Contacts of the helix formed by residues 231 - 243 (chain B) in PDB entry 3UFJ
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 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229B PHE* 3.1 4.0 + - - +
230B ASN* 1.3 68.6 - - - +
232B LYS* 1.3 62.1 + - - +
234B ILE* 2.7 31.2 - - - +
235B TYR 3.9 0.7 + - - -
268B VAL* 4.5 1.1 - - - -
269B MET 2.5 24.3 + - - -
271B SER* 3.2 12.1 - - - +
19C G 3.3 0.4 - - - -
13F T 2.8 23.3 - - - -
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Residues in contact with LYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLY* 1.3 67.3 - - - -
233B CYS* 1.3 65.5 + - - +
235B TYR* 2.8 16.2 + - - +
236B GLU* 2.9 23.8 + - - +
250B LEU* 5.1 11.4 - - + +
252B PHE* 4.2 15.0 - - + -
268B VAL* 4.1 14.1 - - + +
269B MET 4.1 2.2 + - - -
19C G 4.0 14.4 - - - +
13F T 2.9 9.2 + - + -
14F A 4.6 12.3 - - - +
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Residues in contact with CYS 233 (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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139B ILE* 5.6 6.5 - - + -
232B LYS* 1.3 74.2 - - - +
234B ILE* 1.3 62.4 + - - +
236B GLU* 3.2 21.8 + - - +
237B ILE* 3.3 8.7 + - - +
18C A 4.9 0.2 - - - -
12F G 3.6 21.8 - - - -
13F T 2.7 56.8 + - - +
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Residues in contact with ILE 234 (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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137B ILE* 3.4 25.8 - - + +
138B GLY 3.3 28.0 - - - +
139B ILE* 4.4 15.0 - - + +
192B MET* 3.4 31.2 - - + +
229B PHE* 3.8 18.8 - - + -
230B ASN 3.2 19.0 + - - +
231B GLY 2.7 26.2 + - - +
233B CYS* 1.3 78.0 - - - +
235B TYR* 1.3 57.2 + - - +
237B ILE* 3.8 5.5 + - - +
238B PHE* 3.1 24.2 + - - +
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Residues in contact with TYR 235 (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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229B PHE* 4.0 19.5 - + + -
232B LYS* 2.8 13.5 + - - +
234B ILE* 1.3 74.3 - - - +
236B GLU* 1.3 72.5 + - - +
238B PHE* 2.8 28.7 + + - -
239B SER* 2.7 38.5 + - - -
243B PHE* 3.7 19.2 - + - -
247B VAL* 4.2 12.1 - - + +
250B LEU* 4.6 12.1 - - + -
255B GLN* 3.5 37.3 + - + +
256B PRO* 5.1 0.5 - - - +
257B HIS* 4.3 9.9 + - - +
266B CYS* 4.1 16.9 - - + +
268B VAL* 3.5 31.9 - - + -
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Residues in contact with GLU 236 (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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232B LYS* 2.9 23.8 + - - +
233B CYS* 3.2 15.2 - - - +
235B TYR* 1.3 79.2 - - - +
237B ILE* 1.3 64.8 + - - +
239B SER* 3.2 5.0 + - - -
240B LYS* 3.1 19.4 + - - +
245B VAL 4.8 0.3 - - - +
246B LYS* 5.6 0.2 - - - -
247B VAL* 3.7 32.7 + - - +
250B LEU* 4.6 15.2 - - - +
14F A 5.8 0.3 + - - -
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Residues in contact with ILE 237 (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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192B MET* 4.3 13.9 - - + -
208B PHE* 4.9 17.9 - - + -
233B CYS 3.3 6.3 + - - +
234B ILE* 3.9 8.3 - - - +
235B TYR 3.2 0.4 - - - -
236B GLU* 1.3 78.7 - - - +
238B PHE* 1.3 66.3 + - - +
240B LYS* 3.0 10.5 + - - +
241B GLU* 2.9 27.0 + - + +
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Residues in contact with PHE 238 (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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192B MET* 4.5 20.8 - - + +
212B GLY* 4.6 19.5 - - - -
215B LEU* 5.1 10.3 - - + -
216B VAL* 5.1 9.4 - - + -
229B PHE* 3.5 36.8 - + + -
234B ILE 3.1 16.6 + - - +
235B TYR* 2.8 24.4 + + - +
237B ILE* 1.3 75.0 - - - +
239B SER* 1.3 52.0 + - - +
241B GLU* 4.6 4.5 - - + +
242B VAL* 2.7 57.1 + - + +
243B PHE* 3.9 24.2 - + - -
259B ILE* 5.2 7.6 - - + -
260B PRO* 5.2 9.2 - - + -
266B CYS* 4.3 7.0 - - - -
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Residues in contact with SER 239 (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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235B TYR* 2.7 28.8 + - - -
236B GLU 3.5 8.5 - - - -
238B PHE* 1.3 69.1 - - - +
240B LYS* 1.3 51.2 + - - +
241B GLU 3.0 4.3 + - - -
243B PHE* 2.9 26.5 + - - -
244B GLY 2.8 30.0 + - - -
245B VAL* 3.3 18.2 + - - -
247B VAL* 3.9 20.2 - - - -
257B HIS* 6.4 0.2 - - - -
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Residues in contact with LYS 240 (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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236B GLU 3.1 8.1 + - - +
237B ILE* 3.0 11.7 + - - +
239B SER* 1.3 77.3 - - - +
241B GLU* 1.3 57.6 + - + +
244B GLY* 3.3 16.2 - - - -
245B VAL 3.3 18.7 + - - +
246B LYS* 5.1 6.3 - - + -
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Residues in contact with GLU 241 (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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192B MET* 6.5 0.4 - - + -
209B ARG* 4.5 29.6 - - + +
212B GLY* 6.4 2.2 - - - -
237B ILE* 2.9 16.9 + - + +
238B PHE* 4.1 3.1 - - - +
240B LYS* 1.3 79.6 - - - +
242B VAL* 1.3 63.3 + - - +
243B PHE 3.6 0.2 - - - -
244B GLY 4.1 2.3 + - - -
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY 6.4 1.1 - - - -
216B VAL* 6.0 3.6 - - + -
238B PHE* 2.7 54.3 + - + +
241B GLU* 1.3 73.7 - - - +
243B PHE* 1.3 68.8 + - + +
260B PRO* 4.8 14.0 - - + +
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Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B TYR* 3.7 25.1 - + - -
238B PHE* 3.9 29.2 - + - -
239B SER* 2.9 23.6 + - - +
242B VAL* 1.3 81.8 - - + +
244B GLY* 1.3 66.8 + - - +
245B VAL* 3.5 12.2 + - + +
257B HIS* 3.8 33.7 - + + +
258B LYS 3.3 27.4 - - - -
260B PRO* 4.1 15.7 - - + -
266B CYS* 4.1 9.0 - - - -
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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