Contacts of the helix formed by residues 269 - 283 (chain L) in PDB entry 6QX2
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 ASN 269 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113L MET 3.7 4.9 - - - -
114L ASP 3.1 24.6 + - - +
115L GLY* 3.3 17.4 + - - -
267L GLN 3.9 2.6 + - - +
268L VAL* 1.3 70.9 - - - +
270L LYS* 1.3 58.6 + - - +
271L ALA* 3.0 7.3 + - - +
272L ARG* 3.0 64.9 + - + +
273L MET* 2.9 31.0 + - - +
4O C 5.0 1.6 + - - -
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Residues in contact with LYS 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L MET* 3.1 28.3 + - + +
114L ASP* 3.2 26.5 + - - +
264L ILE* 3.9 20.2 - - + -
268L VAL 3.5 3.8 + - - -
269L ASN* 1.3 69.3 - - - +
271L ALA* 1.3 63.2 + - - +
273L MET* 3.2 10.2 + - + +
274L ILE* 3.0 36.1 + - + +
294L ASP* 2.6 31.5 + - - +
296L THR* 3.5 33.0 + - - +
302L VAL* 4.5 15.7 - - + -
304L VAL* 4.3 11.7 - - + -
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Residues in contact with ALA 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L ASP* 3.0 36.9 + - + +
269L ASN* 3.0 9.0 + - - +
270L LYS* 1.3 74.4 - - - +
272L ARG* 1.3 61.1 - - - +
274L ILE* 3.5 9.3 + - - +
275L GLU* 3.1 22.9 + - - +
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Residues in contact with ARG 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267L GLN 6.0 0.2 + - - -
269L ASN* 3.0 51.4 + - + +
271L ALA* 1.3 73.8 - - - +
273L MET* 1.3 58.3 - - - +
275L GLU* 3.1 22.2 + - - +
276L LYS* 2.9 29.5 + - + +
326L PRO* 5.6 3.4 - - + -
3O G 3.8 39.4 + - - -
4O C 2.9 31.7 + - - -
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Residues in contact with MET 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245L SER* 4.6 0.2 - - - -
261L VAL* 5.1 0.7 - - + -
264L ILE* 4.2 25.6 - - + -
268L VAL* 4.1 15.5 - - + -
269L ASN 2.9 18.1 + - - +
270L LYS* 3.5 6.7 - - - +
272L ARG* 1.3 75.7 - - - +
274L ILE* 1.3 75.5 + - + +
276L LYS* 3.4 5.1 + - - +
277L ILE* 3.3 29.8 + - + +
304L VAL* 4.7 14.4 - - + -
325L THR* 5.0 0.7 - - - -
326L PRO* 4.0 32.3 - - + +
327L LEU* 3.5 44.0 - - + +
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Residues in contact with ILE 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270L LYS* 3.0 26.6 + - + +
271L ALA* 3.7 9.9 - - - +
273L MET* 1.3 76.9 - - + +
275L GLU* 1.3 61.6 + - - +
277L ILE* 3.0 10.8 + - + +
278L ALA* 2.9 26.9 + - + +
292L LEU* 3.5 21.6 - - + +
293L ARG 6.1 0.2 - - - -
294L ASP* 3.6 42.8 - - + +
304L VAL* 3.9 26.2 - - + -
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Residues in contact with GLU 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271L ALA 3.1 12.1 + - - +
272L ARG* 3.1 24.9 + - - +
274L ILE* 1.3 77.2 - - + +
276L LYS* 1.3 51.3 + - - +
278L ALA* 3.3 8.5 + - + +
279L GLU* 2.8 48.6 + - + +
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Residues in contact with LYS 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272L ARG* 2.9 12.4 + - + +
273L MET 3.6 10.1 - - - +
274L ILE 3.3 0.4 - - - -
275L GLU* 1.3 76.0 - - - +
277L ILE* 1.3 57.4 + - - +
279L GLU* 3.4 13.9 + - - +
280L LEU* 3.0 35.0 + - + +
324L GLN 5.5 1.3 - - - +
325L THR* 4.5 7.2 - - + -
326L PRO* 4.4 19.1 - - + -
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Residues in contact with ILE 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273L MET* 3.3 22.4 + - + +
274L ILE* 3.0 15.7 + - + +
276L LYS* 1.3 73.9 - - - +
278L ALA* 1.3 64.0 + - - +
280L LEU* 3.2 7.4 + - - +
281L VAL* 3.1 24.5 + - + +
289L ILE* 4.3 14.4 - - + -
292L LEU* 3.7 24.9 - - + -
304L VAL* 5.5 1.6 - - + -
306L ILE* 4.5 15.5 - - + -
321L LEU* 3.9 25.6 - - + -
325L THR* 3.7 23.3 - - + +
327L LEU* 4.5 18.6 - - + -
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Residues in contact with ALA 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274L ILE* 2.9 13.4 + - + +
275L GLU* 3.7 11.0 - - - +
277L ILE* 1.3 74.5 - - - +
279L GLU* 1.3 50.6 - - - +
281L VAL* 3.3 7.7 + - - +
282L ARG* 2.8 38.3 + - - +
292L LEU* 3.6 17.3 - - + +
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Residues in contact with GLU 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275L GLU* 2.8 30.0 + - + +
276L LYS* 3.5 11.7 - - - +
278L ALA* 1.3 74.6 - - - +
280L LEU* 1.3 65.7 + - + +
282L ARG* 3.4 31.3 + - - +
283L ASP* 3.0 46.1 + - - +
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Residues in contact with LEU 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276L LYS* 3.0 16.0 + - + +
277L ILE* 3.2 9.4 + - - +
279L GLU* 1.3 81.6 - - + +
281L VAL* 1.3 60.7 + - - +
283L ASP* 3.5 2.2 + - + +
284L LYS 3.3 2.8 + - - -
285L LYS* 2.8 49.4 + - + -
286L ILE* 3.6 23.5 + - + +
321L LEU* 5.4 0.4 - - + -
324L GLN* 3.5 45.3 - - + +
325L THR* 3.8 19.7 - - + -
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Residues in contact with VAL 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L ILE* 3.1 15.9 + - + +
278L ALA* 3.6 9.6 - - - +
280L LEU* 1.3 72.8 - - - +
282L ARG* 1.3 67.7 + - - +
284L LYS* 2.9 15.6 + - - +
286L ILE* 3.9 21.7 - - + +
289L ILE* 3.8 48.7 - - + +
292L LEU* 6.0 1.1 - - + -
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Residues in contact with ARG 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278L ALA* 2.8 20.0 + - - +
279L GLU* 3.4 35.4 - - - +
281L VAL* 1.3 72.4 - - - +
283L ASP* 1.3 79.4 + - - +
284L LYS* 3.4 3.8 + - - +
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Residues in contact with ASP 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279L GLU* 3.0 35.8 + - - +
280L LEU* 4.2 3.0 - - + +
281L VAL 3.2 0.4 - - - -
282L ARG* 1.3 100.4 + - - +
284L LYS* 1.3 66.7 + - - +
285L LYS* 3.0 13.7 + - + +
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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