Contacts of the helix formed by residues 63 - 70 (chain C) in PDB entry 1Z1G
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 PRO 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B GLU* 3.6 11.2 - - + +
50B GLN* 5.6 9.6 - - + +
61C HIS* 3.2 15.0 - - + +
62C LYS* 1.3 92.9 - - - +
64C LEU* 1.3 57.7 + - - +
65C THR* 3.3 14.8 - - - +
66C ALA* 2.7 37.1 + - + +
67C ARG 3.2 3.1 + - - -
62D LYS* 5.9 4.3 - - + -
64D LEU 5.2 9.6 - - - +
65D THR* 6.3 1.8 - - - -
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Residues in contact with LEU 64 (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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26B TYR* 3.9 29.8 - - + -
35B PHE* 5.1 9.0 - - + -
36B GLY 5.8 0.2 - - - +
37B LEU* 5.1 8.7 - - + -
47B GLU* 2.7 37.7 + - + +
48B ALA 4.9 0.4 - - - +
50B GLN* 5.4 1.0 - - + +
51B ALA* 3.7 30.7 - - + +
63C PRO* 1.3 67.2 - - - +
65C THR* 1.3 72.0 + - - +
66C ALA 2.7 2.4 + - - -
67C ARG* 3.0 29.8 + - + +
68C ILE* 2.7 45.5 + - + +
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Residues in contact with THR 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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50B GLN* 4.7 10.2 + - - +
51B ALA* 5.2 1.6 - - - +
54B GLU* 3.1 48.6 + - + +
63C PRO* 4.2 11.5 - - - +
64C LEU* 1.3 81.5 + - - +
66C ALA* 1.3 65.4 + - - +
68C ILE* 3.3 8.8 + - - +
69C ASN* 3.0 24.6 + - - +
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Residues in contact with ALA 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 LYS* 4.3 27.6 - - + +
63C PRO* 2.7 22.8 + - + +
64C LEU 2.7 2.6 + - - -
65C THR* 1.3 76.6 - - - +
67C ARG* 1.3 49.3 + - - +
68C ILE 2.8 12.0 + - - -
69C ASN* 2.9 13.1 + - - +
70C SER* 2.9 19.2 + - - +
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Residues in contact with ARG 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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35B PHE* 4.7 20.9 - - + +
36B GLY* 2.2 41.4 + - - +
37B LEU* 5.2 5.3 + - - +
47B GLU* 3.5 10.2 + - - -
61C HIS* 6.2 0.6 - - - +
62C LYS* 3.3 27.9 + - + +
63C PRO 3.2 9.9 - - - +
64C LEU* 3.2 27.9 - - + +
66C ALA* 1.3 68.5 - - + +
68C ILE* 1.3 66.2 + - - +
70C SER* 4.0 15.9 + - - -
71C ASP* 4.6 3.8 + - - +
4E G 6.3 0.4 - - - -
5E G 5.6 1.2 + - - -
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Residues in contact with ILE 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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26B TYR* 5.3 9.2 - - + -
28B ASP* 4.4 22.4 - - + +
35B PHE* 4.6 19.9 - - + -
51B ALA* 4.7 11.4 - - + +
54B GLU* 5.8 3.6 - - + -
64C LEU* 2.7 51.1 + - + +
65C THR* 3.5 7.6 - - - +
66C ALA 2.8 0.6 + - - -
67C ARG* 1.3 75.1 - - - +
69C ASN* 1.3 65.5 + - - +
70C SER* 2.7 3.1 + - - -
72C ASN* 2.5 34.6 + - - +
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Residues in contact with ASN 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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65C THR* 3.0 11.3 + - - +
66C ALA* 2.9 8.2 + - - +
68C ILE* 1.3 86.5 - - - +
70C SER* 1.3 67.1 + - - +
72C ASN* 3.1 18.6 - - - +
73C SER* 3.5 12.8 + - - -
117C GLU* 4.6 19.5 + - + +
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Residues in contact with SER 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 ALA* 2.9 17.7 + - - +
67C ARG* 4.0 15.4 + - - -
68C ILE 2.7 3.6 + - - -
69C ASN* 1.3 78.6 - - - +
71C ASP* 1.3 59.9 + - - -
72C ASN 2.7 15.5 + - - -
73C SER* 2.9 19.5 + - - +
115C PRO* 5.0 14.7 - - - +
117C GLU* 5.7 1.9 - - - +
118C ASP* 4.2 15.9 + - - -
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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