Contacts of the helix formed by residues 228 - 240 (chain A) in PDB entry 3L3N
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 SER 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A THR* 3.6 6.6 - - - +
227A PRO* 1.3 78.5 - - - +
229A LEU* 1.3 65.0 + - - +
230A GLU 3.4 2.2 - - - -
231A GLN* 3.2 19.4 + - - +
232A ASP* 2.7 50.1 + - - -
235A ARG* 5.0 3.6 - - - -
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Residues in contact with LEU 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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221A ARG* 3.8 44.2 - - + +
224A TYR* 3.9 37.2 - - + -
226A THR* 2.8 28.1 + - + +
227A PRO 3.2 2.2 + - - -
228A SER* 1.3 76.8 - - - +
230A GLU* 1.3 64.5 + - + +
232A ASP* 3.2 2.5 + - - +
233A LEU* 2.9 59.2 + - + +
469A TRP* 5.0 4.5 - - + -
521A ILE* 5.5 0.4 - - + -
525A VAL* 5.5 0.9 - - + -
587A MET* 4.6 11.4 - - + -
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Residues in contact with GLU 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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221A ARG* 3.1 47.2 + - - +
227A PRO 4.9 1.8 + - - -
228A SER 3.3 1.0 + - - -
229A LEU* 1.3 76.9 - - + +
231A GLN* 1.3 61.2 + - + +
233A LEU* 4.0 4.5 - - - +
234A GLU* 3.0 27.5 + - - +
462A TYR* 4.6 2.1 + - - -
466A GLN* 5.6 1.9 + - - +
469A TRP* 3.7 24.2 - - + +
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Residues in contact with GLN 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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227A PRO 5.5 0.8 + - - -
228A SER* 3.2 19.7 + - - +
230A GLU* 1.3 77.7 - - + +
232A ASP* 1.3 66.9 + - - +
234A GLU* 3.3 6.5 + - - +
235A ARG* 3.0 46.0 + - - +
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Residues in contact with ASP 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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226A THR* 3.5 13.0 - - - +
228A SER* 2.7 46.0 + - - +
229A LEU* 3.6 5.2 - - - +
231A GLN* 1.3 75.3 - - - +
233A LEU* 1.3 64.4 + - - +
235A ARG* 2.6 38.5 + - - +
236A LEU* 3.1 28.4 + - + +
574A TRP* 5.9 0.5 - - - -
587A MET* 4.4 19.3 - - + +
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Residues in contact with LEU 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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224A TYR* 6.5 0.2 - - + -
229A LEU* 2.9 41.5 + - + +
230A GLU* 4.0 4.0 - - - +
232A ASP* 1.3 73.7 - - - +
234A GLU* 1.3 61.7 + - - +
236A LEU* 3.3 14.6 + - + -
237A PHE 2.9 23.9 + - - -
462A TYR* 3.5 21.3 - - + -
466A GLN* 5.6 1.6 - - - +
469A TRP* 4.6 7.9 - - + -
521A ILE* 3.5 35.2 - - + -
524A PHE* 3.7 24.8 - - + -
525A VAL* 4.1 11.0 - - + -
587A MET* 4.1 16.4 - - + -
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Residues in contact with GLU 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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230A GLU 3.0 17.0 + - - +
231A GLN* 3.3 7.2 + - - +
233A LEU* 1.3 76.5 - - - +
235A ARG* 1.3 63.7 + - + +
237A PHE* 3.4 7.4 + - - +
238A GLN* 3.0 53.5 + - + +
462A TYR* 2.8 35.9 + - - +
466A GLN* 5.9 0.2 - - - -
492A TYR* 4.5 9.6 + - - -
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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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228A SER* 5.0 3.4 - - - -
231A GLN* 3.0 31.3 + - - +
232A ASP* 2.6 41.9 + - - +
234A GLU* 1.3 77.9 - - + +
236A LEU* 1.3 61.7 + - + +
238A GLN* 3.2 8.0 + - - +
239A GLU* 2.8 38.7 + - - +
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Residues in contact with LEU 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 ASP* 3.1 18.3 + - + +
233A LEU* 3.8 24.0 - - + +
235A ARG* 1.3 79.6 - - + +
237A PHE* 1.3 62.6 + - - +
239A GLU* 3.3 18.3 + - + +
240A LEU* 3.5 17.5 + - - +
524A PHE* 4.1 4.9 - - + -
525A VAL* 6.4 0.2 - - - -
528A ILE* 4.1 26.5 - - + -
587A MET* 3.9 30.3 - - + +
588A SER* 3.8 13.5 - - - +
589A ALA* 3.6 30.0 - - + +
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Residues in contact with PHE 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 LEU 2.9 18.0 + - - +
234A GLU* 3.6 9.2 - - - +
235A ARG 3.2 0.2 - - - -
236A LEU* 1.3 77.0 - - - +
238A GLN* 1.3 86.0 + - - +
240A LEU* 3.1 14.0 + - - +
241A GLN* 3.5 37.2 + - - +
244A TYR* 6.2 0.2 - + - -
458A ILE* 4.1 17.7 - - + -
459A PRO* 3.7 27.8 - - + -
462A TYR* 3.9 31.9 - + + -
491A LYS 5.6 0.2 - - - -
492A TYR* 3.3 39.7 - + + -
524A PHE* 3.8 6.7 - - + -
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Residues in contact with GLN 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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234A GLU* 3.0 45.2 + - + +
235A ARG* 3.2 7.8 + - - +
237A PHE* 1.3 95.2 - - - +
239A GLU* 1.3 61.7 + - + +
241A GLN* 3.2 34.0 + - - +
242A PRO* 3.9 4.3 - - - +
492A TYR* 5.7 0.8 - - - -
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Residues in contact with GLU 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* 2.8 35.3 + - - +
236A LEU* 3.5 12.6 - - + +
237A PHE 3.2 0.6 - - - -
238A GLN* 1.3 76.3 - - - +
240A LEU* 1.3 60.4 + - - +
241A GLN 3.3 1.2 + - - -
242A PRO* 3.7 11.1 - - - +
589A ALA* 3.9 19.5 - - + +
593A LEU* 3.7 30.0 - - + +
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Residues in contact with LEU 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 LEU 3.5 10.2 + - - +
237A PHE 3.1 11.2 + - - +
239A GLU* 1.3 79.4 - - - +
241A GLN* 1.3 58.9 + - - +
242A PRO 3.5 1.1 - - - -
243A LEU* 3.5 11.5 + - + +
244A TYR* 3.0 29.3 + - + +
455A ILE* 3.5 33.7 - - + -
458A ILE* 4.2 24.2 - - + -
528A ILE* 3.5 32.3 - - + -
589A ALA* 4.1 9.4 - - + -
592A MET* 3.5 24.5 - - + -
593A LEU* 4.4 14.4 - - + -
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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