Contacts of the helix formed by residues 247 - 262 (chain A) in PDB entry 3L43
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 ASP 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASP* 5.9 1.3 - - - -
237A ARG* 4.0 1.5 - - - -
245A LYS 3.7 5.0 + - - +
246A LYS* 1.3 80.7 - - - +
248A ILE* 1.4 60.1 - - - +
249A LYS* 3.7 18.3 - - + +
250A ALA* 3.5 15.2 + - + +
251A ALA* 3.2 23.0 + - - +
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLU* 3.3 28.5 - - + +
50A ASN* 4.1 26.9 - - - +
53A GLY* 3.6 25.3 + - - +
54A ARG* 3.5 22.7 - - - +
55A ASP* 3.4 20.1 + - - +
237A ARG* 3.6 21.8 - - - +
247A ASP* 1.4 70.5 - - - +
249A LYS* 1.4 59.1 + - - +
251A ALA* 3.3 6.2 + - - +
252A MET* 3.1 37.6 + - + +
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Residues in contact with LYS 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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247A ASP* 4.1 16.1 - - + +
248A ILE* 1.4 78.8 - - - +
250A ALA* 1.4 60.4 + - - +
252A MET* 3.5 6.2 + - - +
253A LEU* 3.4 33.3 + - + +
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Residues in contact with ALA 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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246A LYS* 3.9 25.8 - - + -
247A ASP* 3.5 18.1 + - + +
249A LYS* 1.4 77.2 - - - +
251A ALA* 1.4 63.6 + - - +
253A LEU* 3.8 5.9 + - - +
254A ALA* 3.3 24.1 + - - +
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Residues in contact with ALA 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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50A ASN* 4.9 8.5 - - - +
235A VAL 5.1 1.6 - - - +
236A ASN* 5.7 0.7 - - - -
237A ARG* 3.7 29.4 - - + +
246A LYS* 4.4 6.7 - - - +
247A ASP 3.2 14.4 + - - +
248A ILE* 3.4 11.7 - - - +
249A LYS 3.3 0.4 - - - -
250A ALA* 1.4 76.6 - - - +
252A MET* 1.4 59.4 + - + +
254A ALA* 3.3 2.4 + - - +
255A GLU* 2.9 26.7 + - - +
308A UNX 3.0 19.9 - - - -
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Residues in contact with MET 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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50A ASN* 4.2 27.6 - - - +
248A ILE* 3.1 22.2 + - + +
249A LYS* 3.5 6.7 + - - +
251A ALA* 1.4 76.8 - - - +
253A LEU* 1.3 57.9 + - + +
255A GLU* 3.4 24.2 + - - +
256A ARG* 2.9 28.8 + - - +
274A THR* 3.6 32.5 - - + -
275A PRO* 3.8 24.1 - - + +
278A GLN* 4.4 7.2 - - - +
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Residues in contact with LEU 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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249A LYS* 3.4 23.4 + - + +
250A ALA* 4.3 6.1 - - - +
251A ALA 3.4 0.6 - - - -
252A MET* 1.3 74.3 - - + +
254A ALA* 1.4 60.4 + - - +
256A ARG* 3.3 11.0 + - + +
257A LYS* 2.8 30.6 + - - +
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Residues in contact with ALA 254 (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 VAL* 5.9 1.1 - - - -
246A LYS* 4.0 17.7 - - - +
250A ALA 3.3 19.1 + - - +
251A ALA 3.6 4.7 - - - +
253A LEU* 1.4 74.4 - - - +
255A GLU* 1.4 51.6 + - - +
257A LYS* 3.5 11.0 + - - +
258A PHE* 2.9 34.2 + - - +
308A UNX 4.2 5.6 - - - -
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Residues in contact with GLU 255 (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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50A ASN* 5.8 0.2 - - - -
234A VAL* 3.4 3.6 - - - +
235A VAL* 2.9 43.7 + - + +
