Contacts of the helix formed by residues 206 - 224 (chain A) in PDB entry 4Q9U
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 LYS 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PHE* 6.0 1.0 - - - -
203A ARG* 3.3 26.9 + - - +
204A VAL 3.0 0.6 - - - -
205A GLU* 1.3 79.4 - - - +
207A ILE* 1.3 56.1 + - - +
208A MET 3.4 0.4 - - - -
209A ASP* 2.6 31.5 - - - +
210A GLN* 5.1 0.3 - - - +
285A ARG* 6.2 0.9 - - - +
346A ARG* 4.9 0.7 - - - +
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 6.4 0.2 - - + -
145A PHE* 3.4 39.5 - - + -
203A ARG 4.0 2.4 + - - +
204A VAL* 3.0 27.8 + - + +
206A LYS* 1.3 76.2 - - - +
208A MET* 1.3 70.3 + - + +
209A ASP 3.0 2.9 - - - -
210A GLN* 2.9 32.6 + - + -
211A ILE* 3.1 28.6 + - + +
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Residues in contact with MET 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 5.4 12.9 - - + +
189A VAL* 6.1 3.4 - - + -
190A ALA* 5.3 13.2 - - + -
204A VAL* 3.0 30.0 + - + +
205A GLU* 3.9 11.9 - - - +
206A LYS 3.4 0.2 - - - -
207A ILE* 1.3 80.7 - - + +
209A ASP* 1.3 63.8 + - - +
211A ILE* 3.5 26.7 - - + +
212A GLU* 3.7 15.8 - - - +
343A ASN* 3.5 50.0 - - + +
345A SER* 4.5 4.7 - - - +
346A ARG* 4.5 10.7 - - + -
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Residues in contact with ASP 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLU 4.3 1.4 + - - -
206A LYS* 2.6 30.9 - - - +
208A MET* 1.3 79.0 - - - +
210A GLN* 1.3 84.2 + - - +
212A GLU* 3.1 9.1 - - - +
213A LYS* 3.0 26.5 + - - +
285A ARG* 3.0 62.8 + - + +
346A ARG* 3.0 22.4 + - - +
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Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLU* 4.1 11.5 + - - +
142A PHE* 2.9 42.7 - - + +
145A PHE* 3.4 44.8 - - + +
206A LYS 5.1 0.4 - - - +
207A ILE* 2.9 16.7 + - + +
209A ASP* 1.3 85.7 + - - +
211A ILE* 1.3 67.7 + - - +
213A LYS* 2.9 36.1 + - - +
214A TYR 3.1 0.2 + - - -
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Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 3.6 19.5 - - + -
156A ILE* 5.9 6.1 - - + -
160A THR* 6.4 1.8 - - + -
185A PHE* 6.3 3.4 - - + -
186A TYR* 5.6 8.5 - - + -
189A VAL* 6.1 5.4 - - + -
207A ILE* 3.1 38.6 + - + +
208A MET* 3.5 34.8 - - + +
210A GLN* 1.3 77.3 - - - +
212A GLU* 1.3 67.2 + - + +
213A LYS 3.0 0.3 + - - -
214A TYR* 3.0 13.7 + - - +
215A ILE* 3.6 12.5 + - + +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 2.8 29.8 + - + +
208A MET 3.7 11.9 - - - +
209A ASP* 3.1 17.9 - - - +
211A ILE* 1.3 81.8 - - - +
213A LYS* 1.3 62.7 + - - +
215A ILE* 2.9 28.3 - - + +
216A MET* 3.1 17.6 + - + +
283A VAL* 3.5 3.9 - - + +
284A PRO* 3.1 24.1 - - - +
285A ARG* 3.0 35.0 + - - +
288A LEU* 5.0 0.3 - - - +
341A PHE 4.7 0.3 - - - -
342A CYS* 3.5 19.6 - - - -
343A ASN 3.9 1.8 + - - -
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 4.8 4.7 - - + -
142A PHE* 5.5 0.4 - - + -
209A ASP* 3.0 27.2 + - - +
210A GLN* 2.9 28.1 + - - +
212A GLU* 1.3 78.9 - - - +
214A TYR* 1.3 63.0 + - - +
216A MET* 4.0 1.0 - - - +
217A THR* 3.1 27.5 + - - +
282A ARG* 5.4 3.9 - - - +
283A VAL* 3.7 26.1 - - + +
285A ARG* 3.4 40.3 - - + +
286A ASP* 3.1 29.9 + - - +
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Residues in contact with TYR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.5 26.4 - - + +
139A SER* 4.0 27.9 + - - -
142A PHE* 3.2 43.9 - + + -
143A ILE* 6.3 1.6 - - + -
157A TYR* 4.3 21.0 + + - -
161A LYS* 4.1 26.2 + - + -
164A LEU* 4.8 18.6 - - + -
210A GLN 3.1 4.8 + - - -
211A ILE 3.0 5.2 + - - +
213A LYS* 1.3 78.9 - - - +
215A ILE* 1.3 69.7 + - + +
217A THR* 3.4 11.3 + - - -
218A ARG* 3.8 26.7 + - + +
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Residues in contact with ILE 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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164A LEU* 3.4 46.2 - - + -
185A PHE* 4.1 25.1 - - + -
186A TYR* 4.2 11.2 - - + -
211A ILE* 3.6 4.9 + - + +
212A GLU* 2.9 36.8 - - + +
214A TYR* 1.3 79.6 - - + +
216A MET* 1.3 89.1 + - + +
217A THR 3.0 1.0 + - - -
218A ARG* 3.1 7.0 + - - +
219A LEU* 2.8 28.6 + - + +
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Residues in contact with MET 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA* 6.2 2.7 - - + -
