Contacts of the helix formed by residues 256 - 268 (chain B) in PDB entry 6F3T
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 HIS 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B PRO* 3.7 35.5 - - + +
251B LEU* 2.8 27.2 + - + +
254B ASN* 3.5 37.3 + - + +
255B GLN* 1.3 74.1 + - - +
257B GLU* 1.3 57.9 + - - +
258B ASN 3.4 2.5 - - - -
259B GLU* 3.2 27.9 + - + +
260B ALA* 2.9 28.4 + - - +
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Residues in contact with GLU 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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251B LEU 5.3 0.2 - - - -
252B VAL* 5.9 1.3 - - - +
255B GLN* 3.5 6.3 + - - +
256B HIS* 1.3 74.5 - - - +
258B ASN* 1.3 69.1 + - - +
260B ALA* 3.3 6.0 + - + +
261B LYS* 3.0 25.4 + - + +
286B THR* 3.0 50.4 + - - +
287B LYS* 3.2 32.2 + - - +
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Residues in contact with ASN 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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256B HIS 3.4 0.4 - - - -
257B GLU* 1.3 81.6 - - - +
259B GLU* 1.3 71.6 + - - +
261B LYS* 3.4 5.1 + - - +
262B SER* 3.0 25.8 + - - -
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Residues in contact with GLU 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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211B PRO* 3.9 30.3 - - + +
212B THR* 3.8 21.8 - - + +
215B GLU* 4.6 1.4 - - - +
251B LEU* 4.2 8.2 - - + +
256B HIS* 3.2 39.2 + - + +
258B ASN* 1.3 81.4 + - - +
260B ALA* 1.3 57.8 + - - +
262B SER* 3.8 4.8 - - - -
263B PHE* 2.9 30.5 + - - +
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Residues in contact with ALA 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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248B TYR* 3.3 31.9 - - + +
251B LEU* 3.7 24.8 - - + +
252B VAL* 3.8 17.0 - - + +
256B HIS 2.9 16.3 + - - +
257B GLU* 3.7 6.5 - - + +
258B ASN 3.3 0.2 - - - -
259B GLU* 1.3 77.0 - - - +
261B LYS* 1.3 58.2 + - - +
263B PHE* 3.2 1.4 + - - +
264B PHE 2.8 24.8 + - - -
286B THR* 6.2 0.9 - - - -
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Residues in contact with LYS 261 (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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248B TYR* 4.5 2.6 + - - -
257B GLU* 3.0 17.1 + - + +
258B ASN* 4.0 6.1 - - - +
260B ALA* 1.3 75.7 - - - +
262B SER* 1.3 60.2 + - - +
264B PHE* 3.2 7.0 + - + +
265B GLU* 2.9 53.7 + - + +
286B THR* 6.2 4.5 - - + -
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Residues in contact with SER 262 (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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215B GLU* 2.8 25.6 + - - +
258B ASN 3.0 17.7 + - - -
259B GLU* 3.8 5.4 - - - -
261B LYS* 1.3 77.4 - - - +
263B PHE* 1.3 63.1 + - - +
265B GLU* 3.4 9.0 + - - +
266B LYS* 3.1 20.8 + - - +
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Residues in contact with PHE 263 (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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214B TYR* 3.8 24.5 - - + -
215B GLU* 3.2 24.6 + - + +
218B TYR* 3.9 22.2 - + + -
244B PHE* 3.4 41.6 - + - -
247B MET* 3.8 21.3 - - + -
248B TYR* 3.9 20.2 - + + -
251B LEU* 4.1 9.2 - - + -
259B GLU 2.9 19.5 + - - +
260B ALA 3.5 3.6 - - - +
262B SER* 1.3 77.7 - - - +
264B PHE* 1.3 64.4 + - - +
266B LYS* 3.4 1.4 + - - -
267B PHE* 3.3 43.3 + + - -
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Residues in contact with PHE 264 (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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244B PHE* 3.5 28.3 - + - -
248B TYR* 3.8 24.9 - + + -
260B ALA 2.8 16.7 + - - +
261B LYS* 3.2 7.6 + - + +
263B PHE* 1.3 75.1 - - - +
265B GLU* 1.3 67.7 + - + +
266B LYS 3.1 0.2 + - - -
268B HIS* 2.8 63.1 + + + +
279B LEU* 3.3 28.5 - - + -
282B LEU* 3.7 23.8 - - + -
283B SER* 3.8 22.9 - - - -
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Residues in contact with GLU 265 (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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261B LYS* 2.9 50.0 + - + +
262B SER* 3.4 6.9 + - - +
264B PHE* 1.3 79.7 - - + +
266B LYS* 1.3 62.8 + - - +
268B HIS* 3.4 25.8 + - + -
269B GLY 5.1 1.2 + - - -
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Residues in contact with LYS 266 (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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215B GLU* 3.9 25.0 + - - +
219B SER* 3.8 18.5 + - - -
222B LYS* 5.3 0.5 + - - -
262B SER 3.1 17.6 + - - +
263B PHE 3.8 4.3 - - - +
264B PHE 3.1 0.4 - - - -
265B GLU* 1.3 78.3 - - - +
267B PHE* 1.3 87.8 + - + +
269B GLY 5.4 0.8 + - - -
270B ASP* 3.9 8.7 - - - +
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Residues in contact with PHE 267 (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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215B GLU* 3.7 15.9 - - + -
218B TYR* 3.6 49.1 - + + -
219B SER* 3.4 25.4 - - - -
222B LYS* 4.4 13.0 - - + -
244B PHE* 3.7 20.2 - - + -
263B PHE* 3.3 34.7 + + - -
264B PHE 3.3 1.8 + - - -
266B LYS* 1.3 110.7 - - + +
268B HIS* 1.3 63.8 + - - +
269B GLY 3.2 3.4 - - - -
270B ASP* 3.1 26.4 + - - +
271B GLN* 3.1 15.6 + - - -
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Residues in contact with HIS 268 (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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244B PHE* 3.8 13.8 - - + -
264B PHE* 2.8 62.5 + + + +
265B GLU* 3.4 24.9 + - + -
267B PHE* 1.3 77.1 - - - +
269B GLY* 1.3 68.5 + - - +
270B ASP 3.4 0.7 + - - -
271B GLN* 3.6 9.4 + - - +
279B LEU* 3.3 30.2 - - + +
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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