Contacts of the helix formed by residues 220 - 233 (chain A) in PDB entry 3QJQ
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A PHE* 5.2 4.1 - - + -
219A VAL* 1.3 74.7 - - - +
221A PRO* 1.3 66.9 - - - +
222A LEU* 2.9 21.7 + - - +
223A VAL* 3.2 24.9 + - + +
224A ALA* 2.9 28.8 + - - +
553A LEU* 3.7 16.9 - - + +
554A ASN 2.8 36.4 + - - +
555A PRO* 3.9 3.7 - - + +
52B ARG* 2.8 19.2 + - - -
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Residues in contact with PRO 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO* 4.4 19.6 - - + +
138A PRO* 4.8 1.8 - - + -
219A VAL 3.1 11.9 - - - +
220A ASP* 1.3 88.9 - - - +
222A LEU* 1.3 56.2 + - - +
224A ALA* 4.0 5.1 - - + +
225A ARG* 2.9 35.3 + - - +
554A ASN 4.2 5.6 - - - +
556A VAL* 4.1 14.6 - - + -
52B ARG* 6.0 1.3 - - - +
113B ILE* 4.7 2.5 - - + +
128B LEU* 3.9 24.0 - - + -
129B PRO* 3.5 33.2 - - + +
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Residues in contact with LEU 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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220A ASP* 2.9 10.8 + - - +
221A PRO* 1.3 77.0 - - - +
223A VAL* 1.3 58.8 + - - +
225A ARG* 3.9 0.8 - - - -
226A THR* 2.3 39.3 + - - +
284A GLN* 4.0 9.8 + - - +
287A ASP* 4.2 13.9 - - + +
288A PRO* 3.3 31.4 - - + +
289A GLY* 3.6 18.4 - - - +
290A ILE* 4.5 3.6 - - + -
549A LEU* 4.2 12.1 - - + -
50B LEU* 3.8 21.8 - - + -
52B ARG* 4.8 8.7 - - - +
128B LEU* 3.8 21.0 - - + +
131B GLU* 4.2 10.8 - - + +
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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
----------------------------------------------------------
207A PHE* 3.9 35.0 - - + -
220A ASP* 3.2 33.5 + - + +
222A LEU* 1.3 74.5 - - - +
224A ALA* 1.3 62.5 + - + +
226A THR* 3.2 5.1 + - - -
227A LEU* 2.8 36.9 + - + +
546A LEU* 5.8 2.4 - - + +
549A LEU* 3.9 29.8 - - + +
550A PHE* 4.9 13.0 - - + +
553A LEU* 3.5 16.2 - - + -
52B ARG* 4.9 2.0 - - - +
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Residues in contact with ALA 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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137A PRO* 3.8 25.4 - - + -
203A GLU* 3.5 29.0 - - + +
207A PHE* 5.8 2.5 - - + -
219A VAL* 4.1 9.0 - - + -
220A ASP 2.9 18.1 + - - +
221A PRO 4.0 2.5 - - - +
223A VAL* 1.3 78.0 - - + +
225A ARG* 1.3 60.9 + - - +
227A LEU* 5.5 0.4 - - - -
228A PHE* 2.9 32.4 + - - +
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Residues in contact with ARG 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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136A TYR* 3.2 54.9 + - + -
137A PRO* 5.9 1.1 - - + -
221A PRO 2.9 20.8 + - - +
222A LEU* 4.2 0.9 - - - +
224A ALA* 1.3 78.3 - - - +
226A THR* 1.3 56.1 + - - +
228A PHE* 3.8 4.8 - - - +
229A TRP* 2.9 41.4 + - - +
283A HIS 3.9 12.9 + - - -
284A GLN* 3.3 20.7 - - + +
287A ASP* 2.8 37.6 + - - -
376A HIS* 5.7 0.2 - - - -
113B ILE* 4.0 16.5 - - + +
126B GLU* 3.0 29.1 + - - -
128B LEU* 4.1 17.2 - - - +
151B GLN* 4.5 0.8 - - - +
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Residues in contact with THR 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 LEU* 2.3 30.3 + - - +
223A VAL* 3.4 7.0 - - - -
225A ARG* 1.3 73.8 - - - +
227A LEU* 1.3 68.1 + - - +
228A PHE 3.2 0.4 - - - -
229A TRP* 2.9 12.8 + - - +
230A TRP* 3.1 13.1 + - - +
281A PHE* 4.2 17.3 - - + -
284A GLN* 2.8 29.6 + - - +
290A ILE* 4.6 1.7 - - + +
542A TYR* 4.3 12.2 - - + -
545A THR* 4.8 4.0 - - + -
546A LEU* 4.6 13.2 - - + -
549A LEU* 4.2 15.9 - - + +
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Residues in contact with LEU 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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199A GLY* 3.6 33.6 - - - +
