Contacts of the helix formed by residues 236 - 253 (chain A) in PDB entry 4S3F
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 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLY 4.2 0.2 + - - -
235A MET* 1.3 76.7 - - - +
237A VAL* 1.3 63.3 + - - -
239A GLY* 3.2 0.7 + - - -
240A ILE* 3.2 30.2 + - - +
263A LEU* 5.0 3.7 - - - +
264A THR 4.4 4.2 + - - -
266A ALA* 6.0 0.4 - - - +
269A GLU* 5.6 5.2 + - - -
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A MET 3.6 0.2 + - - -
236A GLY* 1.3 68.7 - - - -
238A LYS* 1.3 66.0 + - - +
240A ILE* 3.2 10.6 + - + +
241A VAL* 2.9 39.5 + - + +
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Residues in contact with LYS 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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206A SER 5.4 4.0 + - - -
207A LYS* 5.0 14.4 - - - +
232A GLU 4.3 5.7 + - - -
233A ALA* 2.8 34.7 + - - +
234A GLY* 4.5 4.9 - - - -
235A MET 3.7 9.6 - - - +
236A GLY 3.3 0.4 - - - -
237A VAL* 1.3 78.6 - - - +
239A GLY* 1.3 56.7 + - - +
241A VAL* 4.0 3.6 - - - +
242A ALA* 2.9 42.6 + - + +
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Residues in contact with GLY 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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233A ALA* 3.4 21.4 - - - +
234A GLY 3.8 15.0 - - - -
235A MET 3.2 8.1 + - - -
236A GLY 3.8 3.4 - - - -
238A LYS* 1.3 76.9 - - - +
240A ILE* 1.3 61.5 + - - +
243A SER* 2.7 33.8 + - - -
263A LEU* 3.5 9.9 - - - -
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Residues in contact with ILE 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 GLY* 3.2 21.0 + - - +
237A VAL* 3.2 12.5 + - + +
239A GLY* 1.3 75.7 - - - +
241A VAL* 1.3 68.6 + - + +
243A SER* 3.4 2.1 + - - -
244A ALA* 3.1 24.6 + - + +
263A LEU* 3.7 14.1 - - + +
273A LYS* 5.2 9.0 - - + -
277A VAL* 3.9 39.2 - - + +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A VAL* 2.9 36.5 + - + +
238A LYS* 4.0 3.1 - - - +
240A ILE* 1.3 75.3 - - + +
242A ALA* 1.3 62.5 + - - +
244A ALA* 3.3 5.4 + - - +
245A ALA* 2.8 38.9 + - + +
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER 5.9 0.7 - - - +
208A ALA* 4.4 5.0 - - + +
230A LEU* 3.5 19.2 - - + +
233A ALA 4.6 8.3 - - - +
238A LYS* 2.9 29.0 + - + +
239A GLY 4.1 2.7 - - - +
241A VAL* 1.3 79.1 - - - +
243A SER* 1.3 63.2 + - - +
245A ALA* 3.8 5.3 - - - +
246A ALA* 3.0 26.5 + - - +
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Residues in contact with SER 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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230A LEU* 4.1 13.8 + - - +
233A ALA* 3.3 17.3 - - - +
239A GLY 2.7 23.5 + - - -
240A ILE* 3.7 4.3 - - - -
241A VAL 3.2 0.2 - - - -
242A ALA* 1.3 77.5 - - - +
244A ALA* 1.3 61.7 + - - +
246A ALA 3.4 0.2 + - - -
247A LEU* 3.1 31.5 + - - +
261A VAL* 3.7 30.4 - - - +
262A SER 4.7 1.7 + - - -
277A VAL* 5.0 0.4 - - - -
281A ILE* 4.1 9.4 - - - -
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Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE* 3.1 19.6 + - + +
241A VAL* 3.8 5.2 - - - +
243A SER* 1.3 76.5 - - - +
245A ALA* 1.3 57.8 + - - +
247A LEU* 4.3 0.2 - - - +
248A ALA* 3.0 35.3 + - - +
281A ILE* 3.8 28.2 - - + +
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Residues in contact with ALA 245 (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 ALA* 4.4 8.9 - - + +
212A VAL* 5.3 0.3 - - - +
241A VAL* 2.8 24.5 + - + +
242A ALA* 3.8 6.1 - - - +
244A ALA* 1.3 76.2 - - - +
246A ALA* 1.3 57.2 + - - +
248A ALA* 5.1 1.3 - - - -
249A PRO* 3.0 26.2 - - - +
