Contacts of the helix formed by residues 228 - 242 (chain A) in PDB entry 3SN5
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 PHE 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A VAL* 3.8 26.2 - - + -
218A ALA* 3.7 27.1 - - + -
219A LEU* 4.3 6.7 - - + -
223A LEU* 3.9 27.1 - - + -
224A PRO 3.5 21.1 - - - -
225A ILE* 2.9 19.7 + - - +
226A HIS 4.0 0.4 - - - -
227A MET* 1.3 87.4 - - + +
229A ARG* 1.4 53.2 + - - +
230A THR 3.5 2.5 - - - -
231A ALA* 3.4 18.3 + - + +
232A HIS* 2.8 31.7 + - - +
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Residues in contact with ARG 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 HIS 4.0 11.0 + - - +
227A MET 3.8 3.2 + - - +
228A PHE* 1.4 69.5 - - - +
230A THR* 1.4 63.7 + - - +
232A HIS* 3.0 9.1 + - + +
233A ASN* 3.0 36.9 + - - +
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Residues in contact with THR 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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211A GLN* 3.4 36.3 - - + +
228A PHE 3.5 0.4 - - - -
229A ARG* 1.4 76.4 - - - +
231A ALA* 1.3 57.3 - - - +
233A ASN* 3.5 8.5 + - - +
234A ALA* 3.0 28.3 + - - +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN 3.4 27.3 + - - +
212A PHE* 4.3 4.4 - - - +
215A VAL* 3.6 34.3 - - + -
225A ILE* 3.9 6.1 - - + +
228A PHE* 3.4 11.6 + - + +
229A ARG 3.3 0.2 - - - -
230A THR* 1.3 76.2 - - - +
232A HIS* 1.3 60.3 + - - +
234A ALA* 3.5 5.1 - - - +
235A ARG* 3.0 29.8 + - - +
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Residues in contact with HIS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ILE* 3.5 38.4 - - + +
226A HIS* 4.1 19.3 - - + +
228A PHE 2.8 22.4 + - - +
229A ARG* 3.0 8.0 + - + +
231A ALA* 1.3 69.8 - - - +
233A ASN* 1.4 65.5 + - - +
235A ARG* 3.3 8.9 + - - +
236A GLU* 3.1 48.0 + - + +
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Residues in contact with ASN 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 ARG* 3.0 33.4 + - - +
230A THR* 3.8 7.2 - - - +
232A HIS* 1.4 73.8 - - - +
234A ALA* 1.3 59.8 + - - +
236A GLU* 3.3 6.5 + - - +
237A LYS* 2.9 50.6 + - - +
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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
----------------------------------------------------------
208A ASN* 3.4 41.0 - - - +
211A GLN* 3.8 15.9 - - + -
212A PHE 4.1 1.8 - - - +
230A THR 3.0 18.4 + - - +
231A ALA* 3.5 6.1 - - - +
233A ASN* 1.3 75.7 - - - +
235A ARG* 1.3 55.9 + - - +
237A LYS* 3.2 3.9 + - - +
238A LEU* 2.9 35.8 + - - +
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Residues in contact with ARG 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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107A LYS 4.4 4.2 + - - -
108A ALA 3.1 21.2 + - - -
109A PHE 3.6 21.2 + - - -
110A GLY* 3.7 11.3 - - - +
212A PHE* 3.5 30.5 - - + +
219A LEU* 5.2 0.2 - - - +
225A ILE* 3.6 37.4 - - + +
231A ALA 3.0 17.4 + - - +
232A HIS* 3.6 10.4 + - - +
234A ALA* 1.3 74.6 - - - +
236A GLU* 1.4 82.9 + - - +
238A LEU* 3.4 11.9 + - - +
239A ALA* 3.0 26.9 + - - +
277A LYS* 3.4 9.4 - - - +
280A LEU* 3.5 19.3 - - + +
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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 HIS* 3.1 31.4 + - + +
233A ASN* 3.8 5.8 - - - +
235A ARG* 1.4 97.2 + - - +
237A LYS* 1.4 59.9 + - - +
239A ALA* 3.4 3.7 + - - +
240A GLU* 2.9 29.3 + - - +
273A LEU* 3.8 18.5 - - - +
277A LYS* 2.6 37.5 + - - -
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Residues in contact with LYS 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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208A ASN* 3.5 31.1 + - - +
233A ASN* 2.9 32.6 + - - +
234A ALA* 3.6 2.0 - - - +
236A GLU* 1.4 73.4 - - - +
238A LEU* 1.3 63.6 + - - +
240A GLU* 3.4 8.1 + - - +
241A SER* 3.4 21.1 + - - -
2205A UNX 3.9 5.4 - - - -
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Residues in contact with LEU 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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180A PHE* 5.1 0.2 - - + -
184A TYR* 5.4 0.4 - - + -
205A ASN* 3.7 29.6 - - + +
208A ASN* 3.8 9.2 - - + +
209A PHE* 3.8 26.9 - - + +
212A PHE* 4.1 15.0 - - + -
234A ALA 2.9 19.6 + - - +
235A ARG* 3.6 7.9 - - - +
237A LYS* 1.3 75.9 - - - +
239A ALA* 1.3 60.3 + - - +
241A SER* 2.8 18.3 + - - +
242A LEU* 3.3 17.3 - - - +
280A LEU* 3.9 23.8 - - + -
283A LEU* 4.0 21.1 - - + -
2205A UNX 3.9 12.5 - - - -
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Residues in contact with ALA 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 ARG 3.0 18.2 + - - +
236A GLU* 3.5 6.1 - - - +
238A LEU* 1.3 76.1 - - - +
240A GLU* 1.4 61.0 + - - +
242A LEU* 3.1 13.5 + - - -
273A LEU* 4.1 12.8 - - + -
276A ALA* 3.2 31.1 - - + +
277A LYS* 3.9 33.2 - - + +
280A LEU* 4.7 4.2 - - + +
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Residues in contact with GLU 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 2.9 17.0 + - - +
237A LYS* 3.6 9.4 - - - +
238A LEU 3.4 0.2 - - - -
239A ALA* 1.4 75.2 - - - +
241A SER* 1.3 53.7 + - - +
243A ARG* 2.7 55.5 + - - +
246A ASN* 2.6 33.4 + - - +
273A LEU* 4.9 2.8 - - + +
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Residues in contact with SER 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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184A TYR* 3.7 14.1 + - - -
201A HIS* 4.2 23.6 - - - -
205A ASN* 3.5 14.7 + - - -
237A LYS 3.4 9.1 + - - -
238A LEU* 2.8 19.9 + - - +
240A GLU* 1.3 77.5 - - - +
242A LEU* 1.4 59.4 + - - +
243A ARG 3.5 1.6 - - - -
246A ASN* 3.4 23.8 - - - +
247A LEU* 4.4 5.9 - - - +
250A ARG* 5.5 3.3 + - - -
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Residues in contact with LEU 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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184A TYR* 3.4 26.2 - - + +
188A PHE* 3.6 31.9 - - + -
238A LEU* 3.3 17.3 - - + +
239A ALA 3.1 11.4 + - - +
241A SER* 1.4 76.1 - - - +
243A ARG* 1.3 61.7 + - - +
247A LEU* 3.3 23.6 - - + +
276A ALA* 3.6 12.7 - - - +
279A HIS* 3.5 21.3 - - + +
280A LEU* 3.7 37.9 - - + +
283A LEU* 4.3 15.5 - - + -
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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