Contacts of the helix formed by residues 226 - 241 (chain A) in PDB entry 3IFS
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 ASN 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A GLY 4.0 1.0 + - - +
225A LEU* 1.3 68.7 - - - +
227A ILE* 1.3 61.9 + - - +
228A GLU* 3.0 31.9 + - - +
229A GLU* 3.0 29.6 + - + +
230A MSE 3.3 15.0 + - - +
391A GLU* 2.8 32.1 + - - +
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Residues in contact with ILE 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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60A PHE* 3.5 26.9 - - + -
63A ILE* 3.8 30.5 - - + -
64A GLN* 4.0 21.1 - - + +
217A LEU* 3.7 39.9 - - + +
220A ILE* 3.9 20.9 - - + -
221A ALA* 4.0 16.6 - - + +
225A LEU 3.4 2.0 + - - +
226A ASN* 1.3 70.1 + - - +
228A GLU* 1.3 61.2 + - - +
230A MSE 3.3 7.7 + - - +
231A MSE 3.0 32.4 + - - +
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Residues in contact with GLU 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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55A TYR* 6.0 0.4 - - - -
60A PHE* 4.0 14.3 - - + -
64A GLN* 3.3 32.4 + - - +
226A ASN* 3.0 17.5 + - - +
227A ILE* 1.3 76.2 - - - +
229A GLU* 1.3 61.0 + - + +
231A MSE 3.3 5.7 + - - +
232A LYS* 3.0 41.6 + - - +
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Residues in contact with GLU 229 (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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226A ASN* 3.0 37.3 + - + +
228A GLU* 1.3 74.8 - - + +
230A MSE 1.3 65.4 + - - +
232A LYS* 3.3 33.9 + - - +
233A GLY 3.0 18.5 + - - -
391A GLU* 4.2 11.0 - - + -
392A TYR* 3.4 31.6 - - + +
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Residues in contact with MSE 230 (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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92A ALA* 4.3 1.1 - - + -
96A LEU* 4.1 19.7 - - + -
212A LEU* 4.0 23.8 - - + -
217A LEU* 4.2 11.4 - - + -
220A ILE* 3.8 41.7 - - + -
226A ASN 3.3 9.7 + - - +
227A ILE* 3.5 10.8 - - - +
228A GLU 3.2 0.6 - - - -
229A GLU* 1.3 79.5 - - - +
231A MSE 1.3 62.0 + - - +
233A GLY 3.2 2.1 + - - -
234A ALA* 3.0 19.8 + - - +
391A GLU* 3.4 26.6 - - + +
394A PHE* 3.5 31.2 - - + -
395A GLY* 3.6 12.3 - - - -
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Residues in contact with MSE 231 (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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51A LEU* 3.9 3.4 - - + +
52A PRO* 3.2 44.7 - - + +
55A TYR* 3.7 31.4 - - + +
60A PHE* 3.5 23.1 - - + -
212A LEU* 4.0 40.2 - - + +
217A LEU* 4.4 10.5 - - + -
227A ILE 3.0 21.3 + - - +
228A GLU* 3.3 6.0 + - - +
230A MSE 1.3 76.1 - - - +
232A LYS* 1.3 57.3 + - + +
234A ALA* 3.3 5.3 + - + +
235A ALA* 2.9 30.0 + - - +
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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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228A GLU* 3.0 26.5 + - - +
229A GLU* 3.3 35.0 + - - +
231A MSE 1.3 73.2 - - + +
233A GLY* 1.3 61.5 + - - +
235A ALA* 3.3 7.6 + - - +
236A ALA* 3.0 29.3 + - - +
392A TYR* 3.9 14.3 - - + -
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Residues in contact with GLY 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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229A GLU 3.0 10.7 + - - -
230A MSE 3.2 1.3 + - - -
232A LYS* 1.3 75.1 - - - +
234A ALA* 1.3 62.6 + - - +
236A ALA 3.3 2.1 + - - -
237A GLY 3.1 17.2 + - - -
392A TYR* 3.2 41.6 - - - -
396A TYR* 3.3 19.0 - - - -
