Contacts of the helix formed by residues 209 - 228 (chain A) in PDB entry 1XAI
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 GLY 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A HIS* 3.5 12.3 - - - -
198A PHE* 4.0 0.9 - - - -
207A LEU 3.4 1.0 + - - -
208A ASN* 1.3 81.8 + - - +
210A MET* 1.3 61.5 + - - +
211A ASP* 3.6 1.8 - - - -
212A LYS* 3.8 11.5 + - - +
213A TYR* 2.9 31.5 + - - -
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Residues in contact with MET 210 (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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126A ILE* 4.5 11.9 - - + -
164A LEU* 4.6 8.3 - - + -
172A ILE* 4.7 0.4 - - + -
176A TYR* 3.8 16.6 - - + -
179A VAL* 4.5 13.9 - - - -
198A PHE* 3.8 18.2 - - + -
204A LEU* 3.6 31.0 - - + -
207A LEU* 3.2 40.7 + - + +
208A ASN 3.2 1.6 - - - -
209A GLY* 1.3 74.7 - - - +
211A ASP* 1.3 57.9 + - - +
212A LYS 2.6 17.1 + - - -
213A TYR* 2.7 14.4 + - - +
214A ILE* 3.1 40.1 + - + +
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Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 5.6 0.2 - - - +
18A HIS* 2.2 44.5 + - - -
161A LEU* 4.1 27.1 - - + +
164A LEU* 4.4 9.9 - - - +
207A LEU 4.7 1.4 + - - +
209A GLY* 4.9 0.6 - - - +
210A MET* 1.3 78.8 - - - +
212A LYS* 1.3 59.7 + - - +
214A ILE* 3.8 7.1 + - - +
215A ALA* 3.5 20.6 + - - +
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Residues in contact with LYS 212 (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 ASP* 3.7 9.5 + - - -
209A GLY* 3.8 12.0 + - - +
210A MET 2.6 4.4 + - - -
211A ASP* 1.3 73.9 - - - +
213A TYR* 1.3 111.9 + - + +
214A ILE 3.1 5.5 + - - -
215A ALA* 3.5 5.4 + - - +
216A LYS* 3.2 32.7 + - - +
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Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 3.3 30.7 - - + +
183A ALA* 6.4 0.2 - - + -
190A ALA* 5.1 1.6 - - - -
193A ASP* 3.1 30.0 + - - -
194A ILE* 3.7 34.5 - - + -
197A HIS* 3.6 28.5 + + + +
198A PHE* 3.6 15.7 - + + -
209A GLY 2.9 24.2 - - - -
210A MET* 2.7 11.1 + - - +
212A LYS* 1.3 109.0 + - + +
214A ILE* 1.3 60.7 + - - +
216A LYS* 4.0 21.1 - - + +
217A GLY* 3.4 13.0 + - - -
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Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 5.1 0.7 - - + -
126A ILE* 3.7 31.0 - - + +
129A HIS* 3.7 13.5 - - + -
159A TYR* 3.5 40.4 - - + +
161A LEU* 4.5 7.0 - - + -
164A LEU* 4.1 14.1 - - + -
179A VAL* 4.3 5.8 - - + -
210A MET* 3.4 35.9 - - + +
211A ASP* 4.0 6.7 - - - +
212A LYS 3.1 0.6 - - - -
213A TYR* 1.3 77.9 - - - +
215A ALA* 1.3 58.9 + - - +
216A LYS 3.0 1.3 - - - -
217A GLY* 2.7 19.6 + - - -
218A ILE* 2.8 19.5 + - + +
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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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1A MET* 3.4 34.8 - - + +
16A VAL* 4.9 5.8 - - + +
211A ASP 3.5 14.1 + - - +
212A LYS* 3.5 6.0 + - - +
214A ILE* 1.3 79.4 - - - +
216A LYS* 1.3 57.7 + - - +
218A ILE* 3.5 7.9 + - - +
219A GLU* 3.0 38.3 + - - +
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Residues in contact with LYS 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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183A ALA* 6.0 2.5 - - - +
186A ASN* 3.6 28.2 + - - +
190A ALA* 4.0 21.1 - - - +
193A ASP* 5.8 1.8 - - - -
212A LYS* 3.2 25.7 + - + +
213A TYR* 4.1 28.9 - - + +
214A ILE 3.0 0.4 - - - -
215A ALA* 1.3 80.0 - - - +
217A GLY* 1.3 52.3 + - - +
219A GLU* 4.0 11.6 - - - +
220A THR* 2.4 39.4 + - - +
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Residues in contact with GLY 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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129A HIS* 4.0 6.5 - - - -
179A VAL* 5.7 1.3 - - - -
182A HIS* 3.4 36.7 + - - -
213A TYR 3.4 8.8 + - - -
214A ILE 2.7 10.7 + - - -
216A LYS* 1.3 77.0 - - - +
218A ILE* 1.3 63.8 + - - -
220A THR* 3.3 4.7 + - - -
221A LYS* 3.2 17.2 + - - +
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Residues in contact with ILE 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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3A LEU* 4.1 18.4 - - + -
14A ILE* 4.2 17.3 - - + -
16A VAL* 3.4 33.4 - - + -
129A HIS* 3.7 27.0 - - + +
133A VAL* 4.2 20.5 - - + +
159A TYR* 3.6 24.5 - - + -
182A HIS* 5.5 0.2 - - - -
214A ILE* 2.8 22.0 + - + +
215A ALA* 3.8 7.0 - - - +
217A GLY* 1.3 72.5 - - - +
219A GLU* 1.3 62.3 + - - +
221A LYS* 3.1 7.0 + - - +
222A LEU* 2.9 21.5 + - + +
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Residues in contact with GLU 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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1A MET* 4.0 17.7 - - + +
