Contacts of the helix formed by residues 269 - 283 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C MET 3.4 4.3 - - - -
114C ASP 2.9 30.3 + - - +
115C GLY* 3.2 16.5 - - - +
267C GLN 3.6 4.2 + - - +
268C VAL* 1.3 74.3 - - - +
270C LYS* 1.3 61.2 + - - +
271C ALA 3.0 0.7 + - - -
272C ARG* 2.8 62.8 + - + +
273C MET* 3.0 26.9 + - - +
326C PRO* 5.5 0.2 - - - +
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Residues in contact with LYS 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C MET* 2.6 29.6 + - - +
114C ASP* 3.0 21.1 + - - +
264C ILE* 3.7 23.1 - - + -
268C VAL 3.5 2.0 + - - -
269C ASN* 1.3 69.6 + - - +
271C ALA* 1.3 61.3 + - - +
273C MET* 2.9 20.4 + - + +
274C ILE* 2.8 32.9 + - + +
294C ASP* 3.2 27.6 + - - +
296C THR* 4.1 16.2 + - - +
302C VAL* 4.6 17.9 - - + -
304C VAL* 4.0 23.3 - - + -
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Residues in contact with ALA 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ASP* 3.4 44.7 - - + +
269C ASN* 3.0 0.8 + - - -
270C LYS* 1.3 77.7 - - - +
272C ARG* 1.3 64.1 + - - +
274C ILE* 3.3 10.4 + - - +
275C GLU* 3.0 22.7 + - - +
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Residues in contact with ARG 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C GLY* 5.4 1.6 + - - -
269C ASN* 2.8 46.3 + - + +
271C ALA* 1.3 76.6 - - - +
273C MET* 1.3 65.2 + - - +
275C GLU* 2.7 19.8 + - + +
276C LYS* 2.9 14.1 + - - +
326C PRO* 5.6 1.6 - - + -
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Residues in contact with MET 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C SER* 4.9 0.2 - - - -
261C VAL* 5.3 0.7 - - + -
264C ILE* 4.3 21.3 - - + -
268C VAL* 4.2 7.0 - - + -
269C ASN 3.0 15.7 + - - +
270C LYS* 2.9 18.0 + - + +
272C ARG* 1.3 76.0 - - - +
274C ILE* 1.3 80.8 + - + +
276C LYS* 3.4 4.5 + - - +
277C ILE* 3.2 33.6 + - + +
304C VAL* 4.6 12.3 - - + -
325C THR* 4.9 1.1 - - - +
326C PRO* 4.0 35.3 - - + +
327C LEU* 3.2 44.6 - - + +
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Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C LYS* 2.8 25.9 + - + +
271C ALA* 3.7 8.7 - - - +
273C MET* 1.3 79.5 - - + +
275C GLU* 1.3 58.8 + - - +
277C ILE* 3.3 8.8 + - + +
278C ALA* 3.0 24.8 + - + +
292C LEU* 3.5 28.8 - - + +
294C ASP* 3.5 42.6 - - + +
304C VAL* 4.2 26.9 - - + -
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Residues in contact with GLU 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C ALA 3.0 12.3 + - - +
272C ARG* 2.7 19.6 + - + +
274C ILE* 1.3 70.1 - - - +
276C LYS* 1.3 59.6 + - - +
278C ALA* 4.2 9.3 - - - +
279C GLU* 2.8 35.7 + - + +
282C ARG* 3.5 23.4 + - - -
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Residues in contact with LYS 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ARG 2.9 10.1 + - - +
273C MET* 3.6 9.9 - - - +
275C GLU* 1.3 77.5 - - - +
277C ILE* 1.3 55.8 + - - +
279C GLU* 3.7 29.8 + - - +
280C LEU* 3.0 41.9 + - - +
324C GLN 3.4 27.6 - - - +
325C THR* 4.2 8.7 - - + +
326C PRO* 4.2 16.2 - - + -
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Residues in contact with ILE 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C MET* 3.2 36.5 + - + +
274C ILE* 3.6 10.1 - - - +
275C GLU 3.2 0.2 - - - -
276C LYS* 1.3 73.1 - - - +
278C ALA* 1.3 66.3 + - - +
280C LEU* 3.1 8.0 + - + +
281C VAL* 3.0 27.8 + - + +
286C ILE* 5.9 0.2 - - + -
289C ILE* 4.2 15.9 - - + -
292C LEU* 3.8 24.0 - - + -
304C VAL* 5.5 2.0 - - + -
306C ILE* 4.6 17.7 - - + -
321C LEU* 4.1 23.1 - - + -
325C THR* 4.0 23.3 - - + +
327C LEU* 4.8 6.3 - - + -
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C ILE* 3.0 17.0 + - + +
275C GLU* 3.7 18.4 - - - +
277C ILE* 1.3 76.0 - - - +
279C GLU* 1.3 57.5 + - - +
281C VAL* 3.2 8.5 + - - +
282C ARG* 2.8 33.8 + - - +
292C LEU* 3.7 15.0 - - + +
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Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C GLU* 2.8 21.9 + - - +
276C LYS* 3.7 38.1 + - - +
278C ALA* 1.3 74.0 - - - +
280C LEU* 1.3 68.8 + - - +
282C ARG* 3.2 33.9 + - - +
283C ASP* 2.8 41.8 + - - +
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C LYS* 3.0 34.1 + - - +
277C ILE* 3.5 9.0 - - - +
279C GLU* 1.3 81.1 - - - +
281C VAL* 1.3 62.2 + - - +
283C ASP* 3.6 1.7 + - + -
284C LYS 3.3 2.4 + - - -
285C LYS* 3.0 48.3 + - + -
286C ILE* 3.7 22.5 + - + -
321C LEU* 5.1 1.1 - - + -
324C GLN* 3.6 41.5 - - + +
325C THR* 3.6 21.3 - - + -
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ILE* 3.0 21.9 + - + +
278C ALA* 3.2 10.3 + - - +
280C LEU* 1.3 75.5 - - - +
282C ARG* 1.3 65.9 + - - +
284C LYS* 3.0 19.9 + - - +
286C ILE* 4.2 13.3 - - + +
289C ILE* 3.9 55.0 - - + +
292C LEU* 5.7 1.6 - - + -
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Residues in contact with ARG 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLU* 3.5 22.8 + - - -
278C ALA* 2.8 22.3 + - - +
279C GLU* 3.5 36.2 - - - +
281C VAL* 1.3 76.7 - - - +
283C ASP* 1.3 69.4 + - - +
284C LYS* 3.3 8.5 + - - +
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Residues in contact with ASP 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C GLU* 2.8 40.0 + - - +
280C LEU* 4.4 2.4 - - + +
281C VAL 3.3 0.2 - - - -
282C ARG* 1.3 88.3 + - - +
284C LYS* 1.3 68.9 + - - +
285C LYS* 3.0 10.0 + - + +
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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