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Residues in contact with ALA 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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52A PRO* 3.6 16.5 - - + +
212A LEU* 3.6 26.9 - - + -
230A MSE 3.0 12.3 + - - +
231A MSE 3.7 9.9 - - + +
233A GLY* 1.3 76.8 - - - +
235A ALA* 1.3 56.1 + - - +
237A GLY* 3.2 2.4 + - - -
238A ARG* 2.8 27.0 + - - +
395A GLY 3.4 22.2 - - - +
396A TYR* 4.3 0.7 - - - +
399A TYR* 3.9 7.2 - - + -
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Residues in contact with ALA 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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52A PRO* 3.5 24.0 - - + +
53A LEU* 4.8 10.3 - - + +
231A MSE 2.9 17.8 + - - +
232A LYS* 3.3 8.7 + - - +
234A ALA* 1.3 72.5 - - - +
236A ALA* 1.3 65.1 + - - +
238A ARG* 3.3 7.6 + - - +
239A ASP* 3.0 22.5 + - - +
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Residues in contact with ALA 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 3.0 11.1 + - - +
233A GLY 3.5 8.1 - - - +
235A ALA* 1.3 75.9 - - - +
237A GLY* 1.3 58.7 + - - +
239A ASP* 3.2 7.1 + - - +
240A ASP* 2.9 35.5 + - - +
392A TYR* 3.4 26.2 - - + +
396A TYR* 3.7 11.9 - - + -
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Residues in contact with GLY 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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233A GLY 3.1 11.2 + - - -
234A ALA 3.2 4.9 + - - -
236A ALA* 1.3 73.8 - - - +
238A ARG* 1.3 58.8 + - - +
239A ASP 3.2 0.2 + - - -
241A PHE* 2.8 47.7 + - - +
396A TYR* 3.5 20.1 - - - -
399A TYR* 3.6 13.0 - - - -
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Residues in contact with ARG 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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36A HIS* 5.8 7.4 + - + -
49A VAL* 3.5 17.7 - - + +
50A ASP* 2.7 41.0 + - - +
52A PRO* 4.5 4.0 - - + -
53A LEU* 3.5 41.9 - - - +
234A ALA 2.8 13.7 + - - +
235A ALA* 3.4 12.3 + - - +
237A GLY* 1.3 74.1 - - - +
239A ASP* 1.3 66.5 + - - +
241A PHE 3.8 0.7 - - - -
242A GLY* 3.2 21.5 + - - -
399A TYR* 3.3 24.8 + - + +
403A LYS* 5.6 0.2 + - - -
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Residues in contact with ASP 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 ALA 3.0 12.4 + - - +
236A ALA* 3.4 12.1 - - - +
237A GLY 3.1 0.2 - - - -
238A ARG* 1.3 81.3 - - - +
240A ASP* 1.3 71.1 + - - +
242A GLY* 3.2 14.8 + - - -
243A THR* 4.4 0.7 + - - -
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Residues in contact with ASP 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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2A SER 4.2 5.7 - - - +
3A THR* 3.9 24.4 - - + +
4A HIS 4.3 0.7 + - - -
236A ALA* 2.9 20.9 + - - +
237A GLY 3.9 2.2 - - - +
239A ASP* 1.3 81.3 - - - +
241A PHE* 1.3 65.1 + - + +
242A GLY 3.5 1.9 + - - -
243A THR* 3.8 17.7 - - - +
248A GLU 4.4 5.2 - - - +
249A ASN* 4.5 0.2 + - - -
396A TYR* 2.2 41.5 + - + +
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Residues in contact with PHE 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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3A THR* 4.3 8.1 - - + -
5A VAL 4.5 4.9 - - - -
237A GLY* 2.8 32.4 + - - +
238A ARG 3.8 3.1 - - - -
240A ASP* 1.3 75.5 - - - +
242A GLY* 1.3 59.4 + - - +
243A THR 3.3 2.7 - - - -
249A ASN* 2.9 37.1 + - - +
250A PRO* 3.8 31.0 - - + -
251A ALA* 3.9 8.3 - - + -
252A TYR* 3.8 0.2 + - - -
396A TYR* 3.5 40.2 - + - -
399A TYR* 4.2 6.1 - + + -
400A PHE* 3.7 41.7 - + + -
403A LYS* 3.0 34.9 + - + +
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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