3A LEU* 4.0 22.7 - - + +
215A ALA* 3.0 26.5 + - - +
216A LYS* 4.0 9.2 - - - +
218A ILE* 1.3 79.8 - - - +
220A THR* 1.3 65.9 + - - +
222A LEU* 2.9 20.2 + - - +
223A ASP* 3.1 21.0 + - - +
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Residues in contact with THR 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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182A HIS* 4.0 35.2 + - + +
185A LEU* 5.1 7.6 - - + -
186A ASN* 3.6 23.6 + - + +
216A LYS* 2.4 26.1 + - - +
217A GLY* 3.5 6.4 - - - -
219A GLU* 1.3 78.3 - - - +
221A LYS* 1.3 58.0 + - - +
223A ASP* 3.6 12.5 - - - +
224A ILE* 3.1 29.5 - - + +
238A LEU* 6.1 0.4 - - + -
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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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129A HIS 5.1 0.2 - - - +
130A ASP* 2.6 53.8 + - - +
131A SER* 4.2 3.8 + - - +
133A VAL* 2.6 30.5 + - + +
182A HIS* 4.3 9.4 + - + +
217A GLY 3.2 11.4 + - - +
218A ILE* 3.1 10.2 + - - +
219A GLU 3.0 0.8 - - - -
220A THR* 1.3 71.9 - - - +
222A LEU* 1.3 57.7 + - - +
223A ASP 2.7 16.2 + - - -
224A ILE* 2.7 17.6 + - - -
225A VAL* 2.9 22.0 + - + +
238A LEU* 3.4 27.1 - - + -
500A CRB 2.9 29.5 + - - +
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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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3A LEU* 4.2 18.4 - - + -
4A GLN 3.9 26.0 - - - +
5A THR* 4.3 4.3 - - + +
6A THR* 5.1 5.2 - - + +
14A ILE* 3.6 28.7 - - + -
133A VAL* 4.6 8.2 - - + +
218A ILE* 2.9 12.3 + - + +
219A GLU* 3.3 11.9 - - - +
221A LYS* 1.3 75.0 - - - +
223A ASP* 1.3 70.8 + - - +
225A VAL* 3.6 10.1 - - - -
226A VAL* 2.9 49.2 + - + +
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Residues in contact with ASP 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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219A GLU* 3.3 17.0 - - - +
220A THR* 3.6 11.4 - - - +
221A LYS 2.7 4.9 + - - -
222A LEU* 1.3 88.4 - - - +
224A ILE* 1.3 62.0 + - + +
225A VAL 3.3 0.2 - - - -
226A VAL* 4.2 1.6 - - - +
227A ALA* 3.0 33.1 + - - +
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Residues in contact with ILE 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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185A LEU* 6.1 5.2 - - + -
220A THR* 3.1 25.4 - - + +
221A LYS 2.7 9.2 + - - +
223A ASP* 1.3 76.2 - - + +
225A VAL* 1.3 56.8 + - - +
227A ALA* 4.0 3.7 - - - +
228A ASP* 3.1 27.2 + - - +
234A VAL* 3.9 20.9 - - + +
235A ARG* 3.5 31.7 - - - +
237A PHE* 5.0 7.0 - - + -
238A LEU* 3.7 31.2 - - + -
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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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5A THR* 5.2 1.3 - - + -
7A TYR* 2.7 25.5 + - + +
12A TYR* 4.9 3.6 - - - +
133A VAL* 4.7 3.8 - - + -
134A GLY* 3.8 19.7 - - - +
221A LYS* 2.9 39.5 + - + +
222A LEU* 3.5 15.7 - - + +
224A ILE* 1.3 77.1 - - - +
226A VAL* 1.3 63.2 + - + +
227A ALA 3.3 0.2 - - - -
229A GLU* 2.9 23.2 + - - -
235A ARG* 3.6 40.4 - - - +
238A LEU* 4.1 2.2 - - + -
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Residues in contact with VAL 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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5A THR* 3.9 21.3 - - + -
6A THR* 3.3 57.7 - - - +
7A TYR* 3.3 25.3 - - + -
222A LEU* 2.9 27.2 + - + +
223A ASP* 4.2 2.7 - - - +
225A VAL* 1.3 78.7 - - + +
227A ALA* 1.3 62.7 + - - +
228A ASP 3.4 0.5 + - - -
229A GLU 4.3 1.2 + - - -
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Residues in contact with ALA 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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223A ASP 3.0 20.1 + - - +
224A ILE* 4.3 4.5 - - - +
226A VAL* 1.3 79.7 - - - +
228A ASP* 1.3 59.9 + - + +
234A VAL* 4.9 7.0 - - + +
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Residues in contact with ASP 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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224A ILE 3.1 9.7 + - - +
225A VAL 3.5 2.7 - - - -
227A ALA* 1.3 81.4 - - - +
229A GLU* 1.3 65.3 + - - +
230A LYS 3.3 1.7 + - - -
231A GLU* 3.0 8.8 + - - -
232A GLN* 2.6 50.3 + - - +
233A GLY 3.3 0.5 + - - -
234A VAL* 3.2 29.0 + - + -
235A ARG* 2.8 33.8 + - - +
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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
------------------------------------------------------------
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