Contacts of the helix formed by residues 214 - 227 (chain A) in PDB entry 1ZQ1
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A GLY 4.2 0.5 - - - +
204A ALA* 3.6 1.1 - - - +
205A GLN* 2.9 28.1 + - - +
206A ARG* 2.9 28.9 + - - +
212A SER 3.4 1.2 + - - -
213A SER* 1.3 71.3 - - - +
215A ALA* 1.3 64.7 + - - +
216A ALA 3.5 0.9 - - - -
217A MSE 3.8 3.4 + - - +
218A ASN* 3.0 45.2 + - - +
237A MSE 5.2 1.6 - - - +
238A HIS* 3.4 28.0 + - + +
243A ASP* 5.5 1.1 - - - -
262A ARG* 3.8 24.8 - - - +
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Residues in contact with ALA 215 (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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103A ILE* 3.8 31.0 - - + +
203A GLY 5.2 0.7 - - - -
204A ALA* 3.7 19.5 - - + +
208A SER* 4.0 11.9 - - - +
213A SER* 3.1 18.6 + - - +
214A ASP* 1.3 79.2 + - - +
216A ALA* 1.3 68.4 + - - +
218A ASN* 3.2 6.6 + - - +
219A LEU* 2.9 19.4 + - - +
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Residues in contact with ALA 216 (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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103A ILE 5.0 1.0 + - - -
127A LEU* 3.9 16.2 - - + -
213A SER* 4.4 6.9 + - - +
214A ASP 3.5 0.4 - - - -
215A ALA* 1.3 75.9 - - - +
217A MSE 1.3 55.8 + - - +
219A LEU* 2.7 26.5 + - - +
220A ILE* 3.0 17.5 + - + +
51C ARG* 3.4 48.0 - - - +
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Residues in contact with MSE 217 (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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213A SER 5.4 0.2 + - - -
214A ASP* 3.8 3.6 + - - +
215A ALA 3.6 0.4 - - - -
216A ALA* 1.3 78.6 - - - +
218A ASN* 1.3 61.8 + - - +
220A ILE* 3.9 11.4 - - - +
221A CYS* 3.0 27.5 + - - +
238A HIS* 3.8 31.0 - - + -
243A ASP* 3.2 31.9 - - + +
244A THR 3.9 17.9 - - - +
245A TYR 4.6 1.6 - - - -
246A CYS* 4.3 7.6 - - - -
278A PRO* 3.4 24.0 - - + -
49C ARG* 2.8 41.5 - - - +
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Residues in contact with ASN 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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202A VAL* 3.6 19.8 - - + +
203A GLY 2.9 22.7 - - - +
214A ASP* 3.0 32.2 + - - +
215A ALA* 3.4 4.7 - - - +
216A ALA 2.9 1.0 + - - -
217A MSE 1.3 76.6 - - - +
219A LEU* 1.3 57.3 + - - +
221A CYS* 3.8 1.7 - - - +
222A SER* 2.8 30.7 + - - -
236A VAL* 4.0 3.0 - - - +
237A MSE 3.4 13.8 - - - +
238A HIS* 3.0 32.2 + - - +
246A CYS* 3.5 18.0 - - - -
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Residues in contact with LEU 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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96A ILE* 4.1 20.6 - - + -
103A ILE* 3.4 29.6 - - + -
123A LEU* 5.0 8.3 - - + -
127A LEU* 3.1 28.0 - - + -
130A ILE* 4.1 16.2 - - + -
173A VAL* 4.5 7.4 - - + -
202A VAL* 4.2 5.1 - - + +
215A ALA 2.9 9.0 + - - +
216A ALA 2.7 14.8 + - - +
218A ASN* 1.3 67.6 - - - +
220A ILE* 1.3 67.4 + - - +
222A SER* 2.4 28.0 + - - +
223A VAL* 2.8 26.9 + - + +
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Residues in contact with ILE 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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127A LEU* 3.8 11.0 - - + -
129A GLU* 3.4 46.9 - - + -
130A ILE* 4.3 10.1 - - + +
133A VAL* 5.8 2.0 - - + -
216A ALA* 3.0 16.8 + - + +
217A MSE 3.9 11.0 - - - +
219A LEU* 1.3 77.8 - - - +
221A CYS* 1.3 66.2 + - - +
223A VAL* 3.0 2.1 + - - +
224A ARG* 3.0 36.3 + - + +
278A PRO* 3.4 42.6 - - + +
49C ARG* 5.9 2.0 - - - +
51C ARG* 5.4 0.7 - - - +
