B ARG* 4.5 19.9 - - - +
29B GLU* 6.0 1.6 - - - +
30B ILE* 4.2 8.1 - - + +
182B PRO 3.9 3.1 + - - -
188B PRO 3.5 21.7 + - - -
189B GLN* 4.5 3.3 + - - -
190B GLY* 1.3 76.5 - - - +
192B ARG* 1.3 90.0 + - + +
194B LEU* 3.6 11.2 + - - +
195B ALA* 3.0 28.3 + - - +
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Residues in contact with ARG 192 (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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123B ASP 5.0 1.2 + - - -
124B GLY* 4.4 4.0 - - - -
125B ILE* 3.4 54.1 - - + +
126B GLU 4.4 4.2 + - - +
189B GLN* 3.1 37.7 + - - +
191B HIS* 1.3 98.8 - - + +
193B ILE* 1.3 61.1 + - - +
195B ALA* 3.2 5.6 + - - +
196B HIS* 2.9 42.7 + - + -
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Residues in contact with ILE 193 (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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83B LEU* 5.8 2.2 - - + -
121B LEU* 3.4 41.2 - - + +
122B PHE* 3.9 20.9 - - + -
125B ILE* 3.7 22.0 - - + -
137B LEU* 4.0 16.4 - - + -
139B VAL* 5.9 0.2 - - + -
178B LEU* 4.4 13.9 - - + -
180B PHE* 4.1 19.7 - - + -
182B PRO* 4.7 4.0 - - + -
187B THR* 6.5 0.2 - - - -
189B GLN* 3.6 15.3 - - + +
190B GLY* 3.2 12.7 + - - +
192B ARG* 1.3 76.5 - - - +
194B LEU* 1.3 61.9 + - - +
196B HIS* 3.2 1.7 + - - +
197B PHE* 3.2 17.2 + - - +
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Residues in contact with LEU 194 (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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23B ILE* 4.7 10.5 - - + +
26B ARG* 3.7 36.1 - - + -
27B VAL* 5.3 3.8 - - + +
30B ILE* 4.0 9.4 - - + -
55B ILE* 4.2 17.9 - - + -
83B LEU* 4.1 24.7 - - + -
85B ILE* 4.8 2.0 - - + -
182B PRO* 4.2 16.2 - - + +
183B GLU* 4.4 19.5 - - + +
190B GLY 3.1 12.7 + - - +
191B HIS* 3.7 8.5 - - - +
193B ILE* 1.3 78.5 - - - +
195B ALA* 1.3 64.3 + - - +
197B PHE* 3.2 6.5 + - + +
198B VAL* 3.0 27.0 + - - +
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Residues in contact with ALA 195 (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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30B ILE* 3.7 28.7 - - + -
191B HIS* 3.0 19.4 + - - +
192B ARG* 3.2 9.1 + - - +
194B LEU* 1.3 76.1 - - - +
196B HIS* 1.3 59.5 + - + +
198B VAL* 4.6 0.7 - - - +
199B ILE* 2.8 42.5 + - + +
200B HIS* 5.1 0.4 - - - -
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Residues in contact with HIS 196 (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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120B PHE 3.4 23.4 + - - +
121B LEU* 4.0 9.3 + - - +
123B ASP* 2.9 39.3 + - + -
125B ILE* 3.9 16.4 - - + +
192B ARG* 2.9 30.0 + - + +
193B ILE 3.5 9.6 - - - +
194B LEU 3.2 0.2 - - - -
195B ALA* 1.3 79.6 - - + +
197B PHE* 1.3 64.5 + - - +
200B HIS* 3.1 44.5 + + + +
201B ILE* 3.1 12.7 + - - +
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Residues in contact with PHE 197 (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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10B ILE* 4.5 3.6 - - + -
54B ILE 3.5 29.2 - - - -
55B ILE* 3.8 20.9 - - + -
81B PRO* 3.9 20.2 - - + -
82B VAL 3.8 9.6 - - - -
83B LEU* 3.5 34.5 - - + -
121B LEU* 3.9 14.1 - - + +
176B PHE* 4.4 8.5 - + - -
193B ILE 3.2 7.2 + - - +
194B LEU* 3.6 7.6 - - - +
196B HIS* 1.3 80.0 - - - +
198B VAL* 1.3 68.3 + - + +
201B ILE* 3.3 21.7 + - + +
202B CYS* 2.9 50.8 + - - -
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Residues in contact with VAL 198 (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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10B ILE* 4.0 23.6 - - + -
27B VAL* 4.1 23.1 - - + -
30B ILE* 4.7 7.0 - - + -
32B VAL* 3.3 43.7 - - + -
55B ILE* 4.9 2.0 - - + -
194B LEU* 3.0 19.3 + - + +
195B ALA* 4.2 3.6 - - - +
197B PHE* 1.3 86.7 - - + +
199B ILE* 1.3 61.2 + - + +
202B CYS* 3.6 11.6 - - - +
204B CYS* 3.2 23.8 + - + +
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Residues in contact with ILE 199 (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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30B ILE* 3.9 28.0 - - + +
32B VAL* 4.4 8.3 - - + -
195B ALA* 2.8 28.1 + - + +
198B VAL* 1.3 75.7 - - - +
200B HIS* 1.3 80.1 + - + +
203B GLN* 3.3 20.5 - - - +
204B CYS 3.5 20.6 - - - +
206B PRO* 4.2 25.8 - - + -
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Residues in contact with HIS 200 (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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120B PHE* 5.4 6.7 - - + +
196B HIS* 3.1 46.4 + + + +
199B ILE* 1.3 98.2 + - + +
201B ILE* 1.3 65.7 + - + +
202B CYS 3.6 0.2 - - - -
203B GLN* 2.7 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