Contacts of the helix formed by residues 242 - 256 (chain K) in PDB entry 3D1N
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 THR 242 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240K SER 5.2 1.8 - - - +
241K PHE* 1.3 73.6 - - - +
243K PRO* 1.3 69.3 - - - +
244K GLN* 3.9 9.3 + - - +
245K ALA* 2.9 23.4 + - - +
246K ILE* 2.8 22.2 + - - +
273K TYR* 3.1 12.5 + - + +
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Residues in contact with PRO 243 (chain K).
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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241K PHE 3.5 4.2 - - - +
242K THR* 1.3 82.6 - - - +
244K GLN* 1.3 66.9 + - - +
246K ILE* 3.0 35.3 + - + +
247K GLU* 3.0 16.2 + - - +
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Residues in contact with GLN 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242K THR* 4.0 10.1 - - - +
243K PRO* 1.3 83.3 - - - +
245K ALA* 1.3 59.4 + - - +
247K GLU* 3.5 8.7 + - - +
248K ALA* 3.3 17.5 + - - +
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Residues in contact with ALA 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241K PHE* 4.9 2.0 - - + -
242K THR* 2.9 19.3 + - - +
244K GLN* 1.3 76.4 - - - +
246K ILE* 1.3 64.6 + - - +
247K GLU 3.3 0.2 - - - -
248K ALA* 3.4 10.8 - - - +
249K LEU* 3.2 30.2 + - + +
271K LEU* 3.9 19.0 - - + +
273K TYR* 3.5 28.9 - - + -
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Residues in contact with ILE 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C A 5.1 8.5 - - - +
241K PHE* 3.4 35.0 - - + +
242K THR 2.8 4.6 + - - -
243K PRO* 3.0 30.9 + - + +
245K ALA* 1.3 80.1 - - - +
247K GLU* 1.3 64.9 + - + +
249K LEU* 3.7 16.1 + - + +
250K ASN* 2.7 38.3 + - - +
281K TRP* 4.8 8.2 - - + +
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Residues in contact with GLU 247 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K PRO* 3.0 23.7 + - - +
244K GLN* 4.0 7.1 - - - +
246K ILE* 1.3 85.1 - - + +
248K ALA* 1.3 65.3 + - - +
249K LEU 3.0 2.2 + - - -
250K ASN* 3.1 8.9 + - - +
251K ALA* 2.8 30.5 + - + +
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Residues in contact with ALA 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244K GLN 3.3 13.2 + - - +
245K ALA* 3.4 16.2 - - - +
247K GLU* 1.3 79.2 - - - +
249K LEU* 1.3 65.0 + - - +
251K ALA* 3.5 4.8 - - - +
252K TYR* 3.2 19.4 + - - +
271K LEU* 4.1 21.3 - - + -
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Residues in contact with LEU 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241K PHE* 5.3 4.9 - - + -
245K ALA* 3.2 17.6 + - + +
246K ILE* 3.8 14.8 - - + +
247K GLU 3.0 1.4 + - - -
248K ALA* 1.3 77.1 - - - +
250K ASN* 1.3 51.3 + - - +
251K ALA 3.0 0.9 - - - -
252K TYR* 2.7 13.7 + - - +
253K PHE* 2.6 30.6 + - - +
267K MSE 6.0 2.9 - - + -
271K LEU* 4.8 12.8 - - + -
273K TYR* 6.4 2.2 - - + -
278K VAL* 4.2 24.5 - - + -
281K TRP* 3.3 63.3 - - + +
282K PHE* 4.4 9.2 - - + -
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Residues in contact with ASN 250 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246K ILE* 2.7 31.8 + - - +
247K GLU* 3.1 20.8 + - - +
249K LEU* 1.3 69.8 - - - +
251K ALA* 1.3 60.0 + - - +
253K PHE* 3.2 20.3 - - + -
254K GLU* 2.8 28.6 + - - +
281K TRP* 3.3 19.9 - - + -
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Residues in contact with ALA 251 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247K GLU* 2.8 23.5 + - + +
248K ALA* 3.5 7.0 - - - +
249K LEU 2.9 0.2 + - - -
250K ASN* 1.3 75.4 - - - +
252K TYR* 1.3 59.2 + - - +
253K PHE 2.9 8.7 + - - -
254K GLU* 3.2 4.3 + - - +
255K LYS* 3.0 20.5 + - - +
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Residues in contact with TYR 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248K ALA 3.2 9.1 + - - +
249K LEU* 2.7 11.4 + - - +
251K ALA* 1.3 76.0 - - - +
253K PHE* 1.3 56.1 + - - +
255K LYS* 3.6 8.4 - - - +
256K ASN* 2.8 32.4 + - - +
267K MSE 4.1 26.3 - - + +
282K PHE* 4.1 4.0 - - + -
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Residues in contact with PHE 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249K LEU 2.6 9.3 + - - +
250K ASN* 3.2 25.1 - - + -
251K ALA 2.9 0.2 - - - -
252K TYR* 1.3 72.2 - - - +
254K GLU* 1.3 69.5 + - + +
255K LYS 3.0 1.7 + - - -
257K PRO* 3.4 42.3 - - + +
281K TRP* 3.5 21.3 - + + -
282K PHE* 3.4 26.0 - + + -
285K ARG* 3.9 28.9 - - + -
286K ARG* 4.2 15.9 - - + -
289K LEU* 4.5 17.7 - - + -
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Residues in contact with GLU 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250K ASN 2.8 22.3 + - - +
251K ALA* 3.7 4.9 - - - +
253K PHE* 1.3 76.9 - - - +
255K LYS* 1.3 63.4 - - - +
257K PRO* 4.5 3.6 - - - +
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Residues in contact with LYS 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251K ALA 3.0 15.6 + - - +
252K TYR* 3.6 9.4 - - - +
253K PHE 3.0 0.6 - - - -
254K GLU* 1.3 79.9 - - - +
256K ASN* 1.3 62.7 + - + +
257K PRO* 3.1 11.7 - - - +
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Residues in contact with ASN 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252K TYR 2.8 19.4 + - - +
253K PHE 3.5 3.4 - - - -
255K LYS* 1.3 77.3 - - + +
257K PRO* 1.3 69.9 - - - +
258K LEU 4.2 10.2 + - - +
259K PRO* 3.6 12.2 - - + +
263K GLU* 2.9 28.4 + - - +
267K MSE 6.2 0.9 - - + -
282K PHE* 3.5 11.1 - - - -
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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