Contacts of the helix formed by residues 253 - 267 (chain A) in PDB entry 2FYT
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 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A GLU 3.1 11.2 + - - +
250A MET 3.0 13.4 + - - +
251A LEU 4.2 0.7 - - - -
252A LYS* 1.3 72.3 - - - +
254A LYS* 1.3 59.4 + - - +
255A ILE* 3.6 4.7 + - - +
256A ARG* 3.1 27.0 + - + +
257A THR* 2.9 31.7 + - - -
494A LYS 4.7 0.9 - - - +
495A THR* 3.4 19.7 - - - -
496A HIS* 2.6 51.2 + - + +
497A TRP* 3.9 0.5 - - - -
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Residues in contact with LYS 254 (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 4.9 3.6 - - - +
252A LYS* 3.1 16.2 + - - +
253A ASP* 1.3 70.0 + - - +
255A ILE* 1.3 63.0 + - + +
257A THR* 4.5 2.7 - - - +
258A GLU* 2.9 62.8 + - + +
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Residues in contact with ILE 255 (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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253A ASP* 3.4 7.5 + - - +
254A LYS* 1.3 78.9 - - + +
256A ARG* 1.3 58.5 + - - +
258A GLU* 4.6 2.0 - - - +
259A SER* 2.7 34.3 + - - +
486A PHE* 3.8 26.2 - - + -
487A SER 4.7 3.6 - - - +
493A THR* 3.6 42.2 - - + +
494A LYS 4.2 7.6 - - - +
495A THR* 4.0 17.0 - - + -
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Residues in contact with ARG 256 (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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250A MET* 3.0 33.5 + - - +
251A LEU* 3.9 10.7 - - - +
253A ASP* 3.1 21.9 + - - +
255A ILE* 1.3 82.6 - - - +
257A THR* 1.3 89.1 + - - +
259A SER* 3.3 1.9 + - - -
260A TYR* 3.3 30.7 + - + -
285A ILE* 4.5 1.4 - - - +
286A LEU* 5.2 2.9 - - - +
346A GLU* 3.0 39.4 + - + +
486A PHE* 4.5 11.2 - - + -
495A THR* 5.1 0.4 - - - +
496A HIS* 4.0 10.8 - - - -
497A TRP* 3.7 24.7 - - + -
549A SAH 2.8 40.5 + - - -
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Residues in contact with THR 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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250A MET 3.0 16.3 + - - -
251A LEU* 3.7 15.7 + - + +
253A ASP 2.9 20.6 + - - -
254A LYS* 4.5 1.8 - - - -
256A ARG* 1.3 94.1 + - - +
258A GLU* 1.3 60.4 + - - +
260A TYR* 3.3 7.3 + - - +
261A ARG* 2.9 25.4 + - + +
285A ILE* 4.3 11.0 - - + -
286A LEU* 5.6 1.8 - - + -
289A PHE* 4.0 23.2 - - + -
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Residues in contact with GLU 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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254A LYS* 2.9 48.1 + - + +
255A ILE* 4.6 1.5 - - - +
257A THR* 1.3 73.0 - - + +
259A SER* 1.3 54.8 + - - +
261A ARG* 3.9 39.2 + - - +
262A ASP* 2.7 45.6 + - - +
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Residues in contact with SER 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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255A ILE* 2.7 25.4 + - - +
256A ARG 3.5 3.4 - - - -
257A THR 3.3 0.2 - - - -
258A GLU* 1.3 76.5 - - - +
260A TYR* 1.3 57.7 + - - +
262A ASP* 4.7 2.0 - - - -
263A PHE* 3.0 29.1 + - - +
476A PHE* 4.4 4.0 - - - -
484A VAL* 3.5 24.2 - - - +
485A VAL 4.4 1.6 + - - -
486A PHE* 3.3 38.5 - - - +
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Residues in contact with TYR 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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256A ARG* 3.3 27.3 + - + -
