Contacts of the helix formed by residues 267 - 277 (chain A) in PDB entry 2EZT
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 GLN 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A LYS* 4.5 3.8 - - - +
253A ASP* 4.9 0.4 + - - -
258A TYR* 4.2 12.5 - - - -
259A LEU 3.4 16.6 - - - +
260A GLY* 3.6 23.6 - - - -
261A SER 2.8 10.9 + - - +
266A ALA* 1.3 79.6 - - - +
268A LYS* 1.3 67.7 + - - +
269A PRO 3.3 0.2 - - - -
270A ALA 3.1 13.5 + - - -
271A ASN* 3.5 6.4 + - - +
356A TRP* 2.8 37.1 + - - +
360A LEU* 4.1 9.4 - - - +
402A ASN* 3.4 37.5 + - - +
403A ARG* 4.1 8.6 + - + +
552A ALA* 4.0 3.1 - - - +
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Residues in contact with LYS 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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267A GLN* 1.3 70.5 - - - +
269A PRO* 1.4 71.7 - - + +
270A ALA 3.2 0.3 + - - -
271A ASN* 3.4 3.1 + - - +
272A GLU* 2.6 60.3 + - - +
352A ASN* 3.0 14.1 + - - -
355A ASN* 4.6 1.8 + - - -
356A TRP* 3.6 33.9 - - + +
552A ALA* 3.7 14.6 - - + +
555A LEU* 4.0 25.8 - - + -
557A LEU* 3.6 22.9 - - - -
579A LEU* 4.0 15.5 - - + -
580A GLN 2.7 30.3 + - - -
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Residues in contact with PRO 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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259A LEU* 3.7 30.8 - - + +
267A GLN 3.3 5.6 - - - -
268A LYS* 1.4 90.9 - - + +
270A ALA* 1.3 55.8 + - - +
272A GLU* 4.0 0.5 - - - +
273A ALA* 3.0 33.1 + - - +
349A ASN* 4.7 0.2 - - - +
352A ASN* 3.5 25.6 + - + +
353A VAL* 4.0 16.2 - - + -
356A TRP* 3.5 42.8 - - + -
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Residues in contact with ALA 270 (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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242A MET* 3.9 15.4 - - + +
259A LEU* 3.5 16.9 + - + +
260A GLY 3.4 25.4 - - - +
261A SER 3.2 27.8 - - - +
267A GLN 3.1 3.7 + - - +
269A PRO* 1.3 76.2 - - - +
271A ASN* 1.3 65.1 + - - +
273A ALA* 4.1 0.2 - - - +
274A LEU* 3.0 26.7 + - - +
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Residues in contact with ASN 271 (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* 3.2 10.1 - - - +
263A ASN* 2.7 49.6 + - - +
266A ALA* 4.0 2.7 - - - +
267A GLN 3.5 3.1 + - - +
268A LYS 3.4 7.0 + - - +
270A ALA* 1.3 78.5 - - - +
272A GLU* 1.3 63.8 + - + +
274A LEU* 3.6 4.7 + - - +
275A ALA* 3.3 23.0 + - - +
552A ALA* 3.0 35.5 + - - +
553A GLU* 3.8 4.1 - - - +
555A LEU* 5.3 1.1 - - + -
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Residues in contact with GLU 272 (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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268A LYS* 2.6 51.4 + - - +
269A PRO 4.0 2.2 - - - +
271A ASN* 1.3 72.7 - - - +
273A ALA* 1.3 67.7 + - - +
275A ALA* 3.4 13.5 + - - +
276A GLN* 3.5 18.0 + - - +
352A ASN* 2.8 18.8 + - - +
555A LEU* 3.7 19.1 - - + +
581A PRO* 3.5 8.5 - - - +
582A LEU* 2.8 39.1 + - + +
1613A PYR 4.8 7.1 + - - +
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Residues in contact with ALA 273 (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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216A LEU* 3.8 9.8 - - + +
259A LEU* 3.5 18.8 - - + -
269A PRO 3.0 19.9 + - - +
270A ALA 4.1 1.1 - - - +
272A GLU* 1.3 76.9 - - - +
274A LEU* 1.3 57.6 + - - +
276A GLN* 2.9 19.1 + - - -
277A ALA 3.0 10.6 + - - -
345A TRP* 3.5 12.4 - - + -
349A ASN* 3.4 21.8 - - - +
582A LEU* 3.8 9.6 - - - +
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Residues in contact with LEU 274 (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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216A LEU* 3.7 13.6 - - + +
218A TYR* 4.3 11.9 - - + -
242A MET* 4.0 24.0 - - + -
262A ALA* 4.3 11.2 - - + -
270A ALA 3.0 19.4 + - - +
271A ASN* 3.8 5.6 - - - +
272A GLU 3.4 0.2 - - - -
273A ALA* 1.3 75.3 - - - +
275A ALA* 1.3 61.4 + - - +
276A GLN 3.3 0.9 + - - -
277A ALA* 3.4 12.3 + - - +
280A VAL* 4.0 17.5 - - + -
287A TYR* 5.3 0.2 - - + -
295A ALA* 3.8 39.3 - - + +
296A PHE* 3.8 23.1 - - + -
299A THR* 4.9 4.1 + - - +
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Residues in contact with ALA 275 (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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271A ASN 3.3 10.9 + - - +
272A GLU* 3.5 12.3 - - - +
273A ALA 3.2 0.4 - - - -
274A LEU* 1.3 78.0 - - - +
276A GLN* 1.3 69.8 + - - +
277A ALA 5.0 0.9 - - - +
295A ALA 5.3 3.8 - - - -
298A ASN* 4.5 20.4 + - - +
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Residues in contact with GLN 276 (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 ARG* 2.8 48.3 + - - +
272A GLU 3.5 13.4 + - - +
273A ALA 2.9 8.3 + - - +
275A ALA* 1.3 88.4 - - - +
277A ALA* 1.3 64.1 + - - +
278A ASP* 3.5 1.4 + - - +
345A TRP* 3.7 16.8 - - + -
582A LEU* 4.1 6.3 - - + -
586A LEU* 4.1 13.8 - - + +
593A ASP* 3.1 49.1 + - - +
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Residues in contact with ALA 277 (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 ARG* 3.3 18.6 - - - +
216A LEU* 3.6 31.9 - - + -
273A ALA 3.0 4.5 + - - +
274A LEU 3.4 11.7 + - - +
275A ALA 5.0 1.0 - - - +
276A GLN* 1.3 78.4 - - - +
278A ASP* 1.3 60.4 + - - +
279A VAL 4.2 8.7 - - - +
280A VAL* 4.3 10.8 - - + -
298A ASN* 3.8 6.9 - - - +
299A THR* 3.8 17.4 + - - -
345A TRP* 4.4 1.3 - - + -
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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