Contacts of the helix formed by residues 216 - 229 (chain B) in PDB entry 1XUD
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 LEU 216 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B MET* 3.8 38.4 - - + -
134B VAL* 4.2 10.3 - - + -
137B ALA* 4.1 11.0 - - + -
138B PHE* 4.0 26.5 - - + -
167B PHE* 4.0 24.0 - - + -
201B PHE* 3.9 21.5 - - + -
207B TRP* 3.8 24.9 - - + -
208B THR 3.1 9.5 + - - +
209B SER* 5.1 0.2 - - - +
214B TYR 3.2 3.6 + - - -
215B ASN* 1.3 71.4 - - - +
217B PHE* 1.3 53.9 + - - +
219B VAL 3.3 0.5 + - - -
220B ALA* 2.8 37.6 + - - +
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA* 3.7 25.5 - - + +
140B LYS* 3.3 49.8 - - + -
141B ALA* 3.6 24.7 - - - -
144B VAL* 3.7 15.3 - - + -
208B THR 4.9 0.4 + - - -
209B SER* 5.5 1.7 + - - +
215B ASN* 3.2 6.8 + - - +
216B LEU* 1.3 78.7 - - - +
218B LEU* 1.3 71.0 + - - +
220B ALA* 3.3 2.7 + - - +
221B ALA* 2.8 29.1 + - + +
252B PHE* 3.7 40.2 - + + -
3001B PB4 3.2 29.2 - + - -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASN* 2.8 26.2 + - + +
217B PHE* 1.3 78.0 - - - +
219B VAL* 1.3 61.3 + - - +
221B ALA* 3.4 2.9 + - - +
222B HIS* 3.2 21.5 + - - +
239B LEU* 3.7 19.2 - - + +
244B TYR* 3.5 30.7 - - + +
246B TYR* 4.2 11.0 - - + -
252B PHE* 4.1 13.5 - - + -
3001B PB4 3.6 63.0 - - + +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 4.8 6.7 - - + -
186B ALA* 4.1 11.9 - - + -
201B PHE* 3.8 18.4 - - + -
207B TRP* 3.5 31.9 - - + -
214B TYR* 4.5 3.8 - - + -
215B ASN 3.1 14.9 + - - +
216B LEU 3.8 1.6 - - - +
218B LEU* 1.3 76.0 - - - +
220B ALA* 1.3 58.2 + - - +
222B HIS* 3.2 3.5 + - - +
223B GLU* 2.9 30.3 + - + +
244B TYR* 3.9 19.1 - - + -
3001B PB4 3.4 26.2 - - - -
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 3.7 35.0 - - + -
141B ALA* 3.7 10.3 - - + -
201B PHE* 3.8 13.8 - - + -
216B LEU 2.8 22.2 + - - +
217B PHE* 3.6 4.5 - - - +
219B VAL* 1.3 71.7 - - - +
221B ALA* 1.3 59.9 + - - +
223B GLU 3.2 0.3 + - - -
224B PHE* 2.8 40.8 + - + -
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ALA* 3.6 19.7 - - + +
144B VAL* 4.4 9.2 - - + -
145B TRP* 3.0 30.6 + - - +
217B PHE* 2.8 28.5 + - + +
218B LEU* 3.7 6.3 - - - +
220B ALA* 1.3 73.9 - - - +
222B HIS* 1.3 63.0 + - - +
224B PHE* 4.6 0.9 - - - -
225B GLY 3.2 5.4 + - - -
239B LEU* 3.8 20.2 - - + -
252B PHE* 5.2 1.6 - - + -
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Residues in contact with HIS 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LEU 3.2 3.5 + - - +
219B VAL 3.4 4.5 - - - +
220B ALA 3.2 0.2 - - - -
221B ALA* 1.3 78.8 - - - +
223B GLU* 1.3 78.2 + - - +
225B GLY* 3.0 9.0 + - - -
226B HIS* 3.5 2.1 + - - -
232B HIS* 3.6 2.2 + + - -
239B LEU* 2.7 30.7 + - + +
240B MET* 3.3 39.1 - - + +
241B PHE 3.1 25.4 - - - -
1261B ZN 2.2 35.9 - - - -
3001B PB4 3.3 42.9 - + + +
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Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 6.1 0.2 - - - +
186B ALA* 3.5 37.0 + - + +
187B HIS* 3.3 5.3 - - - +
188B ALA* 3.2 33.8 + - + +
199B ALA* 4.6 5.2 - - + -