251A ALA 2.9 17.9 + - - +
252A MET* 3.4 18.6 - - - +
254A ALA* 1.4 73.5 - - - +
256A ARG* 1.4 62.5 + - - +
258A PHE* 3.4 7.6 + - - +
259A PHE* 3.3 40.3 + - + -
273A GLY* 3.7 5.2 - - - -
274A THR* 2.7 51.4 + - - -
275A PRO* 3.7 5.9 - - - +
308A UNX 3.9 2.8 - - - -
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Residues in contact with ARG 256 (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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252A MET 2.9 16.4 + - - +
253A LEU* 3.7 12.8 - - + +
255A GLU* 1.4 71.7 - - - +
257A LYS* 1.4 65.5 + - - +
259A PHE* 3.5 6.6 + - - +
260A LEU* 3.2 62.2 + - + +
269A ALA* 3.3 24.8 + - - +
270A ASP* 3.1 29.3 + - - +
272A MET 5.3 1.4 + - - -
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Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A LEU 2.8 17.7 + - - +
254A ALA* 3.5 10.8 - - - +
256A ARG* 1.4 77.0 - - - +
258A PHE* 1.4 50.7 + - - +
260A LEU* 3.3 7.8 + - - +
261A SER* 2.8 51.1 + - - +
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Residues in contact with PHE 258 (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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207A LEU* 3.4 43.5 - - + -
208A ASP* 3.8 22.7 - - + -
235A VAL* 3.5 20.0 - - + -
254A ALA 2.9 18.7 + - - +
255A GLU* 3.5 8.5 - - - +
256A ARG 3.4 0.2 - - - -
257A LYS* 1.4 74.9 - - - +
259A PHE* 1.4 67.4 + + - +
261A SER* 3.9 3.4 - - - -
262A HIS* 3.0 53.9 + + + +
265A TYR* 4.0 16.6 - + - -
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Residues in contact with PHE 259 (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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207A LEU* 3.8 20.6 - - + -
220A LEU* 4.8 0.7 - - + -
233A GLY* 3.2 37.5 - - - -
234A VAL* 3.9 2.0 - - - -
235A VAL* 4.3 9.2 - - + -
255A GLU* 3.3 32.8 + - + +
256A ARG* 3.5 6.5 + - - +
257A LYS 3.4 0.2 - - - -
258A PHE* 1.4 83.3 - + - +
260A LEU* 1.3 60.4 + - - +
262A HIS 4.0 2.4 - - - +
265A TYR* 3.6 34.1 - + + +
266A ARG* 3.4 26.7 + - - -
269A ALA* 3.8 18.7 - - + +
272A MET* 3.7 29.2 - - + -
273A GLY* 3.6 14.6 - - - -
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Residues in contact with LEU 260 (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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256A ARG* 3.2 60.2 + - + +
257A LYS* 3.9 6.1 - - - +
259A PHE* 1.3 76.4 - - - +
261A SER* 1.4 61.8 + - - +
262A HIS 3.6 0.2 - - - -
266A ARG* 3.6 29.5 - - + +
269A ALA* 3.8 20.9 - - + -
270A ASP* 5.6 0.2 - - - +
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Residues in contact with SER 261 (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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257A LYS* 2.8 36.3 + - - +
258A PHE* 4.2 2.9 - - - -
260A LEU* 1.4 76.4 - - - +
262A HIS* 1.3 61.7 + - - +
263A PRO* 3.4 10.4 - - - +
266A ARG* 5.3 2.1 + - - -
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Residues in contact with HIS 262 (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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207A LEU 5.5 1.2 + - - -
214A THR 4.9 6.1 + - - -
215A ASP* 4.2 9.9 - - + +
258A PHE* 3.0 39.1 + + - +
259A PHE 4.0 0.6 + - - +
260A LEU 3.6 0.6 - - - -
261A SER* 1.3 74.4 - - - +
263A PRO* 1.4 70.5 - - + +
264A ALA* 3.2 39.6 + - + +
265A TYR* 3.2 41.5 + + + +
266A ARG* 2.9 32.6 + - - +
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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