Contacts of the helix formed by residues 241 - 251 (chain A) in PDB entry 6NFJ
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 ASN 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A TRP* 3.7 9.3 + - + -
240A HIS* 1.3 85.7 - - + +
242A PRO* 1.3 69.6 - - - +
243A TYR* 3.2 18.6 + - - +
244A LEU* 3.3 28.4 + - - +
245A VAL* 3.4 10.2 + - - +
299A THR* 2.7 19.8 + - - +
301A GLY* 3.2 26.8 + - - +
373A SER* 4.9 9.3 + - - -
377A ASN* 4.8 2.8 - - - +
378A ASN* 2.9 28.5 + - - -
416A GLU* 5.4 1.2 + - - +
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Residues in contact with PRO 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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239A ILE* 3.6 20.2 - - + -
240A HIS 3.7 0.4 - - - -
241A ASN* 1.3 86.4 - - - +
243A TYR* 1.3 64.7 + - - +
244A LEU 3.3 0.2 - - - -
245A VAL* 3.2 22.3 + - + +
246A ALA 3.3 8.8 + - - -
273A LEU* 3.7 17.7 - - + +
298A ILE* 3.9 12.1 - - + -
299A THR 3.5 9.6 - - - +
300A LEU* 3.7 18.4 - - + -
301A GLY 5.3 0.2 - - - +
330A PHE* 3.5 38.7 - - + -
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Residues in contact with TYR 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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241A ASN* 3.2 11.1 - - - +
242A PRO* 1.3 82.6 - - + +
244A LEU* 1.3 77.6 + - + +
246A ALA* 4.0 0.7 - - - +
247A TRP* 2.9 67.3 + + + +
248A HIS* 5.7 0.2 - - - -
301A GLY 5.0 3.4 - - - +
325A SER 4.0 3.1 - - - -
326A VAL* 3.6 49.4 - - + +
329A TRP* 3.5 35.4 - + - -
330A PHE* 3.6 15.2 - - + -
378A ASN* 4.6 3.6 - - - -
384A THR* 3.1 31.1 + - + -
385A MET* 4.4 4.6 - - + -
386A ALA 5.3 0.5 + - - -
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Residues in contact with LEU 244 (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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196A TRP* 3.5 37.0 - - + -
241A ASN* 3.3 15.0 + - - +
242A PRO 3.3 0.2 - - - -
243A TYR* 1.3 100.0 - - + +
245A VAL* 1.3 65.6 + - - +
248A HIS* 3.1 45.0 + - + +
249A GLY 3.5 2.4 + - - -
255A HIS* 3.7 17.6 - - + +
377A ASN* 3.4 33.9 - - + +
378A ASN* 3.3 20.4 - - - +
384A THR* 4.6 0.9 - - + -
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TYR* 3.9 28.7 - - + +
196A TRP* 3.3 37.9 - - + +
209A TRP* 4.5 12.3 - - + +
239A ILE* 4.5 2.9 - - + -
240A HIS 4.5 0.4 - - - +
241A ASN 3.4 10.5 - - - +
242A PRO* 3.2 14.5 + - + +
244A LEU* 1.3 78.8 - - - +
246A ALA* 1.3 57.3 + - - +
249A GLY* 3.6 17.1 + - - -
250A TYR* 3.8 10.9 - - + -
255A HIS* 5.7 2.7 - - - -
256A ALA 4.6 5.7 - - - +
269A VAL* 4.9 0.7 - - + -
273A LEU* 3.9 15.5 - - + -
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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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242A PRO 3.3 11.0 + - - +
243A TYR 4.2 1.1 - - - +
244A LEU 3.2 0.4 - - - -
245A VAL* 1.3 79.7 - - - +
247A TRP* 1.3 65.1 + - - +
248A HIS 3.4 0.2 - - - -
250A TYR* 3.0 27.7 + - - +
251A GLY 3.6 1.9 + - - -
266A VAL* 3.5 28.9 - - - +
269A VAL* 3.7 19.5 - - + -
270A GLY* 4.0 7.9 - - - +
329A TRP* 4.2 12.6 - - + -
330A PHE* 4.9 0.2 - - + -
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Residues in contact with TRP 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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243A TYR* 2.9 58.8 + + + +
244A LEU* 4.9 0.2 - - - -
246A ALA* 1.3 74.4 - - - +
248A HIS* 1.3 81.1 + + + +
251A GLY* 3.1 8.9 + - - -
252A THR* 3.0 39.6 + - + +
266A VAL* 4.5 13.9 - - + +
267A TYR* 4.4 16.8 - + - -
325A SER 6.0 0.9 - - - -
329A TRP* 4.6 10.7 - + + -
383A ASN 3.4 16.4 + - - -
384A THR 3.6 7.7 + - - -
385A MET 5.5 6.3 - - - -
386A ALA* 5.6 9.0 - - + -
184D LEU* 3.4 38.8 - - + -
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Residues in contact with HIS 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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243A TYR* 5.7 0.2 - + - -
244A LEU* 3.1 36.5 + - + +
247A TRP* 1.3 94.4 - + - +
249A GLY* 1.3 58.1 + - - +
250A TYR 3.5 0.2 - - - -
252A THR* 3.1 22.4 - - + +
253A GLY 3.6 1.6 + - - -
254A MET* 2.9 18.0 + - + +
255A HIS* 2.7 53.0 + + + +
377A ASN 4.2 3.6 - - - -
381A PRO* 4.7 7.4 - - + +
383A ASN* 4.3 3.8 + - - -
384A THR* 3.1 54.6 + - + +
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Residues in contact with GLY 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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244A LEU 3.5 6.3 + - - -
245A VAL 3.6 12.0 + - - -
247A TRP 3.5 0.2 - - - -
248A HIS* 1.3 78.4 - - - +
250A TYR* 1.3 69.5 + - - +
251A GLY 3.9 0.2 - - - -
255A HIS* 3.6 4.9 - - - -
256A ALA 3.5 22.2 - - - -
257A PRO* 3.5 4.3 - - - +
258A GLY 3.4 7.3 + - - -
259A GLU 3.2 22.1 + - - -
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Residues in contact with TYR 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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203A GLN* 3.2 28.1 + - - -
207A GLY 4.3 5.5 + - - -
209A TRP* 4.3 12.0 + + + -
210A LYS* 4.1 15.3 - - + -
245A VAL* 3.8 16.8 - - + -
246A ALA 3.0 11.4 + - - +
249A GLY* 1.3 82.3 - - - +
251A GLY* 1.3 54.0 + - - +
257A PRO* 3.6 29.2 - - + +
259A GLU* 3.0 39.6 - - + +
262A ASN* 3.3 22.5 + - + +
265A ALA* 3.9 24.2 - - + -
266A VAL* 3.3 16.7 - - + +
269A VAL* 3.5 30.7 - - + -
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Residues in contact with GLY 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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247A TRP* 3.1 14.8 + - - -
250A TYR* 1.3 79.4 - - - +
252A THR* 1.3 63.6 + - - +
253A GLY 3.4 1.1 - - - -
259A GLU 3.4 0.2 + - - -
260A LYS* 3.4 3.3 - - - +
261A GLY* 2.6 28.3 + - - -
266A VAL* 3.5 13.7 - - - +
184D LEU* 4.3 12.3 - - - +
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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