Contacts of the helix formed by residues 278 - 294 (chain B) in PDB entry 2AXT
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 SER 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B GLN 3.5 3.8 + - - -
275B TRP* 3.1 15.1 + - - +
276B ASP 4.6 2.3 + - - -
277B SER* 1.3 79.2 - - - +
279B TYR* 1.3 65.3 + - - +
280B PHE 3.4 2.0 - - - -
281B GLN* 3.1 35.8 + - - +
282B GLN* 2.9 25.5 + - - +
313B ASP* 5.5 0.7 - - - -
358B ARG* 4.5 12.9 + - - +
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PRO* 2.7 30.6 + - - +
172B TYR* 3.2 39.4 + + - -
274B GLN* 2.7 55.2 + - + +
277B SER* 2.8 11.9 + - - +
278B SER* 1.3 78.1 - - - +
280B PHE* 1.3 73.3 + + - +
282B GLN* 3.2 20.6 + - - +
283B GLU* 3.4 8.0 + - - +
62H TRP* 3.4 17.1 - + + +
63H LYS* 4.2 12.8 - - + +
208H DGD 4.4 22.2 - - - -
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Residues in contact with PHE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B TYR* 3.9 34.1 - + + -
265B ILE* 4.0 9.4 - - + -
270B PRO* 4.4 6.3 - - + -
274B GLN* 3.6 53.1 + - + +
275B TRP* 6.0 0.2 - - - -
278B SER 3.4 0.2 - - - -
279B TYR* 1.3 82.5 - + - +
281B GLN* 1.3 64.0 + - - +
282B GLN 3.2 0.3 + - - -
283B GLU* 3.4 3.7 + - - +
284B ILE* 3.1 26.5 + - - +
309B LEU* 4.1 12.8 - - + +
312B TYR* 3.3 60.8 - + + -
313B ASP* 4.0 20.6 - - + +
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Residues in contact with GLN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER* 3.1 33.5 + - - +
280B PHE* 1.3 78.2 - - - +
282B GLN* 1.3 70.0 + - - +
284B ILE* 3.3 5.9 + - - +
285B ASN* 3.1 35.5 + - - +
313B ASP* 3.7 24.5 + - - +
358B ARG* 3.0 33.1 + - - +
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Residues in contact with GLN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B SER* 2.7 31.1 + - - -
278B SER* 2.9 16.8 + - - +
279B TYR* 3.4 12.1 - - - +
281B GLN* 1.3 79.2 - - - +
283B GLU* 1.3 65.4 + - - +
285B ASN* 2.9 9.6 + - - +
286B ARG* 2.8 24.5 + - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B TYR* 3.5 60.9 + - + +
279B TYR 3.4 2.0 + - - +
280B PHE 3.4 6.4 + - - +
282B GLN* 1.3 77.9 - - - +
284B ILE* 1.3 61.5 + - - +
286B ARG* 3.0 45.2 + - - +
287B ARG* 3.0 34.9 + - - +
309B LEU* 4.3 16.8 - - + -
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Residues in contact with ILE 284 (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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280B PHE 3.1 15.5 + - - +
281B GLN* 3.4 8.5 - - - +
282B GLN 3.0 0.8 + - - -
283B GLU* 1.3 73.6 - - - +
285B ASN* 1.3 68.4 + - - +
287B ARG* 2.9 14.0 + - - +
288B VAL* 2.9 12.3 + - - +
302B TRP* 3.5 33.7 - - + -
305B ILE* 3.7 20.2 - - + -
309B LEU* 3.5 30.3 - - + -
310B ALA* 4.1 13.5 - - + +
313B ASP* 3.8 30.1 - - + +
428B GLU* 4.8 5.8 - - + +
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLN* 3.1 35.2 + - - +
282B GLN* 2.9 9.3 + - - +
284B ILE* 1.3 78.7 - - - +
286B ARG* 1.3 58.2 + - - +
287B ARG 2.8 0.3 + - - -
288B VAL* 2.9 7.7 + - - +
289B GLN* 2.6 46.7 + - + +
302B TRP* 4.7 16.8 - - - -
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLN 2.8 16.7 + - - +
283B GLU* 3.0 41.6 + - - +
285B ASN* 1.3 76.0 - - - +
287B ARG* 1.3 80.7 + - - +
289B GLN* 4.3 4.8 - - - +
290B ALA* 3.4 19.8 + - - +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B TYR* 5.8 0.8 - - - -
174B LEU* 3.6 26.1 - - - +
283B GLU* 3.0 34.0 + - - +
284B ILE 2.9 7.0 + - - +
285B ASN 2.8 0.6 + - - -
286B ARG* 1.3 95.9 - - - +
288B VAL* 1.3 55.3 + - - +
290B ALA* 2.9 7.9 + - - +
291B SER* 2.8 40.2 + - - +
304B ALA 5.0 2.2 + - - -
305B ILE* 4.0 19.5 - - + -
306B PRO* 3.5 22.8 - - - +
309B LEU* 4.0 14.8 - - - +
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ILE 2.9 16.1 + - - +
285B ASN* 3.6 10.5 - - - +
287B ARG* 1.3 76.6 - - - +
289B GLN* 1.3 67.0 + - - +
291B SER* 3.1 11.2 + - - -
292B LEU* 3.1 36.2 + - + +
298B LEU* 5.0 2.0 - - + -
301B ALA* 4.3 11.7 - - + +
302B TRP* 3.7 61.2 - - + +
305B ILE* 3.9 13.7 - - + +
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN* 2.6 30.1 + - + +
286B ARG* 4.3 4.5 - - - +
288B VAL* 1.3 75.9 - - - +
290B ALA* 1.3 62.7 + - - +
292B LEU* 3.3 34.2 + - - +
293B ALA* 3.3 16.1 + - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ARG* 3.4 15.9 + - - +
287B ARG* 2.9 11.4 + - - +
289B GLN* 1.3 75.3 - - - +
291B SER* 1.3 57.2 + - - +
292B LEU 3.0 2.0 - - - -
293B ALA* 2.6 32.1 + - - +
294B SER* 3.1 13.4 + - - +
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Residues in contact with SER 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ARG* 2.8 23.2 + - - +
288B VAL* 3.4 10.0 - - - -
290B ALA* 1.3 72.9 - - - +
292B LEU* 1.3 60.2 + - - +
294B SER* 3.3 20.4 + - - -
296B ALA* 3.2 23.1 + - - +
301B ALA* 3.8 27.9 + - - -
304B ALA* 4.7 7.8 - - - +
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Residues in contact with LEU 292 (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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288B VAL* 3.1 22.9 + - + +
289B GLN* 3.3 38.6 - - - +
290B ALA 2.8 0.8 + - - -
291B SER* 1.3 72.6 - - - +
293B ALA* 1.3 56.4 + - - +
294B SER 3.0 4.7 - - - -
295B GLY* 2.7 25.3 + - - -
296B ALA 3.4 23.1 + - - +
298B LEU* 4.2 22.2 - - + +
301B ALA* 3.9 14.8 - - + -
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLN 3.3 8.5 + - - +
290B ALA* 2.6 20.3 + - - +
292B LEU* 1.3 69.1 - - - +
294B SER* 1.3 54.5 + - - +
295B GLY 2.9 8.7 + - - -
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA* 3.1 11.8 + - - +
291B SER* 3.3 15.2 - - - -
292B LEU 3.0 0.4 - - - -
293B ALA* 1.3 76.7 - - - +
295B GLY* 1.3 63.9 + - - +
296B ALA* 5.1 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