Contacts of the helix formed by residues 282 - 297 (chain C) in PDB entry 6FF7
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 GLU 282 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281C ASN* 1.3 69.8 - - - +
283C ASN* 1.3 60.3 + - - +
284C PHE 3.1 1.3 - - - -
285C ALA* 2.9 30.9 + - + +
286C LYS* 3.4 3.5 + - - +
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Residues in contact with ASN 283 (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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797A ASP 5.7 0.9 - - - +
798A GLY* 4.8 15.3 - - - -
799A PRO* 4.9 9.0 - - + +
281C ASN* 3.2 3.2 - - + +
282C GLU* 1.3 74.3 - - - +
284C PHE* 1.3 55.7 + - - +
286C LYS* 3.0 15.9 + - + +
287C LEU* 2.7 31.7 + - - +
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Residues in contact with PHE 284 (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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798A GLY* 5.3 1.5 - - - -
799A PRO* 5.2 7.7 - - - -
281C ASN* 3.4 18.2 + - + +
283C ASN* 1.3 75.9 - - - +
285C ALA* 1.3 51.1 + - - +
287C LEU* 3.0 10.5 + - - +
288C ALA* 2.7 37.5 + - - +
77L LEU* 4.4 19.6 - - + +
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Residues in contact with ALA 285 (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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282C GLU* 2.9 16.7 + - + +
284C PHE* 1.3 77.1 - - - +
286C LYS* 1.3 58.5 + - - +
288C ALA* 3.0 21.3 + - - +
289C GLU* 3.3 17.7 + - + +
290C ALA 4.3 0.7 + - - -
77L LEU* 5.1 4.1 - - + +
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Residues in contact with LYS 286 (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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803A ALA* 3.3 24.7 - - + +
282C GLU 3.4 3.1 + - - +
283C ASN* 3.0 21.8 + - + +
285C ALA* 1.3 77.2 - - - +
287C LEU* 1.3 55.9 + - - +
290C ALA* 3.3 11.4 - - - +
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Residues in contact with LEU 287 (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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799A PRO* 5.0 13.0 - - + -
801A ILE 5.8 1.6 - - - +
802A THR 6.2 0.7 - - - -
803A ALA* 4.7 9.9 - - - +
806A ALA* 6.5 0.9 - - + -
283C ASN 2.7 11.5 + - - +
284C PHE* 3.0 11.4 + - - +
285C ALA 3.5 0.4 - - - -
286C LYS* 1.3 77.5 - - - +
288C ALA* 1.3 59.2 + - - +
290C ALA* 3.0 8.2 + - - +
291C LEU* 2.9 27.2 + - - +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C PHE 2.7 19.6 + - - +
285C ALA* 3.0 6.3 + - - +
287C LEU* 1.3 72.4 - - + +
289C GLU* 1.3 59.9 + - - +
291C LEU* 3.0 11.5 + - - +
292C TYR* 3.0 23.2 + - - +
76L LYS 3.6 24.0 - - - +
77L LEU* 3.7 20.0 - - - +
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Residues in contact with GLU 289 (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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285C ALA* 3.3 10.8 + - + +
288C ALA* 1.3 78.0 - - - +
290C ALA* 1.3 55.8 + - - +
292C TYR* 3.4 10.4 - - + +
293C ILE* 2.8 34.3 + - - +
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Residues in contact with ALA 290 (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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803A ALA* 4.2 17.0 - - + +
807A VAL* 4.6 10.0 - - + +
285C ALA 4.3 1.4 + - - -
286C LYS 3.3 18.2 - - - +
287C LEU 3.0 13.9 + - - +
289C GLU* 1.3 78.6 - - - +
291C LEU* 1.3 57.5 + - - +
293C ILE* 4.7 3.4 - - - +
294C ALA* 3.4 19.1 + - - +
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Residues in contact with LEU 291 (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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806A ALA* 6.2 4.7 - - + -
807A VAL* 5.7 4.7 - - - +
992A LEU* 6.5 0.9 - - - -
995A ARG* 5.1 16.4 - - + -
287C LEU 2.9 11.2 + - - +
288C ALA* 3.0 9.4 + - - +
290C ALA* 1.3 76.6 - - - +
292C TYR* 1.3 60.6 + - - +
294C ALA* 2.9 24.4 + - - +
295C ASP* 3.1 8.0 + - - +
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Residues in contact with TYR 292 (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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288C ALA 3.0 11.6 + - - +
289C GLU* 3.0 15.8 + - + +
291C LEU* 1.3 75.8 - - - +
293C ILE* 1.3 62.6 + - - +
295C ASP* 3.0 20.1 + - - +
296C ARG* 3.3 9.2 + - - +
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Residues in contact with ILE 293 (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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289C GLU 2.8 17.9 + - - +
290C ALA* 4.8 3.4 - - - +
292C TYR* 1.3 72.0 - - - +
294C ALA* 1.3 50.8 + - - +
296C ARG* 3.0 12.1 + - + +
297C LYS* 2.6 36.0 + - - +
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Residues in contact with ALA 294 (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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807A VAL* 4.7 19.5 - - + +
810A TYR* 5.3 8.5 - - + -
290C ALA 3.4 16.5 + - - +
291C LEU* 2.9 17.6 + - - +
293C ILE* 1.3 77.9 - - - +
295C ASP* 1.3 54.4 + - - +
297C LYS* 3.0 10.4 + - - +
298C ALA* 2.8 28.7 + - - +
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Residues in contact with ASP 295 (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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291C LEU 3.1 7.9 + - - +
292C TYR* 3.0 13.7 + - - +
294C ALA* 1.3 75.0 - - - +
296C ARG* 1.3 56.9 + - - +
298C ALA* 2.9 6.5 + - - +
299C ARG* 2.7 41.1 + - + +
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Residues in contact with ARG 296 (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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292C TYR 3.3 6.5 + - - +
293C ILE* 3.0 13.4 + - + +
295C ASP* 1.3 78.4 - - - +
297C LYS* 1.3 56.3 + - - +
298C ALA 3.4 0.7 - - - -
299C ARG* 4.7 4.5 - - - +
300C GLU* 5.4 7.9 - - - +
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Residues in contact with LYS 297 (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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293C ILE 2.6 18.0 + - - +
294C ALA* 3.0 11.8 + - - +
296C ARG* 1.3 74.6 - - - +
298C ALA* 1.3 56.6 + - - +
301C ALA* 4.3 11.2 - - - +
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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