Contacts of the helix formed by residues 259 - 269 (chain A) in PDB entry 6FF7
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 ASP 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A PHE* 3.1 15.2 + - + +
257A LEU 3.5 2.9 - - - +
258A PHE* 1.3 82.6 - - - +
260A LEU* 1.3 65.7 + - - +
261A LYS* 3.3 7.2 - - + +
262A ALA* 4.3 10.5 - - + +
263A PHE* 3.1 23.0 + - - +
330A THR* 4.8 11.0 - - - -
331A TRP* 5.6 5.8 - - + +
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Residues in contact with LEU 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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259A ASP* 1.3 74.6 - - - +
261A LYS* 1.3 57.2 + - - +
263A PHE* 3.4 6.7 + - - +
264A PHE* 2.9 26.0 + - - +
455A VAL* 5.8 3.3 - - - +
458A ALA* 5.2 14.4 - - + -
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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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259A ASP* 3.3 3.2 - - + +
260A LEU* 1.3 77.3 - - - +
262A ALA* 1.3 59.1 + - - +
264A PHE* 3.2 5.5 + - - +
265A THR* 2.9 27.0 + - - -
328A HIS* 3.7 29.9 - - + +
329A LEU 4.1 20.6 - - - +
330A THR* 4.3 7.4 - - - -
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Residues in contact with ALA 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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257A LEU* 3.9 33.0 - - + +
259A ASP* 3.6 16.4 + - + +
260A LEU 3.4 0.2 - - - -
261A LYS* 1.3 78.5 - - - +
263A PHE* 1.3 59.0 + - - +
265A THR* 3.3 8.0 + - - -
266A SER* 2.9 27.1 + - - -
314A ILE* 4.5 18.3 - - + +
328A HIS 5.5 0.2 - - - -
330A THR* 4.3 14.3 - - - -
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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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257A LEU 5.3 2.2 + - - +
258A PHE 5.8 0.9 - - - +
259A ASP 3.1 17.7 + - - +
260A LEU* 3.6 7.2 - - - +
261A LYS 3.3 0.2 - - - -
262A ALA* 1.3 75.4 - - - +
264A PHE* 1.3 59.5 + - - +
266A SER* 3.4 8.1 + - - -
267A LYS* 2.9 28.6 + - - +
277A PRO* 6.5 0.9 - - + -
455A VAL* 4.6 20.5 - - + +
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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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260A LEU 2.9 15.0 + - - +
261A LYS* 3.4 9.6 - - - +
263A PHE* 1.3 75.8 - - - +
265A THR* 1.3 58.1 + - - +
267A LYS* 3.2 8.4 + - - +
268A ALA* 2.9 29.3 + - - +
326A HIS 4.3 6.2 - - - +
328A HIS* 4.0 18.4 - - + +
455A VAL* 6.0 0.2 - - - +
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Residues in contact with THR 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 2.9 13.3 + - - -
262A ALA* 3.5 11.7 - - - -
263A PHE 3.3 0.2 - - - -
264A PHE* 1.3 76.8 - - - +
266A SER* 1.3 55.0 + - - +
268A ALA* 3.3 5.0 + - - +
269A LEU* 2.9 35.5 + - - +
313A LYS 5.5 2.0 - - - -
314A ILE* 4.7 17.7 - - - -
317A PRO* 5.9 5.4 - - - -
327A VAL* 5.1 5.4 - - - +
328A HIS 4.0 21.0 - - - +
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Residues in contact with SER 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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262A ALA 2.9 16.1 + - - -
263A PHE* 3.7 8.5 - - - -
264A PHE 3.3 0.4 - - - -
265A THR* 1.3 76.9 - - - +
267A LYS* 1.3 62.4 + - - +
269A LEU* 3.8 4.0 + - - +
270A ASN* 3.8 0.7 + - - -
271A MET* 2.9 42.6 + - - +
272A ALA* 4.7 7.6 - - - -
273A ILE* 5.2 4.9 - - - -
277A PRO 5.6 2.9 - - - -
279A PHE* 5.5 0.9 + - - +
314A ILE* 5.3 10.9 - - - +
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Residues in contact with LYS 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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263A PHE 2.9 17.9 + - - +
264A PHE* 3.5 8.7 - - - +
265A THR 3.2 0.2 - - - -
266A SER* 1.3 79.7 - - - +
268A ALA* 1.3 60.6 + - - +
270A ASN* 4.0 5.9 + - - -
279A PHE* 4.3 23.2 - - + +
280A GLU 4.3 13.0 - - - +
281A PRO* 4.9 5.0 - - - +
282A LEU* 5.6 1.6 + - - +
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Residues in contact with ALA 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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264A PHE 2.9 12.7 + - - +
265A THR* 4.0 4.7 - - - +
267A LYS* 1.3 77.4 - - - +
269A LEU* 1.3 58.8 + - + +
270A ASN* 3.4 1.8 + - - +
281A PRO* 6.2 0.3 - - - +
282A LEU* 5.8 8.5 + - - +
284A ARG* 6.1 1.0 - - - +
325A HIS 3.7 16.3 - - - +
326A HIS* 3.3 33.0 - - + +
327A VAL* 4.9 2.0 - - + -
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Residues in contact with LEU 269 (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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265A THR* 2.9 17.9 + - - +
266A SER* 3.8 3.5 + - - +
267A LYS 3.4 0.4 - - - -
268A ALA* 1.3 77.6 - - - +
270A ASN* 1.3 69.2 + - - +
271A MET* 3.2 12.4 + - + +
313A LYS* 6.2 4.0 - - + -
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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