Contacts of the helix formed by residues 566 - 576 (chain C) in PDB entry 1EF1
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 566 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565C GLY* 1.3 75.4 - - - -
567C THR* 1.3 62.4 + - - +
568C LYS* 2.9 23.0 + - - +
569C GLN* 2.6 42.8 + - - +
570C ARG* 3.2 27.9 + - - +
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Residues in contact with THR 567 (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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240A PHE* 4.0 16.8 - - + -
244A GLU* 3.6 22.5 + - + +
259A PRO* 4.0 18.4 - - + +
261A ASP* 4.8 4.0 + - - -
264A ALA* 3.6 21.8 - - + -
267A PHE* 5.8 0.4 - - + -
566C ASN* 1.3 75.3 - - - +
568C LYS* 1.3 58.1 + - - +
570C ARG* 3.4 10.1 + - - +
571C ILE* 3.1 45.6 + - + +
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Residues in contact with LYS 568 (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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263A LYS 5.5 2.7 - - - +
264A ALA* 4.1 7.5 - - + +
265A PRO* 3.7 30.5 - - + -
566C ASN* 2.9 13.7 + - - +
567C THR* 1.3 73.4 - - - +
569C GLN* 1.3 68.3 + - + +
571C ILE* 4.0 2.6 - - - +
572C ASP* 2.8 53.2 + - - +
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Residues in contact with GLN 569 (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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565C GLY* 2.9 13.8 - - - -
566C ASN* 2.6 57.6 + - - +
568C LYS* 1.3 79.5 - - + +
570C ARG* 1.3 59.4 + - + +
572C ASP* 3.3 8.6 + - - +
573C GLU* 3.0 26.4 + - - +
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Residues in contact with ARG 570 (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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238A ILE* 3.4 30.6 - - + +
239A GLY 3.2 21.1 + - - -
240A PHE* 3.3 23.6 - - + -
241A PRO* 4.6 0.4 - - - +
244A GLU* 3.1 38.3 + - - -
562C ILE 3.5 19.5 - - - +
563C ARG 3.3 11.0 + - - -
564C GLN 3.3 25.6 + - - +
565C GLY 3.0 18.3 + - - -
566C ASN* 3.2 25.7 + - - +
567C THR* 3.4 5.6 + - - +
569C GLN* 1.3 78.6 - - + +
571C ILE* 1.3 63.5 + - - +
573C GLU* 3.5 8.7 + - - +
574C PHE* 3.1 18.0 + - - +
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Residues in contact with ILE 571 (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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240A PHE* 4.1 10.8 - - + -
259A PRO* 5.6 0.2 - - + -
265A PRO* 3.3 44.2 - - + +
266A ASP 3.8 8.5 - - - +
267A PHE* 3.6 39.3 - - + +
567C THR* 3.1 32.3 + - + +
568C LYS* 4.0 4.5 - - - +
569C GLN 3.3 0.2 - - - -
570C ARG* 1.3 75.8 - - - +
572C ASP* 1.3 62.3 + - - +
574C PHE* 3.3 9.6 - - + +
575C GLU* 3.0 39.2 + - + +
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Residues in contact with ASP 572 (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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568C LYS* 2.8 56.0 + - - +
569C GLN* 3.5 8.4 - - - +
570C ARG 3.2 0.2 - - - -
571C ILE* 1.3 80.8 - - - +
573C GLU* 1.3 63.7 + - - +
575C GLU* 3.5 9.1 + - - +
576C SER* 3.1 22.3 + - - -
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Residues in contact with GLU 573 (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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237A LYS* 4.5 15.6 - - - +
238A ILE* 3.9 22.6 - - + +
569C GLN 3.0 15.6 + - - +
570C ARG* 3.8 11.8 - - - +
571C ILE 3.3 0.2 - - - -
572C ASP* 1.3 75.8 - - - +
574C PHE* 1.3 63.9 + - - +
576C SER* 2.8 26.3 + - - +
577C MSE 3.1 17.3 + - - +
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Residues in contact with PHE 574 (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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208A ILE* 4.1 13.2 - - + -
209A LYS 4.1 0.9 - - - -
210A ASN* 3.2 32.5 + - + -
216A LEU* 3.5 26.9 - - + -
227A ILE* 4.0 16.2 - - + -
238A ILE* 3.4 12.9 - - + +
240A PHE* 6.0 0.9 - - + -
267A PHE* 3.3 30.3 - + + -
268A VAL 3.0 23.8 - - - -
269A PHE* 3.6 23.8 - - + -
570C ARG 3.1 12.8 + - - +
571C ILE* 3.3 12.3 - - + +
573C GLU* 1.3 79.7 - - - +
575C GLU* 1.3 74.3 + - - +
577C MSE 3.1 16.7 + - - +
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Residues in contact with GLU 575 (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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210A ASN* 3.3 16.1 + - - +
211A LYS* 3.0 51.0 + - + +
212A LYS* 3.5 18.4 + - - +
266A ASP 5.7 0.3 - - - +
268A VAL* 3.9 13.7 + - - +
571C ILE* 3.0 28.0 + - + +
572C ASP* 3.9 9.2 - - - +
573C GLU 3.3 0.2 - - - -
574C PHE* 1.3 89.8 - - - +
576C SER* 1.3 61.1 + - - +
577C MSE 3.2 1.1 + - - -
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Residues in contact with SER 576 (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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212A LYS* 3.5 12.7 + - - +
155B GLN* 6.0 1.7 - - - +
572C ASP 3.1 13.0 + - - -
573C GLU* 2.8 24.8 + - - +
575C GLU* 1.3 74.7 - - - +
577C MSE 1.3 63.3 + - - +
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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