257A THR* 3.3 6.0 + - - +
259A SER* 1.3 74.5 - - - +
261A ARG* 1.3 64.7 + - - +
263A PHE* 3.4 3.4 + + - +
264A ILE* 3.0 38.0 + - + +
286A LEU* 3.7 41.5 - - + -
289A PHE* 4.5 0.2 - - - -
344A ILE* 5.4 4.3 - - + -
345A SER 2.6 32.1 + - - -
346A GLU* 3.3 29.0 - - + -
348A MET* 3.4 20.0 - - + +
376A TYR 4.7 0.9 - - - -
377A PRO* 3.3 21.8 - - + +
476A PHE* 3.9 24.9 - + - -
486A PHE* 4.5 6.5 - + - -
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Residues in contact with ARG 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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257A THR 2.9 17.7 + - - +
258A GLU* 3.6 38.4 + - - +
259A SER 3.3 0.2 - - - -
260A TYR* 1.3 76.7 - - - +
262A ASP* 1.3 77.9 + - - +
264A ILE* 3.3 1.3 + - - -
265A TYR* 2.8 65.7 + - + +
289A PHE* 3.6 36.9 - - + -
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Residues in contact with ASP 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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258A GLU* 2.7 29.9 + - - +
259A SER* 4.0 4.7 - - - +
261A ARG* 1.3 99.1 + - - +
263A PHE* 1.3 60.3 + - - +
265A TYR* 4.6 2.6 - - - +
266A GLN* 2.8 59.7 + - - +
484A VAL* 4.2 9.4 - - + -
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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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259A SER 3.0 18.3 + - - +
260A TYR* 3.6 4.3 - + - +
261A ARG 3.3 0.2 - - - -
262A ASP* 1.3 75.8 - - - +
264A ILE* 1.3 77.0 + - + +
267A ASN* 2.9 32.1 + - - +
270A ILE* 3.6 12.6 - - + -
271A PHE* 3.6 27.4 - + - -
344A ILE* 4.5 3.4 - - + -
376A TYR* 3.3 51.1 - + + -
476A PHE* 3.4 39.5 - + + -
480A CYS* 3.5 28.7 - - - -
482A ASN 5.3 0.2 - - - -
484A VAL* 3.8 13.1 - - + +
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Residues in contact with ILE 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 TYR* 3.0 26.4 + - + +
261A ARG 3.9 2.2 - - - +
263A PHE* 1.3 84.0 - - + +
265A TYR* 1.3 63.8 + - + +
267A ASN 3.4 19.6 + - - +
268A PRO* 3.6 6.4 - - - +
271A PHE* 3.6 31.1 - - + -
286A LEU* 4.2 11.2 - - + +
289A PHE* 3.4 55.6 - - + +
290A ALA* 3.9 2.7 - - - +
293A ALA* 3.7 13.4 - - + +
344A ILE* 4.4 16.2 - - + -
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Residues in contact with TYR 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 ARG* 2.8 48.1 + - + +
262A ASP* 4.4 2.7 - - - +
264A ILE* 1.3 76.4 - - + +
266A GLN* 1.3 62.1 + - + +
268A PRO* 3.5 13.5 - - - +
288A MET 5.0 0.2 - - - -
289A PHE* 3.3 51.5 - + + -
292A LYS* 3.6 28.8 - - + +
293A ALA* 4.5 7.6 - - + -
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Residues in contact with GLN 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 ASP* 2.8 42.0 + - - +
265A TYR* 1.3 72.8 - - + +
267A ASN* 1.3 60.4 + - - +
268A PRO* 3.3 7.1 - - - +
481A HIS* 3.2 9.0 + - - -
482A ASN* 2.9 60.2 + - + +
483A ARG 5.3 0.4 + - - -
484A VAL* 4.1 11.1 - - - +
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Residues in contact with ASN 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 37.6 + - - +
264A ILE 3.5 3.6 - - - -
266A GLN* 1.3 81.6 - - - +
268A PRO* 1.3 64.2 - - - +
269A HIS* 3.2 9.6 - - - +
270A ILE* 3.1 34.7 + - + +
271A PHE* 3.8 4.9 - - - -
479A ASN 4.4 0.6 - - - +
480A CYS* 3.3 10.8 - - - -
481A HIS* 3.0 34.1 + - - -
482A ASN* 2.8 31.4 + - - +
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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