Contacts of the helix formed by residues 256 - 268 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A PRO* 3.7 35.0 - - + +
251A LEU* 2.8 26.5 + - + +
254A ASN* 3.5 37.5 + - + +
255A GLN* 1.3 74.7 + - - +
257A GLU* 1.3 59.3 + - - +
258A ASN 3.4 2.2 - - - -
259A GLU* 3.3 26.9 + - + +
260A ALA* 2.9 28.1 + - - +
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Residues in contact with GLU 257 (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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251A LEU 5.2 0.2 - - - -
252A VAL* 5.9 1.3 - - - +
255A GLN* 3.5 7.2 + - - +
256A HIS* 1.3 74.8 - - - +
258A ASN* 1.3 68.8 + - - +
260A ALA* 3.3 7.0 + - + +
261A LYS* 3.0 24.5 + - + +
286A THR* 3.1 46.5 + - - +
287A LYS* 3.4 31.3 + - - +
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Residues in contact with ASN 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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256A HIS 3.4 0.4 - - - -
257A GLU* 1.3 80.7 - - - +
259A GLU* 1.3 72.8 + - - +
261A LYS* 3.3 7.7 + - - +
262A SER* 3.0 24.1 + - - -
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Residues in contact with GLU 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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211A PRO* 3.9 30.5 - - - +
212A THR* 3.9 22.2 - - + +
215A GLU* 4.6 1.4 - - - +
251A LEU* 4.0 8.1 - - + +
256A HIS* 3.4 36.8 + - + +
258A ASN* 1.3 82.0 + - - +
260A ALA* 1.3 57.4 + - - +
262A SER* 3.4 5.6 + - - -
263A PHE* 2.8 30.7 + - - +
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Residues in contact with ALA 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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248A TYR* 3.3 29.9 - - + +
251A LEU* 3.7 25.7 - - + +
252A VAL* 3.8 16.2 - - + +
256A HIS 2.9 17.6 + - - +
257A GLU* 3.7 7.2 - - + +
259A GLU* 1.3 76.6 - - - +
261A LYS* 1.3 57.3 + - - +
263A PHE* 3.2 1.0 + - - +
264A PHE 2.9 25.6 + - - -
286A THR* 6.2 1.1 - - - -
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Residues in contact with LYS 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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248A TYR* 5.0 1.8 - - - -
257A GLU* 3.0 17.6 + - + +
258A ASN* 3.8 7.0 - - - +
260A ALA* 1.3 76.5 - - - +
262A SER* 1.3 61.8 + - - +
264A PHE* 3.3 6.3 + - - +
265A GLU* 3.0 47.0 + - + +
286A THR* 6.4 2.2 - - + -
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Residues in contact with SER 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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215A GLU* 2.5 27.8 + - - +
258A ASN 3.0 15.9 + - - -
259A GLU* 3.7 5.8 - - - -
261A LYS* 1.3 77.1 - - - +
263A PHE* 1.3 63.0 + - - +
265A GLU* 3.3 10.5 + - - +
266A LYS* 3.1 21.3 + - - +
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Residues in contact with PHE 263 (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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214A TYR* 3.6 25.8 - - + -
215A GLU* 3.3 24.1 + - + -
218A TYR* 3.9 21.8 - + + -
244A PHE* 3.4 40.9 - + - -
247A MET* 3.7 19.7 - - + -
248A TYR* 3.9 21.1 - - + -
251A LEU* 4.0 10.5 - - + -
259A GLU 2.8 18.7 + - - +
260A ALA 3.2 4.0 + - - +
262A SER* 1.3 74.8 - - - +
264A PHE* 1.3 62.9 + - - +
266A LYS* 3.4 0.9 + - - -
267A PHE* 3.3 46.2 + + - -
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Residues in contact with PHE 264 (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 PHE* 3.6 27.1 - + - -
248A TYR* 3.7 26.9 - + + +
260A ALA 2.9 17.4 + - - +
261A LYS* 3.7 6.3 - - - +
262A SER 3.3 0.2 - - - -
263A PHE* 1.3 75.1 - - - +
265A GLU* 1.3 66.5 + - + +
268A HIS* 2.8 64.4 + + + +
279A LEU* 3.2 28.3 - - + -
282A LEU* 3.6 24.5 - - + -
283A SER* 3.7 22.7 - - - -
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Residues in contact with GLU 265 (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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261A LYS* 3.0 53.4 + - + +
262A SER* 3.7 7.2 - - - +
264A PHE* 1.3 79.7 - - + +
266A LYS* 1.3 62.8 + - - +
267A PHE 3.5 0.2 + - - -
268A HIS* 3.5 22.1 + - + -
269A GLY 5.1 0.7 + - - -
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Residues in contact with LYS 266 (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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215A GLU* 4.1 23.7 + - - +
219A SER* 3.9 18.2 + - - -
222A LYS* 5.5 0.8 + - - +
262A SER 3.1 16.3 + - - +
263A PHE 3.8 4.7 - - - +
264A PHE 3.1 0.4 - - - -
265A GLU* 1.3 79.1 - - - +
267A PHE* 1.3 87.8 + - + +
269A GLY 5.3 0.6 + - - -
270A ASP* 4.0 9.0 - - - +
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Residues in contact with PHE 267 (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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215A GLU* 3.6 18.6 - - + -
218A TYR* 3.6 43.5 - + + -
219A SER* 3.5 26.0 - - - -
222A LYS* 4.4 10.8 - - + -
244A PHE* 3.6 19.3 - - + -
263A PHE* 3.3 37.8 + + - -
264A PHE 3.3 2.2 + - - -
266A LYS* 1.3 112.2 - - + +
268A HIS* 1.3 65.5 + - - +
269A GLY 3.2 2.9 - - - -
270A ASP* 3.1 26.4 + - - +
271A GLN* 3.1 18.1 + - - +
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Residues in contact with HIS 268 (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 PHE* 3.7 15.6 - - + -
264A PHE* 2.8 62.5 + + + +
265A GLU* 3.5 21.7 + - + -
267A PHE* 1.3 77.5 - - - +
269A GLY* 1.3 67.6 + - - +
270A ASP 3.4 0.7 + - - -
271A GLN* 3.5 9.7 + - - +
279A LEU* 3.5 30.1 - - + +
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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