Contacts of the helix formed by residues 277 - 288 (chain B) in PDB entry 2QNJ
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 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B GLU* 2.8 38.3 + - - -
275B TYR 3.3 3.9 + - - -
276B MET* 1.3 72.8 - - - +
278B THR* 1.3 67.7 + - - +
279B ASP* 3.1 6.1 + - - +
280B CYS* 3.1 14.0 + - - +
281B GLU* 3.1 16.1 + - - +
306B TRP* 4.0 3.8 - - - -
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Residues in contact with THR 278 (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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276B MET 4.4 2.7 - - - +
277B SER* 1.3 74.6 - - - +
279B ASP* 1.3 63.2 + - - +
281B GLU* 3.2 18.0 + - - +
282B ASN* 3.0 37.3 + - - +
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Residues in contact with ASP 279 (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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277B SER* 3.1 5.9 + - - +
278B THR* 1.3 82.3 + - - +
280B CYS* 1.3 58.9 + - - +
282B ASN* 3.1 12.9 + - - +
283B LEU* 2.9 28.4 + - - +
304B ASP* 4.7 1.6 - - - +
305B ARG* 4.4 24.4 - - + +
306B TRP* 3.8 28.2 - - + +
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Residues in contact with CYS 280 (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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152B GLU* 3.8 8.1 - - - +
243B LEU* 4.6 10.3 - - - -
247B VAL* 3.9 28.3 - - - -
276B MET* 3.7 24.7 - - + -
277B SER* 3.1 21.8 + - - +
279B ASP* 1.3 77.1 - - - +
281B GLU* 1.3 64.6 + - - +
282B ASN 3.1 0.2 - - - -
283B LEU* 3.4 3.2 + - - +
284B LEU* 3.1 25.1 + - - +
306B TRP* 3.6 18.2 - - - +
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Residues in contact with GLU 281 (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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270B TYR* 5.0 0.8 + - + -
272B ILE* 3.8 46.5 - - + +
276B MET* 4.3 8.9 - - - +
277B SER 3.1 12.1 + - - +
278B THR* 3.2 21.1 + - - +
280B CYS* 1.3 75.9 - - - +
282B ASN* 1.3 65.1 + - - +
284B LEU* 3.2 15.8 + - - +
285B LYS* 3.3 39.1 + - + +
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Residues in contact with ASN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B THR* 3.0 25.0 + - - +
279B ASP* 3.5 16.7 + - - +
280B CYS 3.1 0.4 - - - -
281B GLU* 1.3 80.6 - - - +
283B LEU* 1.3 66.3 + - - +
285B LYS* 3.2 36.0 + - - +
286B ARG* 3.6 10.6 + - - +
304B ASP* 5.0 4.7 - - - +
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Residues in contact with LEU 283 (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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159B PHE* 4.6 3.1 - - + -
243B LEU* 3.7 16.8 - - + -
279B ASP 2.9 16.3 + - - +
280B CYS* 3.7 6.5 - - - +
281B GLU 3.3 0.2 - - - -
282B ASN* 1.3 76.7 - - - +
284B LEU* 1.3 57.6 + - - +
286B ARG* 2.8 33.1 + - + +
287B PHE* 3.3 27.8 + - + -
301B ILE* 3.9 16.2 - - + -
304B ASP* 3.3 27.1 + - - +
306B TRP* 3.2 35.2 - - + -
307B ILE* 3.8 13.2 - - + -
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Residues in contact with LEU 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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240B GLY* 3.4 28.0 - - - +
243B LEU* 3.7 22.4 - - + -
244B TYR* 3.8 21.1 - - + +
270B TYR* 3.8 24.5 + - + +
272B ILE* 5.1 0.2 - - + -
276B MET* 3.7 37.9 - - + -
280B CYS* 3.1 16.7 + - - +
281B GLU* 3.5 9.2 - - - +
282B ASN 3.2 0.4 - - - -
283B LEU* 1.3 75.3 - - - +
285B LYS* 1.3 58.8 + - - +
286B ARG 3.0 0.9 + - - -
287B PHE* 3.1 5.1 + - - +
288B LEU* 3.0 41.4 + - + +
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Residues in contact with LYS 285 (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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270B TYR* 4.2 11.2 - - - +
281B GLU* 3.6 33.3 + - + +
282B ASN* 3.2 31.6 + - - +
283B LEU 3.1 0.8 - - - -
284B LEU* 1.3 77.4 - - - +
286B ARG* 1.3 57.9 + - + +
288B LEU 4.2 3.8 + - - +
289B VAL* 3.2 26.9 - - - +
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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
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282B ASN 3.9 9.6 - - - +
283B LEU* 2.8 19.5 + - + +
285B LYS* 1.3 79.3 - - + +
287B PHE* 1.3 60.6 + - - +
289B VAL* 4.6 1.1 - - - +
294B LYS 6.1 0.2 - - - -
295B ARG* 3.8 5.5 - - - -
296B GLY* 3.1 33.4 + - - +
300B GLN* 3.9 36.2 + - - +
301B ILE* 4.1 24.2 - - + +
303B LYS* 4.4 3.0 - - - +
304B ASP* 3.5 47.8 + - - +
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Residues in contact with PHE 287 (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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159B PHE* 3.6 28.3 - + - -
163B VAL* 4.5 2.7 - - + -
236B VAL* 3.1 28.9 - - + +
237B TRP* 4.1 6.8 + - - -
239B LEU* 3.7 17.7 - - + -
240B GLY* 3.3 28.3 - - - -
243B LEU* 4.6 4.5 - - + -
283B LEU* 3.3 39.0 + - + -
284B LEU* 3.1 5.3 + - - +
286B ARG* 1.3 79.6 - - - +
288B LEU* 1.3 63.5 + - - +
289B VAL 3.4 1.1 - - - -
295B ARG* 2.9 26.7 - - - -
298B LEU* 3.8 22.0 - - + -
301B ILE* 3.6 25.6 - - + -
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Residues in contact with LEU 288 (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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237B TRP* 3.5 52.5 - - + +
240B GLY* 3.7 8.5 - - - +
241B VAL* 3.7 19.7 - - + +
244B TYR* 5.4 0.4 - - + -
252B PRO* 4.9 7.0 - - + -
253B PHE* 4.3 9.6 - - + -
268B GLY* 5.2 3.9 - - - +
270B TYR* 3.7 45.9 + - + +
284B LEU* 3.0 29.2 + - + +
285B LYS* 4.6 3.2 - - - +
286B ARG 3.8 0.6 - - - -
287B PHE* 1.3 76.8 - - + +
289B VAL* 1.3 62.9 + - - +
290B LEU* 4.2 1.6 + - - +
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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