Contacts of the helix formed by residues 267 - 277 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B LYS* 4.6 2.8 - - - +
253B ASP* 4.9 0.4 + - - -
258B TYR* 4.2 12.7 - - - -
259B LEU 3.5 16.6 - - - +
260B GLY* 3.6 23.2 - - - -
261B SER 2.8 11.1 + - - +
266B ALA* 1.3 80.3 - - - +
268B LYS* 1.3 68.7 + - - +
269B PRO* 3.3 0.9 - - + -
270B ALA 3.2 11.4 + - - -
271B ASN* 3.5 6.2 + - - +
356B TRP* 2.8 36.3 + - - +
360B LEU* 4.1 9.0 - - - +
402B ASN* 3.5 37.7 + - - +
403B ARG* 4.1 10.3 + - + +
552B ALA* 4.1 3.8 - - - -
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Residues in contact with LYS 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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267B GLN* 1.3 69.2 - - - +
269B PRO* 1.4 66.8 - - + +
270B ALA 3.2 0.7 + - - -
271B ASN* 3.3 4.1 + - - +
272B GLU* 2.8 58.5 + - - +
352B ASN* 2.8 18.4 + - - -
355B ASN* 4.4 3.4 + - - -
356B TRP* 3.5 39.5 - - + -
552B ALA* 3.9 12.7 - - + +
555B LEU* 3.8 22.2 - - + -
557B LEU* 3.6 21.1 - - - -
579B LEU* 4.0 17.2 - - + +
580B GLN 2.6 30.2 + - - -
581B PRO* 4.0 0.2 - - - +
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Residues in contact with PRO 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 3.8 19.5 - - + +
267B GLN 3.4 5.2 - - - -
268B LYS* 1.4 94.3 - - + +
270B ALA* 1.3 54.3 + - - +
272B GLU* 3.9 0.9 - - - +
273B ALA* 2.9 32.4 + - - +
349B ASN* 4.7 0.5 - - - +
352B ASN* 3.5 31.4 + - + +
353B VAL* 4.0 23.6 - - + +
356B TRP* 3.6 38.4 - - + -
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Residues in contact with ALA 270 (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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242B MET* 4.1 13.3 - - + +
259B LEU* 3.5 17.3 + - + +
260B GLY 3.6 23.8 - - - +
261B SER* 3.3 28.0 - - - +
262B ALA* 4.2 1.3 - - - +
267B GLN 3.2 3.6 + - - +
269B PRO* 1.3 75.6 - - - +
271B ASN* 1.3 61.6 + - - +
274B LEU* 3.0 32.2 + - - +
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Residues in contact with ASN 271 (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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262B ALA* 3.1 11.6 - - - +
263B ASN* 2.7 48.8 + - - +
266B ALA* 3.9 1.0 - - - +
267B GLN 3.5 4.4 + - - +
268B LYS 3.3 8.3 + - - +
270B ALA* 1.3 80.1 - - - +
272B GLU* 1.3 62.5 + - + +
274B LEU* 3.8 5.6 - - - +
275B ALA* 3.3 22.2 + - - +
552B ALA* 3.1 35.9 + - - +
553B GLU* 3.7 4.6 - - - +
555B LEU* 5.2 1.6 - - + -
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Residues in contact with GLU 272 (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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268B LYS* 2.8 49.1 + - - +
269B PRO 3.9 2.2 - - - +
271B ASN* 1.3 74.1 - - - +
273B ALA* 1.3 66.5 + - - +
275B ALA* 3.3 14.6 + - - +
276B GLN* 3.4 17.3 + - - +
352B ASN* 2.8 19.7 + - - +
555B LEU* 3.6 20.6 - - + +
561B MET* 5.9 2.0 - - + +
581B PRO* 3.5 12.0 - - - +
582B LEU* 2.9 37.6 + - + +
1616B PYR 4.7 6.4 + - - +
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Residues in contact with ALA 273 (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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216B LEU* 3.7 11.9 - - + +
259B LEU* 3.4 26.0 - - + -
269B PRO 2.9 20.0 + - - +
270B ALA 4.2 0.2 - - - +
272B GLU* 1.3 73.1 - - - +
274B LEU* 1.3 67.9 + - - +
276B GLN* 2.9 13.9 + - - +
277B ALA 2.9 11.6 + - - -
345B TRP* 3.6 7.7 - - + -
349B ASN* 3.4 17.0 - - - +
582B LEU* 3.8 8.9 - - - +
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Residues in contact with LEU 274 (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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216B LEU* 3.6 7.5 - - + +
218B TYR* 4.5 4.3 - - + -
242B MET* 4.2 20.9 - - + -
262B ALA* 4.2 21.8 - - + -
270B ALA 3.0 20.3 + - - +
271B ASN* 3.8 5.6 - - - +
273B ALA* 1.3 77.0 - - - +
275B ALA* 1.3 61.2 - - - +
276B GLN 3.4 0.3 + - - -
277B ALA* 3.5 11.4 + - - +
280B VAL* 3.9 18.2 - - + -
295B ALA* 3.8 38.4 - - + +
296B PHE* 3.7 29.2 - - + -
298B ASN* 6.0 0.5 - - - +
299B THR* 5.0 3.7 + - - +
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Residues in contact with ALA 275 (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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271B ASN 3.3 10.3 + - - +
272B GLU* 3.3 12.0 + - - +
273B ALA 3.1 0.8 - - - -
274B LEU* 1.3 78.9 - - - +
276B GLN* 1.3 67.9 + - - +
277B ALA 5.1 0.2 - - - -
295B ALA 5.4 2.7 - - - -
298B ASN* 3.6 33.2 + - - +
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Residues in contact with GLN 276 (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 ARG* 2.8 36.9 + - - +
272B GLU 3.4 12.7 + - - +
273B ALA 2.9 7.9 + - - +
275B ALA* 1.3 86.8 - - - +
277B ALA* 1.3 62.4 + - - +
298B ASN* 6.1 0.2 - - - -
345B TRP* 3.7 19.5 - - + -
582B LEU* 4.1 13.5 - - + -
586B LEU* 4.1 10.3 - - + +
592B ASP 4.1 4.9 + - - -
593B ASP* 3.5 50.9 - - - +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG* 3.3 19.2 + - - +
216B LEU* 3.6 31.9 - - + -
273B ALA 2.9 6.3 + - - +
274B LEU 3.5 9.6 + - - +
275B ALA 4.9 1.0 - - - +
276B GLN* 1.3 78.7 - - - +
278B ASP* 1.3 60.4 + - - +
279B VAL 4.2 9.2 - - - +
280B VAL* 4.2 9.4 - - + -
298B ASN 3.7 16.8 - - - +
299B THR* 3.8 9.1 + - - -
345B TRP* 4.4 0.9 - - - -
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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