186A TYR* 4.5 11.0 - - + +
212A GLU* 3.1 17.6 + - + +
213A LYS 4.3 0.9 - - - +
215A ILE* 1.3 103.4 - - + +
217A THR* 1.3 63.2 - - - +
219A LEU* 4.1 15.5 - - + -
220A TYR* 2.8 27.5 + - - +
223A VAL* 5.0 4.5 - - - -
282A ARG* 4.1 10.0 - - - +
283A VAL* 4.2 9.4 - - - -
284A PRO* 3.7 16.4 - - + -
337A TYR* 3.2 27.8 - - + +
341A PHE* 4.0 28.5 - - + -
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Residues in contact with THR 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU* 3.1 38.8 - - + +
135A THR* 3.8 18.0 + - - +
138A VAL* 3.0 33.1 - - + +
213A LYS* 3.1 11.9 + - - +
214A TYR* 3.7 9.4 - - + -
215A ILE 3.0 1.4 + - - -
216A MET* 1.3 78.0 - - - +
218A ARG* 1.3 61.7 + - + +
220A TYR* 4.6 3.5 + - - +
221A LYS 5.7 0.2 + - - -
282A ARG* 4.6 19.5 + - - +
283A VAL* 5.9 0.7 - - - +
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Residues in contact with ARG 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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135A THR* 3.6 34.4 + - + +
139A SER* 5.6 5.3 + - - -
161A LYS* 3.5 35.6 - - - +
214A TYR* 3.8 25.2 + - + +
215A ILE* 3.1 7.2 + - - +
217A THR* 1.3 81.5 - - + +
219A LEU* 1.3 65.3 + - + +
220A TYR 3.7 0.6 + - - -
221A LYS* 3.0 37.6 + - - +
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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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164A LEU* 4.9 13.9 - - + -
167A MET* 4.8 21.1 - - + -
168A HIS* 5.8 1.1 - - + +
215A ILE* 2.8 25.0 + - + +
216A MET* 3.0 14.3 + - + -
218A ARG* 1.3 81.9 - - + +
220A TYR* 1.3 66.8 + - - +
221A LYS* 3.1 3.6 - - - -
222A TYR* 2.8 41.7 + - + +
223A VAL* 3.0 31.3 + - + +
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Residues in contact with TYR 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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216A MET* 2.8 20.4 + - - +
217A THR 5.0 2.7 - - - +
218A ARG 3.7 0.6 - - - -
219A LEU* 1.3 70.8 - - - +
221A LYS* 1.3 57.0 + - + +
223A VAL* 3.0 8.7 + - - -
224A PHE* 2.8 69.2 + + + -
279A ASP* 4.4 13.0 + - - -
280A SER 6.0 1.1 - - - -
281A LYS 5.3 0.4 - - - -
282A ARG* 4.3 29.2 - - + +
287A LYS* 4.9 10.1 - - - -
330A ARG* 3.7 23.7 + - - -
334A ASN* 5.4 2.6 + - - -
337A TYR* 3.1 36.3 - + - +
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Residues in contact with LYS 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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135A THR* 3.8 28.0 + - - +
218A ARG* 3.0 29.2 + - - +
219A LEU* 6.0 0.7 - - - -
220A TYR* 1.3 82.7 - - + +
222A TYR* 1.3 90.3 + - + +
224A PHE* 2.9 29.1 - - + +
227A GLU* 5.4 2.9 - - - +
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Residues in contact with TYR 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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167A MET 4.4 4.7 - - - -
168A HIS* 2.9 51.2 + - + +
171A ARG* 3.7 36.1 - - + -
178A GLN* 5.4 2.3 - - - +
219A LEU* 2.8 29.5 + - + +
221A LYS* 1.3 105.6 - - + +
223A VAL* 1.3 70.4 + - + +
224A PHE 3.7 3.0 + - - +
226A PRO* 5.4 5.9 - - - +
227A GLU* 5.1 7.6 - - - +
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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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175A ILE* 5.5 0.2 - - - +
178A GLN* 5.0 10.5 - - - +
216A MET* 5.0 2.5 - - - -
219A LEU* 3.1 39.3 - - + +
220A TYR* 3.0 12.8 + - - +
222A TYR* 1.3 88.0 - - + +
224A PHE* 1.3 66.3 + - - +
225A CYS 3.7 1.6 + - - -
226A PRO* 3.9 14.0 - - - +
337A TYR* 4.0 13.5 - - + +
340A ARG* 4.7 5.2 + - - -
341A PHE* 3.3 44.4 - - + -
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Residues in contact with PHE 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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220A TYR* 2.8 63.9 + + + -
221A LYS* 2.9 28.3 - - + -
222A TYR 4.4 2.6 - - - +
223A VAL* 1.3 74.1 - - - +
225A CYS* 1.3 82.4 + - + +
226A PRO* 3.4 1.6 - - - +
227A GLU* 4.7 10.1 - - - +
330A ARG* 3.5 28.9 - - - -
333A SER* 4.7 2.0 - - - +
337A TYR* 3.8 13.0 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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