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Residues in contact with CYS 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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217A MSE 3.0 18.8 + - - +
218A ASN 3.9 0.2 - - - +
220A ILE* 1.3 80.7 - - - +
222A SER* 1.3 63.9 + - - +
224A ARG* 3.4 7.8 + - - +
225A MSE 3.2 16.1 + - - +
236A VAL* 3.8 1.3 - - + -
246A CYS* 3.4 29.4 - - - -
276A ILE* 3.2 38.0 - - + +
277A TRP 3.7 6.3 - - - -
278A PRO* 3.5 34.5 - - - -
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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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173A VAL* 4.0 7.2 - - - +
200A VAL* 3.5 13.0 - - - +
202A VAL* 3.0 36.4 - - - +
218A ASN 2.8 14.1 + - - -
219A LEU* 2.4 39.0 + - - +
221A CYS* 1.3 78.2 - - - +
223A VAL* 1.3 55.7 + - - +
225A MSE 3.0 5.7 + - - +
226A ALA* 2.9 25.1 + - - +
236A VAL* 3.7 9.2 - - - +
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Residues in contact with VAL 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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94A VAL* 4.1 26.7 - - + -
96A ILE* 5.0 6.1 - - + -
130A ILE* 3.3 34.3 - - + +
133A VAL* 4.1 19.7 - - + -
134A ALA* 4.3 7.6 - - + -
136A VAL* 5.2 1.3 - - + -
173A VAL* 4.2 9.0 - - + -
219A LEU* 2.8 28.0 + - + +
220A ILE 3.7 5.4 - - - +
222A SER* 1.3 67.7 - - - +
224A ARG* 1.3 65.9 + - + +
225A MSE 2.9 4.7 - - - -
226A ALA* 2.8 18.9 + - - +
227A THR* 3.0 12.0 + - - +
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Residues in contact with ARG 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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129A GLU* 5.5 2.2 + - - +
132A GLU 5.3 0.4 + - - -
133A VAL* 3.7 39.0 - - + +
220A ILE* 3.0 28.8 + - + +
221A CYS* 3.6 9.6 - - - +
223A VAL* 1.3 75.3 - - - +
225A MSE 1.3 57.8 + - - +
227A THR* 3.3 22.3 - - - +
228A SER* 3.1 12.7 + - - -
276A ILE* 4.9 10.8 - - + -
277A TRP 4.8 3.8 - - - +
278A PRO 3.2 26.2 + - - +
279A ASN* 3.5 15.9 + - - +
280A GLY* 3.9 21.1 - - - +
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Residues in contact with MSE 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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198A PRO* 3.3 11.5 - - - +
200A VAL* 4.2 2.7 - - + -
221A CYS 3.2 1.8 + - - +
222A SER 3.0 9.1 + - - +
223A VAL 2.9 1.0 - - - -
224A ARG* 1.3 74.9 - - - +
226A ALA* 1.3 55.0 + - - +
227A THR 2.8 5.8 - - - -
228A SER* 2.8 43.0 + - - +
230A VAL* 4.0 16.8 - - + -
234A MSE 3.2 47.0 - - + +
236A VAL* 4.1 8.1 - - + -
248A ALA* 4.0 11.0 - - + -
273A ILE* 4.8 3.6 - - + -
274A ALA* 5.4 2.5 - - + -
276A ILE* 3.2 54.5 - - + -
282A ILE* 4.1 9.9 - - + -
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Residues in contact with ALA 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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94A VAL* 4.0 19.3 - - + -
170A TYR 4.2 0.3 - - - -
171A GLY* 3.5 14.5 + - - -
172A VAL 4.0 8.1 - - - +
173A VAL* 3.5 30.1 - - + -
198A PRO* 3.2 29.3 - - - +
200A VAL* 4.0 4.0 - - - +
222A SER 2.9 4.9 + - - -
223A VAL 2.8 9.7 + - - +
225A MSE 1.3 75.6 - - - +
227A THR* 1.3 56.4 + - - +
292A ARG* 3.3 8.3 + - - -
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Residues in contact with THR 227 (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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92A PRO* 4.4 6.2 - - + +
94A VAL* 4.5 3.8 - - - +
133A VAL* 4.3 20.8 + - + +
134A ALA* 4.4 9.9 - - - +
170A TYR* 3.8 24.7 + - + -
223A VAL 3.0 9.8 + - - -
224A ARG* 3.3 16.8 - - - +
226A ALA* 1.3 77.1 - - - +
228A SER* 1.3 61.6 + - - +
292A ARG* 3.7 10.1 + - - +
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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