Contacts of the helix formed by residues 189 - 200 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A LEU* 4.2 11.4 - - - +
394A ALA* 3.8 12.9 - - - +
398A TYR* 6.0 0.3 - - - -
125C ILE* 3.4 29.6 - - + -
126C GLU 4.3 7.0 - - - +
127C ASP* 2.4 31.1 + - - +
137C LEU* 3.7 18.4 - - + -
138C ASP 5.2 1.1 + - - +
187C THR 3.2 0.8 - - - -
188C PRO* 1.3 85.4 - - - +
190C GLY* 1.3 63.4 + - - +
191C HIS* 3.3 6.8 - - - -
192C ARG* 3.0 52.4 + - - +
193C ILE* 3.4 9.1 + - + +
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Residues in contact with GLY 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C PRO* 3.3 28.5 - - - +
187C THR* 2.7 28.3 + - - -
188C PRO 3.3 0.6 - - - -
189C GLN* 1.3 78.0 - - - +
191C HIS* 1.3 60.7 + - - +
193C ILE* 3.1 11.7 + - - +
194C LEU* 3.1 19.6 + - - +
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Residues in contact with HIS 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ARG* 4.4 21.3 - - + +
29C GLU* 6.1 0.2 - - - +
30C ILE* 4.2 6.8 - - + +
182C PRO 3.8 4.2 + - - -
187C THR 4.7 0.4 + - - -
188C PRO 3.5 22.3 + - - -
189C GLN* 3.9 4.2 - - - -
190C GLY* 1.3 76.0 - - - +
192C ARG* 1.3 85.9 + - + +
194C LEU* 3.6 11.2 + - - +
195C ALA* 3.1 26.5 + - - +
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Residues in contact with ARG 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LEU* 2.9 52.7 + - - +
389A GLU* 4.2 15.4 + - - +
392A LEU 5.3 1.0 + - - -
123C ASP 4.7 1.4 + - - -
124C GLY* 4.2 3.0 - - - -
125C ILE* 3.2 51.5 - - + +
126C GLU 4.2 3.2 + - - +
189C GLN* 3.0 40.3 + - - +
191C HIS* 1.3 98.7 - - + +
193C ILE* 1.3 66.1 + - - +
195C ALA* 3.4 5.2 + - - +
196C HIS* 3.0 35.8 + - + -
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Residues in contact with ILE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 5.6 2.2 - - + -
121C LEU* 3.9 33.1 - - + +
122C PHE* 3.7 22.9 - - + -
125C ILE* 3.8 22.0 - - + -
137C LEU* 4.6 11.0 - - + -
139C VAL* 5.8 0.4 - - + -
178C LEU* 4.2 17.3 - - + -
180C PHE* 3.8 24.7 - - + -
182C PRO* 4.5 5.2 - - + -
189C GLN 4.0 8.1 - - - +
190C GLY* 3.1 15.8 + - - +
192C ARG* 1.3 77.3 - - - +
194C LEU* 1.3 64.0 + - + +
196C HIS* 3.1 13.3 + - - +
197C PHE 3.1 9.9 + - - -
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Residues in contact with LEU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 4.7 7.6 - - + +
26C ARG* 3.8 27.1 - - + -
27C VAL* 5.4 4.5 - - + -
30C ILE* 3.8 10.8 - - + -
55C ILE* 4.4 16.6 - - + -
83C LEU* 4.2 19.5 - - + -
85C ILE* 4.6 6.5 - - + -
182C PRO* 3.9 43.5 - - + +
183C GLU* 4.1 9.2 - - + +
190C GLY 3.1 11.6 + - - +
191C HIS* 3.8 9.9 - - - +
193C ILE* 1.3 77.6 - - - +
195C ALA* 1.3 56.9 + - - +
197C PHE* 3.3 6.5 + - - +
198C VAL* 3.0 31.7 + - - +
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Residues in contact with ALA 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE* 3.4 28.5 - - + +
191C HIS* 3.1 19.4 + - + +
192C ARG* 3.8 7.2 - - - +
193C ILE 3.2 0.2 - - - -
194C LEU* 1.3 73.6 - - - +
196C HIS* 1.3 64.3 + - + +
198C VAL* 4.4 0.7 - - - +
199C ILE* 2.8 38.3 + - + +
200C HIS* 5.3 0.2 - - - -
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Residues in contact with HIS 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A GLU* 4.5 14.6 + - - -
120C PHE 3.3 23.6 + - - +
121C LEU* 4.0 9.2 + - - +
123C ASP* 2.9 42.8 + - + +
125C ILE* 4.3 9.3 - - + +
192C ARG* 3.0 32.0 + - + +
193C ILE 3.1 8.5 + - - +
195C ALA* 1.3 80.3 - - + +
197C PHE* 1.3 57.5 + - - +
200C HIS* 3.2 34.1 + + - +
201C ILE* 3.0 28.7 + - - +
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Residues in contact with PHE 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 5.1 1.6 - - + -
53C GLY 5.0 0.7 - - - -
54C ILE 3.8 8.7 - - - -
55C ILE* 3.6 30.7 - - + -
81C PRO* 3.9 18.2 - - + -
82C VAL 3.7 12.8 - - - -
83C LEU* 3.5 47.8 - - + -
121C LEU* 3.7 16.9 - - + +
176C PHE* 4.4 6.1 - + - -
193C ILE 3.1 7.2 + - - +
194C LEU* 3.6 8.1 - - + +
195C ALA 3.3 0.2 - - - -
196C HIS* 1.3 78.5 - - - +
198C VAL* 1.3 66.8 + - + +
201C ILE* 3.4 21.8 - - + +
202C CYS* 2.9 47.0 + - - -
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Residues in contact with VAL 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 4.0 22.9 - - + -
27C VAL* 4.3 21.3 - - + -
30C ILE* 4.4 11.2 - - + -
32C VAL* 3.4 41.5 - - + -
55C ILE* 4.8 2.9 - - + -
194C LEU 3.0 20.6 + - - +
195C ALA* 4.3 3.4 - - - +
197C PHE* 1.3 86.7 - - + +
199C ILE* 1.3 65.8 + - - +
202C CYS* 3.4 12.7 - - - +
204C CYS* 3.3 20.1 + - + +
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Residues in contact with ILE 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LYS* 4.7 11.4 - - - +
30C ILE* 3.8 23.1 - - + +
32C VAL* 4.4 6.1 - - + -
195C ALA* 2.8 25.2 + - + +
198C VAL* 1.3 72.3 - - - +
200C HIS* 1.3 80.6 + - + +
203C GLN* 3.2 24.1 - - - -
204C CYS 3.3 22.0 + - - +
206C PRO* 3.7 34.5 - - + -
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Residues in contact with HIS 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LYS* 4.2 27.8 + - - +
389A GLU* 5.3 4.0 - - - -
120C PHE* 5.3 4.3 - - + +
195C ALA 6.0 0.2 - - - -
196C HIS* 3.2 46.3 + + + +
199C ILE* 1.3 89.3 - - + +
201C ILE* 1.3 66.4 + - + +
203C GLN* 3.0 26.3 + - - +
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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
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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