Contacts of the helix formed by residues 50 - 58 (chain C) in PDB entry 3LOC
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 SER 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C ALA* 3.8 1.3 - - - -
49C VAL* 1.3 81.2 - - - +
51C LYS* 1.3 58.0 + - - +
52C THR* 3.5 11.1 + - - -
53C ASN* 3.0 28.0 + - - +
54C LEU* 2.9 24.4 + - - +
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Residues in contact with LYS 51 (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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39C ARG* 5.8 2.0 - - - +
40C LEU* 4.2 34.7 - - + +
41C GLU* 4.6 21.6 - - + +
44C ALA* 3.8 15.5 - - + +
50C SER* 1.3 72.4 - - - +
52C THR* 1.3 59.0 + - - +
54C LEU* 3.3 5.3 + - + +
55C LEU* 3.0 53.2 + - + +
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Residues in contact with THR 52 (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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50C SER* 3.1 10.0 + - - -
51C LYS* 1.3 81.3 - - - +
53C ASN* 1.3 61.4 + - - +
55C LEU* 3.5 13.6 + - + +
56C TYR* 3.4 30.4 + - + -
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Residues in contact with ASN 53 (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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18C LYS* 2.8 38.8 + - - +
22C ILE* 5.1 0.4 - - - -
49C VAL* 4.4 5.3 - - + +
50C SER* 3.0 27.4 + - - +
52C THR* 1.3 76.4 - - - +
54C LEU* 1.3 65.3 + - - +
56C TYR* 2.9 20.9 + - - +
57C TYR* 3.3 33.3 - - - -
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Residues in contact with LEU 54 (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 ILE* 4.0 28.3 - - + -
40C LEU* 3.8 37.5 - - + +
43C ILE* 3.7 30.5 - - + -
44C ALA* 3.7 19.5 - - + +
49C VAL* 4.3 7.0 - - + +
50C SER 2.9 12.0 + - - +
51C LYS* 3.4 10.1 - - - +
53C ASN* 1.3 74.7 - - - +
55C LEU* 1.3 60.8 + - + +
57C TYR* 2.9 19.6 + - - +
58C PHE* 2.9 23.9 + - + +
60C SER 5.7 0.2 - - - +
64C LEU* 4.1 10.5 - - + -
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C LEU* 3.6 28.7 - - + -
51C LYS* 3.0 45.3 + - + +
52C THR* 3.7 12.1 - - + +
53C ASN 3.2 0.4 - - - -
54C LEU* 1.3 77.7 - - + +
56C TYR* 1.3 62.6 + - + +
58C PHE 3.2 21.2 - - - +
59C PRO* 3.4 38.0 - - + +
60C SER* 4.5 0.7 - - - -
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Residues in contact with TYR 56 (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 THR* 3.4 22.3 + - + +
53C ASN* 2.9 21.8 + - - +
55C LEU* 1.3 78.3 - - + +
57C TYR* 1.3 65.7 + - + +
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Residues in contact with TYR 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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15C VAL* 3.6 54.5 + - + +
18C LYS* 3.8 28.0 + - + +
19C LYS* 4.2 29.4 + - + -
22C ILE* 3.9 14.1 - - + -
53C ASN* 3.3 32.3 - - - -
54C LEU 2.9 7.6 + - - +
56C TYR* 1.3 83.8 - - + +
58C PHE* 1.3 85.8 + - + +
59C PRO* 4.3 2.7 - - - +
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Residues in contact with PHE 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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19C LYS* 3.4 32.8 - - + -
22C ILE* 3.7 33.0 - - + -
23C LEU* 3.7 20.9 - - + -
54C LEU* 2.9 12.1 + - + +
55C LEU* 3.2 20.2 - - - +
56C TYR 3.6 0.2 - - - -
57C TYR* 1.3 96.9 - - + +
59C PRO* 1.3 66.6 - - + +
60C SER 3.2 10.1 + - - +
63C ALA* 4.4 3.8 - - + -
64C LEU* 3.9 30.3 - - + +
67C ALA* 3.6 29.2 - - + -
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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