202A LEU* 4.1 24.5 - - + -
203A GLU* 3.7 33.0 - - + +
206A LEU* 5.7 0.4 - - + -
207A PHE* 4.1 21.8 - - + -
223A VAL* 2.8 23.3 + - + +
224A ALA 4.1 0.7 - - - +
226A THR* 1.3 70.7 - - - +
228A PHE* 1.3 66.4 - - - +
230A TRP* 3.1 29.2 + - + +
546A LEU* 4.1 24.8 - - + +
550A PHE* 4.6 13.9 - - + -
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Residues in contact with PHE 228 (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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133A TYR* 4.2 4.5 - + - -
134A THR* 3.8 33.9 - - + -
135A PHE* 3.7 27.1 - + - -
136A TYR* 4.3 8.3 - + + -
200A LEU* 3.9 16.8 - - + +
203A GLU* 3.1 25.7 + - - +
224A ALA 2.9 21.6 + - - +
225A ARG* 3.8 4.0 - - - +
227A LEU* 1.3 80.1 - - - +
229A TRP* 1.3 110.4 + + - +
231A THR* 3.1 14.0 + - - -
232A GLY* 3.2 14.4 + - - -
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Residues in contact with TRP 229 (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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133A TYR* 5.4 1.3 - + - -
134A THR* 4.3 3.1 - - + -
136A TYR* 3.1 30.4 + - - -
225A ARG* 2.9 36.3 + - + +
226A THR 2.9 6.7 + - - +
228A PHE* 1.3 90.7 - + - +
230A TRP* 1.3 56.5 + - - +
231A THR 2.8 11.4 + - - -
232A GLY* 2.8 47.1 - - - -
233A HIS* 3.3 16.5 + - - +
234A PRO* 4.4 0.2 - - - +
280A GLY* 3.7 25.7 - - - +
283A HIS* 3.3 47.7 + + + +
284A GLN* 4.1 15.7 - - + +
542A TYR* 3.9 2.7 - - - -
801A HAS 3.5 32.3 - - + -
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Residues in contact with TRP 230 (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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195A LEU* 3.1 24.5 + - + -
196A ALA* 3.2 12.8 + - - +
198A LEU* 3.8 24.0 - - + -
199A GLY* 3.1 20.2 - - - +
202A LEU* 5.4 7.9 - - + -
226A THR 3.1 8.5 + - - +
227A LEU* 3.1 24.7 + - + +
229A TRP* 1.3 74.7 - - - +
231A THR* 1.3 54.1 + - - +
234A PRO* 3.4 19.2 - - - +
277A THR* 3.6 11.2 - - + +
538A VAL* 4.0 23.1 - - + -
542A TYR* 3.3 50.3 + + + -
546A LEU* 3.7 26.9 - - + -
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Residues in contact with THR 231 (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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193A TRP* 4.1 22.9 - - + -
196A ALA 2.7 25.4 + - - +
197A SER* 4.4 2.5 - - - -
199A GLY* 3.3 5.2 - - - -
200A LEU* 2.9 46.2 + - + +
228A PHE 3.4 9.0 - - - -
229A TRP 2.8 0.4 - - - -
230A TRP* 1.3 77.9 - - - +
232A GLY* 1.3 58.9 + - - +
233A HIS 3.1 6.0 + - - -
234A PRO* 3.2 5.1 - - - +
235A ILE* 2.8 32.0 + - + +
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Residues in contact with GLY 232 (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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228A PHE* 3.2 16.0 + - - -
229A TRP* 2.8 37.2 + - - -
231A THR* 1.3 79.2 - - - +
233A HIS* 1.3 59.5 + - - +
235A ILE* 3.6 21.6 - - - +
236A VAL* 4.2 6.4 - - - +
283A HIS* 3.8 3.8 - - - -
801A HAS 5.7 0.3 - - - +
803A CU1 4.1 0.2 - - - -
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Residues in contact with HIS 233 (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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229A TRP* 3.3 8.9 + - - +
231A THR 3.1 0.2 - - - -
232A GLY* 1.3 78.5 - - - +
234A PRO* 1.3 77.1 - - + +
235A ILE 3.2 1.1 - - - -
236A VAL* 3.0 28.2 + - + +
237A TYR* 1.8 54.3 + + - -
276A SER 3.4 13.9 - - - -
279A VAL* 3.6 16.5 - - + +
280A GLY* 4.8 2.5 - - - -
282A HIS* 2.9 17.9 - + + +
283A HIS* 3.4 8.7 - - + +
305A VAL* 4.7 2.3 - - + +
563A CMO 3.3 9.8 + - - -
801A HAS 4.6 1.8 - + - -
803A CU1 1.9 32.0 - - - -
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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