Contacts of the helix formed by residues 54 - 68 (chain C) in PDB entry 4A12
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 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C ARG* 3.5 10.0 - - - +
53C PRO* 1.3 76.0 - - - +
55C LEU* 1.3 65.2 + - - +
56C ARG* 3.8 32.3 + - - +
57C LYS* 2.9 43.5 + - + +
58C ARG* 3.0 11.7 + - - +
15F A 4.3 4.0 - - - +
16F C 3.2 56.4 + - - +
17F T 3.8 10.1 + - - +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PRO 3.6 7.2 - - - +
26C PHE 3.3 31.0 - - - +
27C ILE 3.3 13.0 - - - +
28C THR* 3.8 23.1 - - + -
54C GLU* 1.3 68.3 - - - +
56C ARG* 1.3 59.2 - - + +
58C ARG* 3.0 19.4 + - - +
59C ILE* 2.8 56.0 + - + +
15F A 3.8 26.2 - - - +
16F C 3.0 21.2 + - - +
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Residues in contact with ARG 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLU* 3.3 21.0 + - - +
55C LEU* 1.3 82.4 - - + +
57C LYS* 1.3 58.5 + - + +
59C ILE* 3.7 9.1 + - + +
60C LYS* 3.1 27.2 + - - +
56D ARG* 3.4 56.3 - - + +
59D ILE* 5.4 0.9 - - - +
14F T 2.8 39.0 + - - -
15F A 3.2 53.1 + - - -
28G G 5.2 0.6 - - - +
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Residues in contact with LYS 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C PRO* 3.7 22.2 - - + -
54C GLU* 2.9 36.4 + - + +
56C ARG* 1.3 74.5 - - + +
58C ARG* 1.4 63.3 + - - +
60C LYS* 3.5 9.6 + - + +
61C LEU* 3.2 31.3 + - + +
17F T 6.0 3.1 - - - -
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Residues in contact with ARG 58 (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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21C ILE* 3.6 32.0 - - - +
25C PRO* 3.0 35.9 + - + +
27C ILE* 2.6 38.6 + - - +
28C THR* 5.0 0.6 - - - +
29C ASP* 4.8 3.2 + - - -
32C LEU* 5.3 0.2 - - - +
47C ARG* 3.6 18.4 - - - +
52C ILE* 3.8 6.0 - - - +
53C PRO* 2.7 46.1 + - + +
54C GLU* 3.0 14.0 + - - +
55C LEU* 3.2 26.7 - - - +
57C LYS* 1.4 72.9 - - - +
59C ILE* 1.4 64.5 + - - +
61C LEU* 3.1 13.3 + - + +
62C VAL* 3.1 26.5 + - - +
16F C 4.5 2.0 + - - -
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Residues in contact with ILE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PRO* 4.7 2.5 - - + +
26C PHE* 3.7 30.7 - - + +
55C LEU* 2.8 48.6 + - + +
56C ARG* 4.1 9.2 - - + +
58C ARG* 1.4 73.9 - - - +
60C LYS* 1.4 56.2 + - - +
62C VAL* 3.3 7.2 + - - -
63C ALA* 3.0 24.8 + - - +
56D ARG 5.4 1.1 - - - +
59D ILE* 4.1 5.2 - - + +
60D LYS* 3.6 47.3 - - + +
63D ALA* 3.5 13.3 - - + +
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Residues in contact with LYS 60 (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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56C ARG 3.1 19.0 + - - +
57C LYS* 3.6 10.3 - - + +
58C ARG 3.2 0.2 - - - -
59C ILE* 1.4 75.3 - - - +
61C LEU* 1.3 52.0 + - + +
63C ALA* 3.2 3.3 + - - +
64C GLU* 2.8 67.5 + - - +
26D PHE* 4.2 17.3 - - + -
59D ILE* 3.6 29.6 - - + +
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Residues in contact with LEU 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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53C PRO* 4.3 17.7 - - + -
57C LYS* 3.2 22.1 + - + +
58C ARG* 3.1 10.0 + - - +
60C LYS* 1.3 76.6 - - + +
62C VAL* 1.3 61.1 + - + +
64C GLU* 3.9 17.1 - - + +
65C LYS* 3.2 45.0 + - + +
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Residues in contact with VAL 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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25C PRO* 4.2 25.4 - - + -
26C PHE* 4.5 8.3 - - + -
58C ARG 3.1 16.9 + - - +
59C ILE* 3.6 8.7 - - - +
60C LYS 3.3 0.2 - - - -
61C LEU* 1.3 76.4 - - + +
63C ALA* 1.3 61.3 - - - +
65C LYS* 3.5 8.1 + - + +
66C ASN* 3.2 31.2 + - - +
63D ALA* 3.8 27.8 - - + +
66D ASN 4.6 4.9 - - - +
67D TYR* 4.6 9.6 - - + -
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Residues in contact with ALA 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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59C ILE 3.0 10.6 + - - +
60C LYS 3.5 7.6 - - - +
62C VAL* 1.3 75.5 - - - +
64C GLU* 1.4 52.2 + - - +
66C ASN* 3.3 2.5 + - - +
67C TYR* 2.8 34.7 + - - +
26D PHE* 3.8 12.8 - - + -
59D ILE* 3.4 35.7 - - + +
62D VAL* 3.5 10.5 - - + +
63D ALA* 3.7 14.3 - - - +
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Residues in contact with GLU 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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60C LYS* 2.8 53.9 + - - +
61C LEU* 3.9 21.9 - - + +
63C ALA* 1.4 68.5 - - - +
65C LYS* 1.3 58.7 + - + +
67C TYR* 3.9 3.7 - - + +
68C ASP* 3.0 43.5 + - - +
26D PHE* 3.8 23.2 - - + -
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Residues in contact with LYS 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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61C LEU* 3.2 34.8 + - - +
62C VAL* 3.8 8.7 - - - +
63C ALA 3.4 0.2 - - - -
64C GLU* 1.3 74.2 - - + +
66C ASN* 1.4 64.1 + - - +
69C GLN 3.4 3.8 + - - -
70C ILE* 3.2 53.2 + - + +
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Residues in contact with ASN 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 VAL* 3.2 17.4 + - - +
63C ALA 3.3 6.2 + - - +
65C LYS* 1.4 77.7 - - - +
67C TYR* 1.4 63.1 + - - +
69C GLN* 3.3 19.6 + - - +
70C ILE 5.3 1.6 - - - +
62D VAL* 3.3 28.5 + - + +
63D ALA* 3.5 8.3 + - - +
66D ASN* 3.2 56.2 + - + +
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Residues in contact with TYR 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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63C ALA 2.8 20.4 + - - +
64C GLU* 3.9 5.2 - - + +
65C LYS 3.5 0.2 - - - -
66C ASN* 1.4 70.0 - - - +
68C ASP* 1.4 64.1 + - - +
69C GLN* 3.0 21.1 + - - +
22D ASP 5.5 2.0 - - - -
23D SER 2.6 27.7 + - - -
24D ASN* 4.0 7.7 + - - +
25D PRO* 3.9 22.9 - - + -
26D PHE* 3.6 31.9 - + + -
62D VAL* 4.5 9.1 - - + +
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Residues in contact with ASP 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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64C GLU* 3.0 30.4 + - - +
66C ASN 3.5 0.2 - - - -
67C TYR* 1.4 79.8 - - - +
69C GLN* 1.4 67.2 + - - +
70C ILE* 3.4 25.0 + - + +
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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