Contacts of the helix formed by residues 252 - 260 (chain B) in PDB entry 6CNB
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 PRO 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B ILE 3.6 9.2 - - - +
241B TYR* 3.4 20.9 - - + -
251B ILE* 1.3 89.4 - - + +
253B ILE* 1.3 66.0 + - - +
254B ALA* 3.0 6.1 - - + +
255B ILE* 2.9 45.8 + - + +
256B VAL 3.4 4.0 + - - -
286B ASN* 4.9 3.4 - - - +
289B GLU* 3.6 30.3 - - + +
290B SER 5.5 1.3 - - - +
293B LEU* 6.1 0.7 - - + -
304B TYR* 4.2 11.4 - - + +
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Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B GLN* 6.0 0.4 - - - +
232B TYR* 3.2 38.4 - - + +
240B ILE* 3.4 8.3 + - + -
242B LEU* 3.7 24.2 - - + -
251B ILE 3.3 5.2 + - - -
252B PRO* 1.3 72.5 - - - +
254B ALA* 1.3 63.0 + - - +
256B VAL* 3.5 5.1 + - + +
257B LEU* 2.9 30.7 + - + +
283B PHE* 4.6 5.6 - - + -
286B ASN* 3.1 30.9 - - - +
349B ILE* 4.1 20.4 - - + -
353B THR* 3.8 25.4 - - + +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B PRO* 3.0 3.9 - - + +
253B ILE* 1.3 84.3 - - + +
255B ILE* 1.3 62.6 + - - +
257B LEU* 3.4 5.4 + - - +
258B LYS* 2.9 31.1 + - + +
265B ASP* 6.1 0.2 - - - +
268B ILE* 4.3 12.3 - - + +
283B PHE* 5.6 4.7 - - + -
286B ASN* 4.6 12.9 - - - +
287B LEU* 4.6 16.2 - - + -
290B SER* 3.7 25.6 - - - +
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ILE* 3.8 1.6 - - + -
252B PRO* 2.9 32.7 + - + +
254B ALA* 1.3 76.6 - - - +
256B VAL* 1.3 64.4 + - - +
258B LYS* 3.0 12.0 + - - +
259B ALA* 2.9 19.9 + - - +
289B GLU 5.7 0.2 - - - +
290B SER* 4.3 17.9 - - - +
293B LEU* 4.1 20.4 - - + -
294B ASP* 5.1 6.3 - - + +
301B ALA* 4.1 15.9 - - + +
304B TYR* 3.6 31.0 - - + -
305B ILE* 3.8 25.4 - - + -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B LEU* 3.6 34.3 - - + -
251B ILE* 3.4 31.2 - - + -
252B PRO 3.4 3.0 + - - +
253B ILE* 3.9 10.3 - - + +
255B ILE* 1.3 75.8 - - - +
257B LEU* 1.3 52.9 + - - +
259B ALA* 2.9 9.4 + - + +
260B CYS* 2.4 57.4 + - - -
305B ILE* 4.2 11.2 - - + -
329B THR* 6.1 1.6 - - + -
332B ILE* 6.0 3.4 - - + -
349B ILE* 4.8 6.1 - - + -
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Residues in contact with LEU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B ILE* 2.9 27.4 + - + +
254B ALA* 3.9 3.6 - - - +
256B VAL* 1.3 75.6 - - - +
258B LYS* 1.3 65.1 + - - +
260B CYS* 3.3 17.1 - - + +
262B ILE* 3.2 37.8 - - + +
268B ILE* 3.5 39.3 - - + -
271B LEU* 5.5 2.5 - - + -
272B VAL* 4.3 17.7 - - + -
283B PHE* 5.7 0.9 - - + -
346B ALA 3.6 27.1 - - - +
349B ILE* 5.2 4.7 - - + -
350B ALA* 4.3 12.3 - - + +
353B THR* 6.0 1.3 - - + +
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Residues in contact with LYS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ALA* 2.9 28.0 + - - +
255B ILE* 3.1 9.9 - - - +
257B LEU* 1.3 74.4 - - - +
259B ALA* 1.3 53.7 + - - +
261B GLY* 2.6 30.0 + - - -
262B ILE 3.4 18.3 + - - +
263B LEU* 4.1 13.7 - - + +
265B ASP* 3.5 45.1 + - - +
268B ILE* 3.9 8.5 - - + +
290B SER* 3.8 19.0 + - - +
294B ASP 5.9 0.2 - - - +
295B ILE* 3.7 32.1 - - + +
296B TYR 5.6 1.3 - - - +
297B THR* 3.7 13.7 - - + +
301B ALA* 4.9 11.2 - - + -
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Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B ILE 2.9 14.1 + - - +
256B VAL* 3.5 10.3 - - + +
258B LYS* 1.3 72.5 - - - +
260B CYS* 1.3 56.1 + - - +
261B GLY 3.0 4.3 + - - -
297B THR* 3.2 22.0 + - - +
301B ALA* 4.1 6.2 - - - +
302B LEU* 3.5 42.9 - - + +
305B ILE* 4.6 7.2 - - + -
329B THR* 3.8 11.1 - - + +
342B PHE* 3.8 6.8 - - - -
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Residues in contact with CYS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B VAL* 2.4 57.4 + - - +
257B LEU* 3.3 16.8 - - - +
258B LYS 3.0 0.4 + - - -
259B ALA* 1.3 67.8 - - - +
261B GLY* 1.3 57.2 + - - +
262B ILE 3.5 1.1 - - - -
329B THR* 4.1 17.7 - - - -
342B PHE* 2.9 23.4 - - - +
345B LYS* 5.3 2.7 - - - -
346B ALA* 3.1 32.2 - - + +
349B ILE* 3.9 22.0 - - - -
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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