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Residues in contact with ALA 246 (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 ALA* 3.6 30.5 - - + +
211A LEU* 3.8 19.1 - - + +
212A VAL* 3.7 16.1 - - - +
230A LEU* 3.9 11.7 - - + -
242A ALA 3.0 18.5 + - - +
243A SER 3.8 3.6 - - - +
245A ALA* 1.3 75.4 - - - +
247A LEU* 1.3 64.9 + - + +
249A PRO* 3.6 6.6 - - - +
250A LEU* 3.9 9.2 - - - +
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Residues in contact with LEU 247 (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 LEU* 3.9 20.2 - - + -
228A LEU* 3.9 24.5 - - + +
229A GLY* 4.1 1.8 - - - -
230A LEU* 4.0 16.4 - - + +
243A SER* 3.1 19.5 + - - +
244A ALA 4.3 1.3 - - - +
246A ALA* 1.3 81.7 - - + +
248A ALA* 1.3 62.7 + - - +
250A LEU* 3.1 5.4 + - - +
251A LEU* 2.9 39.9 + - + +
259A ILE* 4.1 37.5 - - + -
260A ARG 5.0 1.8 - - - +
261A VAL* 4.9 7.4 - - + -
281A ILE* 4.2 20.0 - - + -
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Residues in contact with ALA 248 (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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244A ALA 3.0 18.5 + - - +
245A ALA* 4.7 1.6 - - - +
247A LEU* 1.3 76.3 - - - +
249A PRO* 1.3 68.7 - - + +
251A LEU* 4.0 0.2 - - - +
252A LEU* 2.9 31.3 + - + +
281A ILE* 5.2 1.7 - - + +
285A LEU* 3.9 32.3 - - + -
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Residues in contact with PRO 249 (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 VAL* 4.1 24.7 - - + -
216A ARG* 5.0 5.8 - - - +
245A ALA 3.0 23.1 - - - +
246A ALA 3.6 4.5 - - - +
247A LEU 3.5 3.4 - - - -
248A ALA* 1.3 92.9 - - + +
250A LEU* 1.3 59.9 + - - +
252A LEU* 3.9 7.0 - - + +
253A GLU* 3.3 31.6 + - - +
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Residues in contact with LEU 250 (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 LEU* 3.9 13.0 - - + +
212A VAL* 3.8 29.6 - - + +
215A TYR* 3.7 27.1 - - + -
216A ARG* 4.2 6.1 - - + +
228A LEU* 3.6 32.5 - - + -
246A ALA 3.9 14.4 - - - +
247A LEU 3.1 6.3 + - - +
249A PRO* 1.3 75.6 - - - +
251A LEU* 1.3 65.2 + - - +
253A GLU* 3.1 14.1 + - - +
254A GLY 3.2 0.2 + - - -
255A ILE* 3.0 51.6 + - + +
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Residues in contact with LEU 251 (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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24A ILE* 3.9 25.8 - - + -
228A LEU* 4.0 13.0 - - + -
247A LEU* 2.9 29.1 + - + +
250A LEU* 1.3 76.2 - - - +
252A LEU* 1.3 62.1 + - - +
254A GLY* 3.1 14.2 + - - -
255A ILE 3.5 16.8 - - - +
256A GLY* 4.5 4.0 - - - +
259A ILE* 4.4 12.3 - - + -
281A ILE* 3.9 28.0 - - + -
282A LEU* 3.9 15.7 - - + -
285A LEU* 4.0 10.3 - - + -
287A LEU* 3.7 25.0 - - + +
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Residues in contact with LEU 252 (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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4A MET* 4.6 12.3 - - - +
248A ALA* 2.9 22.2 + - + +
249A PRO* 3.9 7.2 - - + +
251A LEU* 1.3 78.7 - - - +
253A GLU* 1.3 57.7 + - + +
254A GLY 3.2 1.0 + - - -
285A LEU* 4.1 37.7 - - + +
287A LEU* 6.0 3.6 - - + -
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Residues in contact with GLU 253 (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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4A MET* 3.5 38.7 - - + +
6A ARG* 5.9 0.2 - - - +
216A ARG* 2.6 54.4 + - - +
249A PRO* 3.3 14.7 + - - +
250A LEU* 3.1 13.2 + - - +
252A LEU* 1.3 76.4 - - + +
254A GLY* 1.3 59.0 + - - +
255A ILE* 3.4 16.2 + - + +
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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