Contacts of the helix formed by residues 56 - 69 (chain C) in PDB entry 5Y7G
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 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C GLU 3.7 3.6 - - - +
55C LEU* 1.3 96.4 - - + +
57C GLU* 1.3 60.0 + - - +
58C ALA* 3.3 4.3 - - + +
59C SER* 3.6 29.2 - - - +
60C GLN* 2.8 28.4 + - - +
93C PRO* 4.3 14.8 - - + -
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Residues in contact with GLU 57 (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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20C PHE* 5.4 2.0 - - - -
23C LEU* 4.3 6.8 - - - +
24C HIS* 6.1 0.2 - - - -
27C ARG* 3.5 24.8 + - - -
55C LEU 3.8 0.4 + - - +
56C PRO* 1.3 73.5 - - - +
58C ALA* 1.3 57.2 + - - +
60C GLN* 3.6 11.5 - - - +
61C ALA* 3.0 30.3 + - - +
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Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PRO* 4.3 3.5 - - + +
57C GLU* 1.3 79.3 - - - +
59C SER* 1.3 59.4 + - - +
61C ALA* 3.3 6.6 + - - +
62C LEU* 3.0 22.7 + - - +
83C GLU 5.7 0.9 - - - -
84C ILE* 3.9 24.2 - - - +
90C ALA* 3.6 15.8 - - + +
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Residues in contact with SER 59 (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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55C LEU* 5.0 0.2 - - - -
56C PRO* 3.3 28.1 + - - +
58C ALA* 1.3 76.0 - - - +
60C GLN* 1.3 64.4 + - - +
62C LEU* 3.2 4.7 + - - +
63C LEU 3.1 17.8 + - - -
89C ALA 4.7 0.2 + - - -
90C ALA* 3.0 32.4 + - - -
93C PRO* 3.3 22.5 - - - +
94C LEU* 3.6 19.1 - - - +
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Residues in contact with GLN 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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23C LEU* 3.5 17.9 - - + +
27C ARG* 3.1 35.0 + - - +
52C PHE 4.2 12.5 + - - +
53C ALA* 4.5 7.9 + - - +
55C LEU* 3.8 31.6 + - + +
56C PRO 2.8 24.0 + - - +
57C GLU* 3.6 15.1 - - - +
59C SER* 1.3 70.4 - - - +
61C ALA* 1.3 67.2 + - - +
62C LEU 3.3 0.2 - - - -
63C LEU* 3.6 7.9 + - - +
64C VAL* 3.2 27.9 + - - +
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Residues in contact with ALA 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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20C PHE* 4.0 16.4 - - + -
22C TYR* 3.4 31.3 + - - +
23C LEU* 4.1 12.3 - - + -
57C GLU 3.0 21.9 + - - +
58C ALA* 3.5 7.2 - - - +
60C GLN* 1.3 77.4 - - - +
62C LEU* 1.3 62.5 + - - +
64C VAL 3.4 6.2 + - - -
65C ARG* 3.8 4.9 + - - +
84C ILE* 3.7 18.6 - - + +
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Residues in contact with LEU 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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58C ALA 3.0 13.6 + - - +
59C SER 3.2 8.7 + - - +
61C ALA* 1.3 77.9 - - - +
63C LEU* 1.3 63.9 + - - +
64C VAL 3.3 1.0 + - - -
65C ARG* 3.3 11.6 + - - +
66C MET* 3.5 40.1 + - + +
79C LEU* 4.4 11.9 - - + +
81C TYR* 4.6 6.7 - - + -
84C ILE* 3.6 28.4 - - + +
87C THR* 3.6 18.4 - - + +
90C ALA* 3.7 9.0 - - + +
91C VAL* 3.5 33.4 - - + +
94C LEU* 4.7 2.5 - - + -
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Residues in contact with LEU 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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52C PHE* 6.4 0.4 - - + -
55C LEU* 4.5 7.0 - - + -
59C SER 3.1 10.0 + - - +
60C GLN* 3.9 9.0 - - - +
61C ALA 3.3 0.4 - - - -
62C LEU* 1.3 76.5 - - - +
64C VAL* 1.3 65.1 + - + +
66C MET* 3.2 10.2 + - + +
67C VAL* 3.1 46.6 + - + +
94C LEU* 3.8 36.5 - - + +
99C TRP* 4.5 24.0 - - + +
100C VAL* 4.2 16.4 - - + -
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Residues in contact with VAL 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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22C TYR* 3.4 41.5 - - + +
23C LEU* 3.6 23.1 - - + -
26C PHE* 4.4 24.0 - - + -
60C GLN 3.2 17.3 - - - +
61C ALA 3.4 2.4 + - - +
62C LEU 3.2 1.0 - - - -
63C LEU* 1.3 77.9 - - + +
65C ARG* 1.3 63.7 + - - +
67C VAL* 3.5 4.9 + - - +
68C MET* 3.0 38.6 + - + +
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Residues in contact with ARG 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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19C PRO 4.8 0.4 + - - -
21C TYR* 3.6 24.0 + - - -
22C TYR* 3.2 40.9 - - + +
61C ALA 3.8 12.1 + - - +
62C LEU* 3.3 8.2 + - + +
63C LEU 3.3 0.6 - - - -
64C VAL* 1.3 77.2 - - - +
66C MET* 1.3 62.8 + - + +
68C MET* 3.3 37.8 + - - +
69C ARG* 3.5 11.8 + - - +
74C PHE* 5.6 0.2 - - - -
79C LEU* 5.6 0.9 - - + -
81C TYR* 3.5 58.5 + - + +
83C GLU* 3.5 17.2 + - - -
84C ILE* 5.3 0.2 - - + -
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Residues in contact with MET 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 LEU* 3.5 43.3 + - + +
63C LEU* 3.2 13.7 + - + +
65C ARG* 1.3 77.0 - - - +
67C VAL* 1.3 61.4 + - + +
69C ARG 2.9 23.4 + - - +
71C GLY 4.3 1.2 - - - +
74C PHE* 3.3 34.6 - - + -
79C LEU* 3.6 39.5 - - + -
87C THR* 5.4 0.9 - - + -
91C VAL* 4.1 15.9 - - + -
94C LEU* 5.2 0.4 - - + -
100C VAL* 4.1 25.1 - - + -
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Residues in contact with VAL 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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26C PHE* 6.3 2.9 - - + -
63C LEU* 3.1 39.1 + - + +
64C VAL* 4.2 4.7 - - - +
66C MET* 1.3 77.9 - - + +
68C MET* 1.3 61.6 + - + +
69C ARG 3.3 8.5 + - - +
70C LYS* 5.0 1.6 - - - -
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Residues in contact with MET 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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21C TYR* 5.3 2.9 - - + +
22C TYR* 4.0 17.0 - - + +
26C PHE* 6.4 1.1 - - + -
64C VAL* 3.0 33.4 + - + +
65C ARG* 3.3 44.4 + - - +
66C MET 3.2 0.6 - - - -
67C VAL* 1.3 77.8 - - + +
69C ARG* 1.3 57.2 - - - +
70C LYS* 4.1 5.9 + - - +
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Residues in contact with ARG 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 ARG 3.5 6.6 + - - +
66C MET 2.9 18.0 + - - +
67C VAL* 3.1 7.6 - - - +
68C MET* 1.3 80.1 - - - +
70C LYS* 1.3 93.9 + - - +
71C GLY* 2.8 35.1 + - - +
74C PHE* 3.4 32.7 - - + -
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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