Contacts of the helix formed by residues 243 - 262 (chain B) in PDB entry 4IA4
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 TRP 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LYS* 3.5 29.4 - - + +
165B LEU* 3.5 41.5 - - + -
239B TRP 4.5 0.6 + - - -
240B ASP 3.3 24.9 + - - +
241B ASP 2.9 3.4 + - - -
242B GLN* 1.3 79.1 - - - +
244B ILE* 1.3 77.3 + - + +
246B TRP* 3.4 7.2 + - - +
247B VAL* 3.2 38.9 + - + +
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Residues in contact with ILE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 3.7 29.6 - - + -
161B LYS* 3.9 20.6 - - + +
164B ALA* 3.9 12.8 - - + -
165B LEU* 3.2 44.2 - - + +
168B GLU* 4.2 7.8 - - + +
241B ASP* 2.8 20.2 + - + +
243B TRP* 1.3 103.8 - - + +
245B PHE* 1.3 63.8 + - + +
246B TRP 3.1 0.4 + - - -
248B GLY* 2.8 30.1 + - - -
249B PRO* 3.6 0.3 - - - +
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Residues in contact with PHE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASN* 3.2 45.1 - - + -
154B SER* 3.3 24.0 - - - -
155B VAL* 5.5 1.6 - - + -
168B GLU* 3.5 35.0 - - + -
217B THR* 3.8 13.5 - - + -
220B GLY* 4.6 0.4 - - - -
222B ASN 3.6 3.5 - - - +
223B PRO* 3.6 9.9 - - - +
226B SER* 3.6 25.6 - - - +
241B ASP* 3.8 22.0 - - + -
242B GLN* 3.2 24.1 + - - +
244B ILE* 1.3 80.4 - - + +
246B TRP* 1.3 59.6 + - + +
249B PRO* 2.8 26.5 - - - +
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Residues in contact with TRP 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PRO* 5.5 2.5 - - + -
123B MET* 6.2 1.8 - - - -
127B CYS* 3.9 19.3 - - - -
223B PRO* 3.9 16.4 + - + -
227B PHE* 3.9 34.5 - + + +
242B GLN* 3.0 44.1 + - + +
243B TRP* 3.4 7.6 + - - +
244B ILE 3.1 0.4 - - - -
245B PHE* 1.3 82.6 - - + +
247B VAL* 1.3 68.2 + - + +
248B GLY 3.4 0.4 - - - -
249B PRO* 3.4 0.3 - - - +
250B PHE* 2.8 64.8 + + + -
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 4.1 10.5 - - + -
243B TRP* 3.2 40.2 + - + +
246B TRP* 1.3 76.5 - - + +
248B GLY* 1.3 61.3 + - - +
250B PHE* 4.0 2.9 - - - +
251B ILE* 2.8 58.1 + - + +
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Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.9 9.1 - - - +
168B GLU* 4.2 7.2 - - - -
169B ILE* 3.4 32.1 - - - +
244B ILE 2.8 19.0 + - - -
247B VAL* 1.3 75.5 - - - +
249B PRO* 1.4 60.5 - - - +
252B GLY 2.8 24.9 + - - -
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Residues in contact with PRO 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA* 3.8 20.9 - - + -
168B GLU* 4.0 14.8 - - - +
172B THR* 3.4 25.9 - - + +
222B ASN 4.3 7.2 - - - +
223B PRO* 3.8 15.7 - - + -
244B ILE 3.6 1.6 - - - +
245B PHE* 2.8 34.8 - - - +
246B TRP 3.4 3.1 - - - +
248B GLY* 1.4 88.3 - - - +
250B PHE* 1.3 54.2 + - - +
252B GLY* 3.0 2.4 + - - -
253B ALA* 2.7 35.3 + - - +
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PRO* 4.5 10.1 - - + -
103B ALA* 4.9 2.7 - - + -
106B PHE* 3.3 64.2 - + + -
123B MET* 4.3 20.4 - - + -
223B PRO* 3.7 15.9 - - + -
246B TRP* 2.8 61.5 + + + +
247B VAL* 4.0 3.6 - - - +
249B PRO* 1.3 78.4 - - - +
251B ILE* 1.3 63.1 + - + +
253B ALA* 4.4 1.6 - - - -
254B ALA* 3.1 22.9 + - - +
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Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 5.4 3.4 - - + -
169B ILE* 3.5 32.1 - - + -
247B VAL* 2.8 49.7 + - + +
248B GLY 3.4 3.8 - - - +
250B PHE* 1.3 74.1 - - + +
252B GLY* 1.3 66.5 + - - +
254B ALA* 3.2 6.4 + - - +
255B VAL* 2.9 39.3 + - + +
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Residues in contact with GLY 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 3.9 28.2 - - - +
172B THR* 4.5 0.9 - - - -
173B PHE* 3.9 13.6 - - - -
248B GLY 2.8 14.7 + - - -
249B PRO 3.5 2.2 - - - -
251B ILE* 1.3 78.6 - - - +
253B ALA* 1.3 51.4 + - - +
255B VAL* 3.3 5.1 + - - +
256B ALA* 2.8 35.5 + - - +
