Contacts of the helix formed by residues 60 - 74 (chain C) in PDB entry 4RE1
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 ASP 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B VAL* 5.6 0.4 - - - +
59C GLY* 1.3 67.4 - - - -
61C SER* 1.3 57.1 + - - +
62C GLU* 3.8 7.1 + - - +
63C THR* 3.2 34.3 + - + +
64C ASP* 3.0 28.5 + - - +
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Residues in contact with SER 61 (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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318B VAL* 4.5 7.9 - - - -
319B VAL* 5.3 0.9 - - - -
346B TYR* 3.6 30.1 - - - -
57C VAL* 3.9 24.5 - - - +
59C GLY 3.1 3.5 + - - -
60C ASP* 1.3 71.5 + - - +
62C GLU* 1.3 65.4 + - - +
64C ASP* 4.2 6.3 - - - -
65C LEU* 2.9 26.0 + - - +
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Residues in contact with GLU 62 (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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60C ASP* 3.3 6.8 + - - +
61C SER* 1.3 80.6 + - - +
63C THR* 1.3 64.6 + - - +
65C LEU* 3.2 6.9 + - - +
66C GLU* 3.1 21.7 + - - +
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Residues in contact with THR 63 (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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60C ASP* 3.2 33.7 + - + +
62C GLU* 1.3 78.6 - - - +
64C ASP* 1.3 63.1 + - - +
66C GLU* 3.3 8.8 + - - +
67C ALA* 3.1 21.4 + - + +
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Residues in contact with ASP 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B SER* 2.6 30.8 + - - +
314B PHE* 4.9 6.8 - - - -
316B LYS* 6.2 0.2 - - - +
318B VAL* 3.9 16.0 - - + +
346B TYR* 2.8 19.9 + - - -
60C ASP 3.0 17.2 + - - +
61C SER* 3.7 9.0 - - - +
62C GLU 3.3 0.2 - - - -
63C THR* 1.3 78.2 - - - +
65C LEU* 1.3 62.0 + - - +
67C ALA* 3.2 11.4 + - - +
68C LEU* 3.1 18.5 + - - +
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Residues in contact with LEU 65 (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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346B TYR* 3.6 52.9 - - + +
349B ASN* 3.8 16.2 - - + +
350B PHE* 3.6 40.6 - - + +
353B LYS* 5.7 1.3 - - + -
61C SER 2.9 15.0 + - - +
62C GLU* 3.6 6.7 - - - +
64C ASP* 1.3 74.1 + - - +
66C GLU* 1.3 65.4 + - - +
68C LEU* 3.2 15.9 + - + +
69C PHE* 3.2 33.2 - - + -
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Residues in contact with GLU 66 (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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62C GLU 3.1 12.3 + - - +
63C THR* 3.3 11.2 + - - +
65C LEU* 1.3 75.1 - - - +
67C ALA* 1.3 58.5 + - - +
69C PHE* 3.1 8.9 + - - +
70C ASN* 2.9 39.9 + - - +
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Residues in contact with ALA 67 (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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314B PHE* 3.7 15.3 - - + -
63C THR* 3.1 13.9 + - + +
64C ASP* 3.2 13.9 + - - +
66C GLU* 1.3 73.3 - - - +
68C LEU* 1.3 64.4 + - - +
70C ASN* 4.4 7.9 - - - +
71C ALA* 3.2 24.4 + - - +
80C VAL* 4.0 13.1 - - + +
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Residues in contact with LEU 68 (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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313B SER* 3.7 17.7 - - - -
314B PHE* 3.5 26.9 - - + -
346B TYR* 3.6 23.8 - - + +
350B PHE* 4.1 20.0 - - + -
366B VAL* 3.5 30.0 - - + +
369B ASN* 3.9 22.3 + - + +
370B PHE* 4.2 15.5 - - + -
64C ASP 3.1 8.1 + - - +
65C LEU* 3.3 15.3 - - + +
67C ALA* 1.3 77.1 - - - +
69C PHE* 1.3 64.8 + - + +
71C ALA* 4.0 9.9 - - - +
72C VAL* 4.4 1.6 - - - +
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Residues in contact with PHE 69 (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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350B PHE* 3.8 15.5 - + - -
353B LYS* 3.4 46.0 - - + -
354B LEU* 3.5 12.3 - - - -
357B LEU* 3.8 26.5 - - + -
366B VAL* 4.0 24.5 - - + -
65C LEU* 3.2 40.2 - - + -
66C GLU* 3.1 8.8 + - - +
68C LEU* 1.3 78.5 - - + +
70C ASN* 1.3 63.2 + - - +
71C ALA 3.1 2.0 - - - -
72C VAL* 3.0 6.8 + - - +
73C MET* 2.8 36.7 + - + +
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Residues in contact with ASN 70 (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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66C GLU* 2.9 30.6 + - - +
67C ALA* 3.6 6.3 + - - +
69C PHE* 1.3 73.6 - - - +
71C ALA* 1.3 60.5 + - - +
72C VAL 3.0 1.8 - - - -
73C MET* 4.0 5.2 - - - +
74C ASN* 2.8 58.5 + - + +
78C ALA* 3.9 13.0 - - + -
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Residues in contact with ALA 71 (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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314B PHE* 4.1 11.9 - - + -
369B ASN* 4.6 9.2 - - - +
67C ALA 3.2 17.5 + - - +
68C LEU 4.0 8.7 - - - +
69C PHE 3.1 0.6 - - - -
70C ASN* 1.3 76.2 - - - +
72C VAL* 1.3 62.9 + - + +
75C PRO* 3.7 18.1 - - - +
78C ALA* 4.0 11.1 - - - +
80C VAL* 3.7 23.6 - - + +
82C GLN* 5.7 3.1 + - - -
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Residues in contact with VAL 72 (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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362B MET* 4.2 9.0 - - + +
365B SER* 3.5 51.1 - - - +
366B VAL* 3.7 14.1 - - + +
369B ASN* 5.5 2.5 - - - +
68C LEU 4.4 4.7 - - - +
69C PHE 3.0 6.3 + - - +
71C ALA* 1.3 86.7 - - + +
73C MET* 1.3 80.0 + - + +
74C ASN 3.5 0.7 - - - -
75C PRO* 3.8 10.9 - - - +
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Residues in contact with MET 73 (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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357B LEU* 3.8 32.8 - - + -
358B PRO* 5.8 1.1 - - - -
362B MET* 4.1 23.3 - - + +
366B VAL* 5.0 1.3 - - + -
69C PHE* 2.8 27.8 + - + +
70C ASN* 4.3 7.9 - - - +
72C VAL* 1.3 107.7 - - + +
74C ASN* 1.3 71.2 + - - +
75C PRO* 3.5 6.6 - - - +
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Residues in contact with ASN 74 (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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70C ASN* 2.8 38.9 + - + +
73C MET* 1.3 99.7 - - - +
75C PRO* 1.3 59.6 - - - +
76C LYS 3.3 2.5 - - - -
77C THR* 3.0 29.6 + - + +
78C ALA 2.9 24.2 + - - +
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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