Contacts of the helix formed by residues 217 - 226 (chain A) in PDB entry 1TQN
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 ASP 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A ASP* 3.0 34.4 + - + +
215A PHE 3.4 0.2 - - - -
216A LEU* 1.3 81.2 - - - +
218A PRO* 1.3 75.7 - - + +
219A PHE* 3.4 8.0 + - - +
220A PHE* 3.0 31.5 + - - -
221A LEU* 2.9 18.3 + - - +
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Residues in contact with PRO 218 (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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216A LEU 3.9 1.5 - - - +
217A ASP* 1.3 88.7 - - + +
219A PHE* 1.3 58.2 + - - +
221A LEU* 3.3 9.4 + - + +
222A SER* 2.8 36.5 + - - +
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Residues in contact with PHE 219 (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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109A GLY* 5.6 0.2 - - - -
110A PRO* 4.1 13.2 - - + -
217A ASP* 3.2 9.4 + - - +
218A PRO* 1.3 78.0 - - - +
220A PHE* 1.3 82.7 + + - +
222A SER* 3.1 9.5 + - - -
223A ILE* 2.9 48.9 + - + +
233A LEU* 4.0 26.2 - - + -
238A ILE* 5.6 5.8 - - + -
240A VAL* 3.8 24.9 - - + -
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Residues in contact with PHE 220 (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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108A PHE* 3.8 22.7 - + - -
213A PHE* 3.9 33.0 - + + -
214A ASP 3.3 11.9 - - - -
215A PHE* 3.5 51.8 - + + +
217A ASP* 3.0 31.7 + - - +
219A PHE* 1.3 89.2 - + - +
221A LEU* 1.3 66.1 + - - +
223A ILE* 3.2 5.0 + - + +
224A THR* 2.9 29.3 + - - +
240A VAL* 3.7 31.9 - - + -
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Residues in contact with LEU 221 (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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50A ILE* 4.4 32.1 - - + +
53A TYR* 5.1 1.3 - - + -
215A PHE 4.0 5.2 - - - +
216A LEU* 3.2 46.7 - - + +
217A ASP 2.9 18.1 + - - +
218A PRO* 3.8 7.2 - - + +
220A PHE* 1.3 75.9 - - - +
222A SER* 1.3 63.8 + - - +
224A THR* 3.2 8.0 + - + +
225A VAL* 3.0 30.0 + - + +
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Residues in contact with SER 222 (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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218A PRO* 2.8 24.8 + - - +
219A PHE* 3.1 8.0 + - - -
221A LEU* 1.3 78.6 - - - +
223A ILE* 1.3 53.8 + - - +
225A VAL* 3.1 4.6 + - - +
226A PHE* 2.7 60.7 + - - -
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Residues in contact with ILE 223 (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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108A PHE 4.0 15.5 - - - +
109A GLY* 4.5 0.4 - - - -
110A PRO* 5.1 1.3 - - + -
219A PHE* 2.9 43.4 + - + +
220A PHE* 3.2 8.5 + - + +
222A SER* 1.3 77.7 - - - +
224A THR* 1.3 59.2 + - - +
226A PHE* 4.1 10.8 - - + +
227A PRO* 2.9 29.0 - - + +
229A LEU* 4.3 14.6 - - + -
230A ILE* 3.5 35.7 - - + -
233A LEU* 3.9 24.2 - - + -
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Residues in contact with THR 224 (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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50A ILE* 4.1 14.6 - - + -
76A ASP* 3.6 40.8 - - + +
77A GLY* 3.9 11.1 - - - +
78A GLN 4.9 1.2 + - - -
106A ARG* 5.9 0.2 - - - +
215A PHE 5.2 2.3 + - - -
220A PHE* 2.9 17.9 + - - +
221A LEU* 3.4 16.2 - - + +
222A SER 3.1 0.2 - - - -
223A ILE* 1.3 78.1 - - - +
225A VAL* 1.3 62.7 + - + +
227A PRO* 3.2 14.1 - - - +
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Residues in contact with VAL 225 (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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46A PHE* 3.9 32.3 - - + +
47A LEU* 4.0 19.7 - - + +
50A ILE* 3.5 28.9 - - + -
77A GLY* 4.9 1.3 - - - -
78A GLN* 6.0 2.1 - - - +
221A LEU 3.0 17.5 + - - +
222A SER* 3.8 5.4 - - - +
224A THR* 1.3 79.3 - - + +
226A PHE* 1.3 79.4 + - + +
227A PRO* 3.3 6.4 - - - +
228A PHE* 4.3 5.0 - - - -
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Residues in contact with PHE 226 (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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222A SER* 2.7 42.1 + - - +
223A ILE* 3.2 9.1 - - - +
225A VAL* 1.3 95.8 - - + +
227A PRO* 1.3 59.5 - - - +
228A PHE* 3.0 24.5 - + + -
229A LEU* 2.8 54.0 + - + +
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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