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA* 3.2 29.4 - - + +
106B PHE* 4.3 4.7 - - + -
107B GLY* 4.2 12.1 - - - +
172B THR* 4.2 2.4 - - - +
176B VAL* 3.8 24.6 - - + +
249B PRO 2.7 19.1 + - - +
250B PHE 3.8 4.7 - - - +
252B GLY* 1.3 71.4 - - - +
254B ALA* 1.3 57.5 + - - +
256B ALA* 3.2 2.3 + - - +
257B ALA* 2.8 30.1 + - - +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 4.3 2.9 - - + -
110B LEU* 3.8 25.3 - - + +
250B PHE 3.1 15.3 + - - +
251B ILE* 3.3 11.4 - - + +
253B ALA* 1.3 73.2 - - - +
255B VAL* 1.3 68.3 + - + +
257B ALA* 3.0 5.0 + - - +
258B ALA* 2.9 24.7 + - - +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 5.4 4.7 - - + -
173B PHE* 3.9 14.8 - - + -
251B ILE* 2.9 28.9 + - + +
252B GLY* 3.6 7.0 - - - +
254B ALA* 1.3 76.8 - - + +
256B ALA* 1.3 57.5 + - - +
258B ALA* 3.8 7.9 - - + +
259B TYR* 2.9 28.5 + - + +
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 3.3 24.6 - - + +
176B VAL* 4.0 10.1 - - + -
177B TYR* 3.9 27.2 - - - +
180B PHE* 4.2 2.9 - - - -
252B GLY 2.8 17.1 + - - +
253B ALA 3.4 6.3 - - - +
254B ALA 3.0 0.2 - - - -
255B VAL* 1.3 74.9 - - - +
257B ALA* 1.3 67.3 + - - +
259B TYR* 2.9 3.6 + - - +
260B HIS* 2.8 25.3 + - - +
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Residues in contact with ALA 257 (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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107B GLY 3.6 23.6 - - - +
110B LEU* 4.5 11.7 - - + -
111B ALA* 5.1 1.8 - - - +
180B PHE* 3.2 19.2 - - + -
253B ALA 2.8 17.2 + - - +
254B ALA* 3.4 11.0 - - - +
256B ALA* 1.3 71.5 - - - +
258B ALA* 1.3 54.0 + - - +
260B HIS 3.1 0.3 + - - -
261B GLN* 2.6 45.5 + - + +
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Residues in contact with ALA 258 (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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254B ALA 2.9 14.3 + - - +
255B VAL* 3.8 8.1 - - - +
257B ALA* 1.3 77.6 - - - +
259B TYR* 1.3 58.9 + - - +
261B GLN* 4.7 1.3 - - - -
262B TYR* 2.6 38.8 + - + +
263B VAL* 3.0 10.0 + - + +
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Residues in contact with TYR 259 (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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173B PHE* 3.7 24.9 - + + -
177B TYR* 3.7 30.2 + + - -
255B VAL* 2.9 21.2 + - + +
256B ALA 2.9 4.0 + - - +
258B ALA* 1.3 76.6 - - - +
260B HIS* 1.3 59.5 + - - +
263B VAL* 3.0 36.9 - - + +
264B LEU* 2.8 54.2 + - + +
42D ILE* 3.6 8.0 + - + +
43D ALA* 3.5 20.8 - - - +
46D ILE* 3.5 37.7 - - + +
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Residues in contact with HIS 260 (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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113B LYS* 5.0 6.5 - - - -
177B TYR* 4.9 12.6 - + + -
180B PHE* 3.5 59.7 + + + +
181B SER* 4.6 9.3 + - - -
183B THR* 5.3 1.3 - - - -
256B ALA 2.8 19.0 + - - +
257B ALA 3.7 1.6 - - - +
259B TYR* 1.3 77.7 - - - +
261B GLN* 1.3 69.7 + - - +
264B LEU* 2.6 44.9 - - + +
265B ARG* 3.7 20.8 - - + +
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Residues in contact with GLN 261 (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 ALA* 3.2 42.8 - - + +
113B LYS* 4.1 20.6 - - - +
180B PHE* 4.5 3.1 - - + -
257B ALA* 2.6 28.0 + - + +
258B ALA* 4.7 1.1 - - - -
260B HIS* 1.3 88.2 + - - +
262B TYR* 1.3 61.5 + - + +
264B LEU 2.8 15.7 - - - +
265B ARG* 3.5 43.5 + - - +
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Residues in contact with TYR 262 (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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258B ALA* 2.6 25.9 + - + +
261B GLN* 1.3 77.6 - - - +
263B VAL* 1.3 65.6 + - + +
264B LEU 4.2 1.0 - - - +
39D ARG* 4.9 3.3 + - - -
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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