201B PHE* 4.3 11.4 - - + -
219B VAL* 2.9 23.0 + - + +
220B ALA* 3.7 5.8 - - - +
222B HIS* 1.3 91.0 - - - +
224B PHE* 1.3 62.7 + - - +
225B GLY 3.0 1.3 - - - -
226B HIS* 2.9 32.1 + - - +
227B SER* 3.0 13.4 + - - -
3001B PB4 4.2 8.3 - - - +
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Residues in contact with PHE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 3.8 15.5 - + - -
141B ALA* 3.6 29.4 - - + -
142B PHE* 3.5 55.2 - + + -
145B TRP* 3.8 18.2 - - + +
163B ILE* 4.5 3.4 - - + -
165B ILE* 3.6 19.5 - - + -
199B ALA* 3.9 22.2 - - + -
201B PHE* 4.7 4.7 - + - -
220B ALA* 2.8 25.3 + - + +
223B GLU* 1.3 74.1 - - - +
225B GLY* 1.3 62.8 + - - +
227B SER* 3.4 14.8 - - - -
228B LEU* 3.0 31.5 + - + +
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Residues in contact with GLY 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B TRP* 3.6 25.1 - - - -
221B ALA 3.2 6.1 + - - -
222B HIS 3.0 9.8 + - - -
223B GLU 3.0 1.4 - - - -
224B PHE* 1.3 77.6 - - - +
226B HIS* 1.3 58.5 + - - +
228B LEU* 3.2 12.1 + - - +
229B GLY 3.3 0.9 + - - -
230B LEU* 3.0 32.3 + - - +
240B MET* 4.0 6.5 - - - -
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Residues in contact with HIS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PHE* 3.5 25.8 - + + -
187B HIS* 6.1 0.2 - - - -
188B ALA* 4.1 17.5 - - + +
189B PHE 4.4 2.2 - - - -
190B PRO* 3.6 7.4 - - - +
222B HIS* 3.5 10.3 + + - -
223B GLU* 2.9 25.8 + - - +
225B GLY* 1.3 72.2 - - - +
227B SER* 1.3 64.3 + - - +
228B LEU 3.0 1.8 - - - -
229B GLY 3.0 10.7 + - - -
230B LEU 2.7 26.0 + - - -
231B ASP* 4.0 8.5 - - - -
232B HIS* 3.4 16.5 + + - -
240B MET* 3.3 16.5 - - + +
1261B ZN 2.2 36.4 - - - -
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 2.9 23.4 + - - -
163B ILE* 4.2 14.6 - - - -
188B ALA* 3.5 10.2 - - - +
189B PHE 3.6 11.4 + - - -
191B PRO* 3.2 12.6 - - - +
197B GLY* 2.8 27.1 + - - -
199B ALA* 4.5 0.5 - - - +
223B GLU 3.0 11.6 + - - -
224B PHE* 3.4 22.1 - - - -
226B HIS* 1.3 75.8 - - - +
228B LEU* 1.3 58.0 + - - +
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU 4.2 1.0 - - - +
113B TRP* 3.9 9.0 - - + +
118B LEU* 3.8 29.2 - - + -
142B PHE* 6.5 0.2 - - + -
145B TRP* 3.6 41.5 - - + -
151B LEU* 3.8 20.4 - - + -
153B PHE* 4.0 11.7 - - + -
163B ILE* 4.8 5.2 - - + -
191B PRO* 3.5 6.0 - - - +
224B PHE* 3.0 19.1 + - + +
225B GLY 3.7 4.9 - - - +
226B HIS 3.0 0.2 - - - -
227B SER* 1.3 80.8 - - - +
229B GLY* 1.3 56.5 + - - +
230B LEU 3.8 0.2 - - - -
262B ILE* 3.9 16.6 - - + -
265B LEU* 4.0 4.4 - - - +
266B TYR* 2.6 31.3 + - - +
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Residues in contact with GLY 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 3.7 1.4 - - - +
107A PHE* 3.2 31.3 + - - +
111B LEU 4.0 11.4 - - - +
191B PRO* 3.6 17.7 - - - +
226B HIS 3.0 7.7 + - - -
227B SER 3.4 0.4 - - - -
228B LEU* 1.3 81.1 - - - +
230B LEU* 1.3 60.2 + - - +
265B LEU* 3.6 15.9 - - - +
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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