Contacts of the helix formed by residues 269 - 283 (chain A) in PDB entry 6FQS
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A MET 3.9 5.6 - - - -
114A ASP 2.8 25.2 + - - +
115A GLY* 3.2 16.0 - - - -
267A GLN 4.0 2.8 + - - -
268A VAL* 1.3 81.8 - - - +
270A LYS* 1.3 58.6 + - - +
271A ALA* 2.7 16.7 + - - +
272A ARG* 2.7 72.8 + - + +
273A MET* 3.1 18.5 + - - +
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Residues in contact with LYS 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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113A MET* 3.5 23.8 + - + +
114A ASP* 2.6 35.2 + - - +
264A ILE* 3.7 27.1 - - + -
268A VAL 3.2 3.2 + - - -
269A ASN* 1.3 74.5 + - - +
271A ALA* 1.3 64.9 + - - +
273A MET* 2.9 17.9 + - + +
274A ILE* 2.9 23.4 + - + +
294A ASP* 2.6 27.3 + - - +
296A THR* 3.8 23.3 + - - +
302A VAL* 4.3 19.1 - - + -
304A VAL* 4.3 15.5 - - + -
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP* 3.4 38.1 + - + +
269A ASN* 2.7 5.4 + - - -
270A LYS* 1.3 75.6 - - - +
272A ARG* 1.3 61.2 + - - +
274A ILE* 3.3 13.5 + - - +
275A GLU* 3.1 29.1 + - - +
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Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLN 5.7 1.4 + - - -
269A ASN* 2.7 60.1 + - + +
271A ALA* 1.3 72.7 - - - +
273A MET* 1.3 61.8 + - - +
275A GLU* 3.2 18.9 + - - +
276A LYS* 3.1 44.8 + - + +
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Residues in contact with MET 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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245A SER* 4.9 0.7 - - - -
261A VAL* 5.4 2.5 - - + -
264A ILE* 4.3 25.4 - - + -
268A VAL* 4.3 9.9 - - + -
269A ASN 3.1 15.1 + - - +
270A LYS* 2.9 12.6 + - + +
272A ARG* 1.3 77.6 - - - +
274A ILE* 1.3 71.0 + - + +
276A LYS* 3.3 3.7 + - - +
277A ILE* 3.1 33.7 + - + +
304A VAL* 5.1 13.0 - - + -
326A PRO* 4.0 34.3 - - + +
327A LEU* 3.3 45.8 - - + +
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Residues in contact with ILE 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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270A LYS* 2.9 26.1 + - + +
271A ALA* 3.6 11.9 - - - +
273A MET* 1.3 80.8 - - + +
275A GLU* 1.3 59.0 + - + +
277A ILE* 3.1 10.6 + - - +
278A ALA* 2.7 28.8 + - + +
292A LEU* 3.9 24.7 - - + +
293A ARG 5.6 0.4 - - - -
294A ASP* 3.6 43.5 - - + +
304A VAL* 4.5 19.3 - - + -
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Residues in contact with GLU 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 ALA* 3.1 21.8 + - - +
272A ARG* 3.2 19.5 + - - +
274A ILE* 1.3 78.3 - - + +
276A LYS* 1.3 57.1 + - + +
278A ALA* 3.0 9.8 + - - +
279A GLU* 2.7 30.3 + - - +
282A ARG* 5.3 1.2 + - - -
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Residues in contact with LYS 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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272A ARG* 3.1 34.1 + - + +
273A MET* 3.6 6.7 - - - +
274A ILE 3.2 0.2 - - - -
275A GLU* 1.3 77.1 - - + +
277A ILE* 1.3 63.5 + - - +
279A GLU* 3.2 14.0 + - - +
280A LEU* 3.1 29.0 + - - +
324A GLN 5.9 0.4 - - - +
325A THR* 4.7 4.5 - - + -
326A PRO* 3.5 36.3 - - + +
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Residues in contact with ILE 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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273A MET* 3.1 26.0 + - + +
274A ILE* 3.5 9.0 - - - +
276A LYS* 1.3 72.9 - - - +
278A ALA* 1.3 67.5 + - - +
280A LEU* 3.5 7.0 - - + +
281A VAL* 3.3 21.6 + - + +
286A ILE* 6.0 0.2 - - + -
289A ILE* 4.6 13.2 - - + -
292A LEU* 4.0 24.0 - - + -
304A VAL* 5.6 2.5 - - + -
306A ILE* 4.6 14.1 - - + -
321A LEU* 3.8 25.4 - - + -
325A THR* 3.9 18.4 - - + -
327A LEU* 4.3 22.4 - - + -
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Residues in contact with ALA 278 (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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274A ILE* 2.7 19.1 + - + +
275A GLU* 3.3 13.2 - - - +
277A ILE* 1.3 72.9 - - - +
279A GLU* 1.3 57.0 + - - +
281A VAL* 3.2 7.8 + - - +
282A ARG* 2.9 40.2 + - - +
292A LEU* 3.7 16.5 - - + +
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Residues in contact with GLU 279 (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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275A GLU 2.7 19.5 + - - +
276A LYS* 3.6 13.6 - - - +
277A ILE 3.2 0.2 - - - -
278A ALA* 1.3 70.7 - - - +
280A LEU* 1.3 68.8 + - + +
282A ARG* 3.1 28.3 + - - +
283A ASP* 2.8 49.3 + - - +
285A LYS* 5.6 4.3 + - - +
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Residues in contact with LEU 280 (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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276A LYS 3.1 17.0 + - - +
277A ILE* 3.5 7.6 - - + +
279A GLU* 1.3 88.1 - - + +
281A VAL* 1.3 64.1 + - - +
283A ASP* 3.2 1.7 + - - -
284A LYS 3.1 2.8 + - - -
285A LYS* 3.0 59.4 + - + +
286A ILE* 4.0 26.0 - - + -
321A LEU* 5.3 1.1 - - + -
324A GLN* 3.1 47.6 - - + +
325A THR* 4.6 7.0 - - + -
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Residues in contact with VAL 281 (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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277A ILE* 3.3 11.4 + - + +
278A ALA* 3.2 10.8 + - - +
279A GLU 3.1 0.6 - - - -
280A LEU* 1.3 78.6 - - - +
282A ARG* 1.3 58.4 + - - +
284A LYS* 2.7 32.6 + - - +
286A ILE* 3.6 26.1 - - + +
289A ILE* 3.8 41.3 - - + +
292A LEU* 6.0 2.5 - - + -
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Residues in contact with ARG 282 (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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275A GLU 5.3 1.0 + - - -
278A ALA* 2.9 26.3 + - - +
279A GLU* 3.4 35.4 + - - +
281A VAL* 1.3 78.5 - - - +
283A ASP* 1.3 66.5 + - - +
284A LYS* 3.4 14.8 + - - +
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Residues in contact with ASP 283 (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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279A GLU* 2.8 42.2 + - - +
280A LEU* 3.9 3.1 - - - +
281A VAL 3.1 0.2 - - - -
282A ARG* 1.3 85.7 + - - +
284A LYS* 1.3 64.1 + - - +
285A LYS* 2.9 34.1 + - + +
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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