Contacts of the helix formed by residues 231 - 243 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A PHE* 3.0 6.1 + - - +
230A ASN* 1.3 69.7 - - - +
232A LYS* 1.3 62.5 + - - +
233A CYS 3.3 2.2 - - - -
234A ILE* 2.8 30.0 - - - +
235A TYR 3.9 1.0 + - - -
268A VAL* 4.4 1.3 - - - +
269A MET 2.5 23.5 + - - -
271A SER* 3.3 11.6 - - - +
13D T 2.9 20.2 - - - -
19E G 3.4 0.2 - - - -
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Residues in contact with LYS 232 (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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231A GLY* 1.3 69.2 - - - -
233A CYS* 1.3 65.3 + - - +
235A TYR* 2.8 14.4 + - - +
236A GLU* 2.9 15.7 + - + +
250A LEU* 4.2 20.8 - - + +
252A PHE* 4.2 14.9 - - + -
268A VAL* 4.1 11.4 - - + +
269A MET 4.1 2.0 + - - -
13D T 2.9 8.8 + - + -
14D A 4.7 13.5 - - - +
19E G 4.1 13.9 - - - +
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Residues in contact with CYS 233 (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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139A ILE* 5.8 4.7 - - + -
208A PHE* 6.4 0.9 - - + -
232A LYS* 1.3 72.6 - - - +
234A ILE* 1.3 63.2 + - - +
236A GLU* 3.3 8.4 + - - +
237A ILE* 3.1 22.9 + - - +
12D G 3.8 20.9 - - - -
13D T 2.6 59.4 + - - +
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Residues in contact with ILE 234 (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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137A ILE* 3.5 23.1 - - + +
138A GLY 3.4 22.9 - - - +
139A ILE* 4.4 16.1 - - + +
192A MET* 3.2 42.6 - - + +
208A PHE* 5.6 6.3 - - + -
229A PHE* 4.0 15.5 - - + -
230A ASN 3.2 17.5 - - - +
231A GLY 2.8 25.5 + - - +
233A CYS* 1.3 79.7 - - - +
235A TYR* 1.3 56.9 + - - +
237A ILE* 3.8 3.0 + - - -
238A PHE* 3.1 24.8 + - - +
13D T 4.4 0.2 + - - -
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Residues in contact with TYR 235 (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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229A PHE* 3.9 22.9 - + + -
231A GLY 4.7 0.2 - - - +
232A LYS 2.8 9.2 + - - +
234A ILE* 1.3 78.3 - - - +
236A GLU* 1.3 57.7 + - - +
237A ILE 3.1 1.8 - - - -
238A PHE* 2.8 29.0 + + - -
239A SER* 2.6 49.6 + - - -
243A PHE* 3.8 16.4 - + - -
247A VAL* 5.5 4.5 - - + -
250A LEU* 4.0 15.9 - - + -
255A GLN* 3.4 42.0 + - + +
257A HIS* 4.4 9.9 + - - -
266A CYS* 4.1 19.4 - - + +
268A VAL* 3.5 26.0 - - + -
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Residues in contact with GLU 236 (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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232A LYS* 2.9 12.6 + - + +
233A CYS* 3.5 12.1 - - - +
235A TYR* 1.3 76.7 - - - +
237A ILE* 1.3 62.3 + - - +
239A SER* 4.0 4.5 - - - -
240A LYS* 3.2 21.8 + - - +
245A VAL 4.6 1.4 - - - +
246A LYS* 5.3 2.8 - - - -
247A VAL* 5.8 6.7 - - + +
250A LEU* 4.6 11.6 - - + +
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Residues in contact with ILE 237 (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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192A MET* 4.4 13.2 - - + -
208A PHE* 4.9 18.4 - - + -
233A CYS 3.1 14.7 + - - +
234A ILE* 4.0 5.2 - - - +
235A TYR 3.1 0.4 - - - -
236A GLU* 1.3 75.0 - - - +
238A PHE* 1.3 64.8 + - - +
240A LYS* 3.0 9.6 + - - +
241A GLU* 2.9 27.7 + - + +
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Residues in contact with PHE 238 (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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192A MET* 4.4 12.7 - - + +
212A GLY* 4.3 18.8 - - - -
215A LEU* 4.5 9.2 - - + -
216A VAL* 3.6 33.2 - - + -
219A LEU* 5.6 1.1 - - + -
229A PHE* 3.6 33.9 - + + -
234A ILE 3.1 18.0 + - - +
235A TYR* 2.8 23.7 + + - +
237A ILE* 1.3 75.5 - - - +
239A SER* 1.3 52.5 + - - +
241A GLU* 4.7 3.1 - - - -
242A VAL* 2.7 49.3 + - + +
243A PHE* 4.0 19.3 - + - -
259A ILE* 3.7 27.6 - - + -
260A PRO* 5.6 1.1 - - + -
266A CYS* 4.4 0.2 - - - -
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Residues in contact with SER 239 (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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235A TYR* 2.6 36.8 + - - -
236A GLU* 4.0 4.3 - - - -
238A PHE* 1.3 69.1 - - - +
240A LYS* 1.3 51.7 + - - +
241A GLU 2.9 5.0 + - - -
243A PHE* 2.8 31.8 + - - -
244A GLY 2.8 30.7 + - - -
245A VAL* 3.4 18.3 + - - -
247A VAL* 5.3 6.5 - - - -
257A HIS* 6.2 0.9 - - - -
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Residues in contact with LYS 240 (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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236A GLU 3.2 16.1 + - - +
237A ILE* 3.0 8.6 + - - +
239A SER* 1.3 76.7 - - - +
241A GLU* 1.3 56.5 + - + +
244A GLY* 3.4 14.3 - - - -
245A VAL 3.4 19.4 + - - +
246A LYS* 4.9 7.2 - - + -
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Residues in contact with GLU 241 (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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192A MET* 6.3 1.6 - - + -
208A PHE 5.9 0.2 - - - +
209A ARG* 4.9 22.0 - - + +
212A GLY* 6.1 4.3 - - - -
237A ILE* 2.9 16.2 + - + +
238A PHE* 4.1 3.6 - - + +
240A LYS* 1.3 80.3 - - + +
242A VAL* 1.3 61.5 + - - +
243A PHE 3.6 0.2 - - - -
244A GLY* 4.3 2.0 - - - -
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Residues in contact with VAL 242 (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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212A GLY 6.0 1.6 - - - -
216A VAL* 4.1 13.2 - - + -
238A PHE* 2.7 51.0 + - + +
241A GLU* 1.3 74.8 - - - +
243A PHE* 1.3 69.5 + - + +
244A GLY 3.7 0.2 - - - -
260A PRO* 5.0 11.1 - - + +
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Residues in contact with PHE 243 (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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235A TYR* 3.8 20.2 - + - -
238A PHE* 4.0 27.6 - + - -
239A SER* 2.8 27.3 + - - +
242A VAL* 1.3 81.4 - - + +
244A GLY* 1.3 66.3 + - - +
245A VAL* 4.5 11.3 - - + +
257A HIS* 3.7 37.9 - + + -
258A LYS 3.4 27.8 - - - -
259A ILE* 5.0 0.2 - - + -
260A PRO* 4.2 16.8 - - + -
266A CYS* 4.8 3.4 - - - -
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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