Contacts of the helix formed by residues 189 - 200 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ILE* 3.8 19.1 - - + -
126A GLU 4.4 14.7 + - - +
127A ASP* 3.3 37.2 + - - +
137A LEU* 4.9 5.2 - - + -
138A ASP 5.3 0.2 + - - -
187A THR 3.3 0.8 - - - -
188A PRO* 1.3 78.8 - - - +
190A GLY* 1.3 64.2 + - - +
191A HIS* 3.2 10.0 - - - -
192A ARG* 2.9 56.5 + - - +
193A ILE* 3.3 13.5 + - - +
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO* 3.2 35.0 - - - +
187A THR* 2.8 23.1 + - - -
188A PRO 3.2 0.4 - - - -
189A GLN* 1.3 76.7 - - - +
191A HIS* 1.3 61.8 + - - +
193A ILE* 3.1 10.8 + - - +
194A LEU* 3.1 20.5 + - - +
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Residues in contact with HIS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 4.6 20.8 - - - +
30A ILE* 4.3 6.4 - - + +
182A PRO 3.9 3.1 + - - -
187A THR 4.8 0.2 + - - -
188A PRO 3.2 23.4 + - - -
189A GLN* 3.9 6.7 - - - -
190A GLY* 1.3 76.5 - - - +
192A ARG* 1.3 84.6 + - + +
194A LEU* 3.6 9.5 + - - +
195A ALA* 3.0 27.8 + - + +
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASP 4.6 2.0 + - - -
124A GLY* 4.3 5.9 - - - -
125A ILE* 3.1 50.0 - - + +
126A GLU 4.5 2.8 + - - +
189A GLN* 2.9 39.8 + - - +
191A HIS* 1.3 101.2 - - + +
193A ILE* 1.3 58.9 + - - +
195A ALA* 3.2 6.4 + - - +
196A HIS* 2.8 42.2 + - + -
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 5.8 1.6 - - + -
121A LEU* 3.6 40.2 - - + +
122A PHE* 3.9 13.2 - - + -
125A ILE* 4.1 14.8 - - + -
137A LEU* 3.7 27.4 - - + -
178A LEU* 4.1 18.6 - - + -
180A PHE* 4.0 18.8 - - + -
182A PRO* 4.6 4.5 - - + -
187A THR* 5.5 0.7 - - - +
189A GLN 3.7 12.1 - - - +
190A GLY* 3.1 14.7 + - - +
192A ARG* 1.3 77.9 - - - +
194A LEU* 1.3 62.3 + - + +
196A HIS* 3.1 5.4 + - - +
197A PHE 3.1 17.2 + - - -
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.6 9.9 - - + +
26A ARG* 4.1 24.5 - - + -
27A VAL* 5.0 5.2 - - + -
30A ILE* 4.0 11.4 - - + -
55A ILE* 3.9 27.1 - - + -
83A LEU* 4.0 16.8 - - + -
85A ILE* 4.8 1.8 - - + -
182A PRO* 4.1 25.6 - - + +
183A GLU* 4.1 17.5 - - + +
190A GLY 3.1 19.1 + - - +
191A HIS* 3.9 5.4 - - - +
193A ILE* 1.3 74.0 - - + +
195A ALA* 1.3 60.9 + - - +
197A PHE* 3.2 5.0 + - + +
198A VAL* 3.0 34.9 + - + +
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.6 25.8 - - + +
191A HIS* 3.0 20.3 + - + +
192A ARG* 3.5 8.5 - - - +
194A LEU* 1.3 77.4 - - - +
196A HIS* 1.3 62.0 + - + +
198A VAL 4.0 0.2 - - - -
199A ILE* 3.0 37.5 + - + +
200A HIS* 4.5 1.3 - - - -
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Residues in contact with HIS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE 3.3 24.3 + - - +
121A LEU* 4.1 12.3 + - - +
123A ASP* 2.9 40.2 + - + -
125A ILE* 4.3 9.3 - - + +
192A ARG* 2.8 33.4 + - + +
193A ILE 3.1 9.4 + - - +
195A ALA* 1.3 79.6 - - + +
197A PHE* 1.3 64.6 + - - +
200A HIS* 3.2 32.5 + + + +
201A ILE* 3.1 24.9 + - - +
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Residues in contact with PHE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 5.1 2.0 - - + -
53A GLY 4.8 1.1 - - - -
54A ILE 3.5 27.8 - - - -
55A ILE* 3.7 21.1 - - + -
81A PRO* 3.8 20.0 - - + -
82A VAL 3.6 11.4 - - - -
83A LEU* 3.5 37.5 - - + -
121A LEU* 3.8 17.4 - - + +
176A PHE* 4.2 9.9 - + - -
193A ILE 3.1 8.2 + - - +
194A LEU* 3.2 7.4 + - - +
196A HIS* 1.3 78.8 - - - +
198A VAL* 1.3 63.7 + - + +
201A ILE* 3.4 17.6 - - + +
202A CYS* 2.9 52.7 + - - -
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Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 4.1 21.5 - - + -
27A VAL* 4.3 22.7 - - + -
30A ILE* 4.6 11.9 - - + -
32A VAL* 3.7 35.7 - - + -
55A ILE* 5.0 3.4 - - + -
194A LEU* 3.0 18.4 + - + +
195A ALA 4.5 0.9 - - - +
197A PHE* 1.3 86.3 - - + +
199A ILE* 1.3 64.9 + - + +
202A CYS* 3.4 16.7 - - - +
204A CYS* 3.2 20.9 + - + +
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.7 31.4 - - + +
32A VAL* 4.4 7.0 - - + -
195A ALA* 3.0 20.5 + - + +
198A VAL* 1.3 76.2 - - - +
200A HIS* 1.3 80.9 + - + +
203A GLN* 3.3 23.2 + - - -
204A CYS 3.6 21.5 + - - +
206A PRO* 3.9 25.6 - - + -
211C LYS* 4.6 10.8 - - - +
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Residues in contact with HIS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 5.6 3.4 - - + +
195A ALA 4.5 2.7 - - - -
196A HIS* 3.2 49.5 + + + +
199A ILE* 1.3 87.8 + - + +
201A ILE* 1.3 68.2 + - + +
203A GLN* 3.5 24.9 + - - +
211C LYS* 3.9 29.6 + - - -
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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