Contacts of the helix formed by residues 44 - 57 (chain L) in PDB entry 5MS0
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 44 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5L ALA* 3.3 15.1 + - + +
6L ARG* 4.3 25.1 - - + +
9L ALA* 3.8 6.4 - - - +
43L VAL* 1.3 66.9 - - - +
45L VAL* 1.3 63.4 + - - +
46L LEU 3.3 3.7 + - - +
47L TYR* 3.6 11.8 + - + +
48L PHE* 3.3 19.9 + - - +
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Residues in contact with VAL 45 (chain L).
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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43L VAL* 3.1 14.5 + - + +
44L ASP* 1.3 71.4 - - - +
46L LEU* 1.3 60.6 + - - +
48L PHE* 3.5 9.5 - - + +
49L ARG* 2.9 30.5 + - - +
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Residues in contact with LEU 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L ASP* 3.3 1.6 - - + -
45L VAL* 1.3 75.8 - - - +
47L TYR* 1.3 59.9 + - - +
49L ARG* 4.1 3.3 - - - +
50L GLU* 2.9 29.6 + - - +
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Residues in contact with TYR 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L ARG* 5.9 5.2 - - + -
9L ALA* 5.9 2.9 - - + -
44L ASP* 3.6 15.6 + - + +
46L LEU* 1.3 75.7 - - - +
48L PHE* 1.3 60.3 + - - +
50L GLU* 3.8 6.8 - - - +
51L LEU* 2.9 31.0 + - - +
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Residues in contact with PHE 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ALA* 4.8 17.2 - - + +
13L ALA* 5.8 6.5 - - + +
43L VAL* 5.9 2.7 - - + -
44L ASP 3.3 17.4 + - - +
45L VAL* 3.5 11.2 - - + +
46L LEU 3.2 0.2 - - - -
47L TYR* 1.3 77.1 - - - +
49L ARG* 1.3 58.8 + - - +
51L LEU* 3.4 4.5 + - - +
52L LEU* 3.0 29.5 + - - +
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Residues in contact with ARG 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L VAL 2.9 17.4 + - - +
46L LEU* 4.2 3.6 - - - +
48L PHE* 1.3 73.5 - - - +
50L GLU* 1.3 59.5 + - - +
52L LEU* 4.1 4.6 - - - +
53L ALA* 2.9 31.9 + - - +
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Residues in contact with GLU 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L LEU 2.9 20.0 + - - +
47L TYR* 3.8 7.9 - - - +
48L PHE 3.3 0.2 - - - -
49L ARG* 1.3 77.9 - - - +
51L LEU* 1.3 56.3 + - - +
53L ALA* 3.7 4.6 + - - +
54L GLY* 2.9 23.7 + - - -
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Residues in contact with LEU 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L ALA* 5.8 8.1 - - + -
47L TYR 2.9 18.9 + - - +
48L PHE* 4.0 4.3 - - - +
50L GLU* 1.3 75.1 - - - +
52L LEU* 1.3 59.2 + - - +
54L GLY* 4.7 1.6 - - - -
55L VAL* 2.9 32.4 + - - +
87L ILE* 6.1 4.9 - - + -
90L TYR* 6.2 4.7 - - + -
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Residues in contact with LEU 52 (chain L).
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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16L ALA* 6.2 3.8 - - + -
27L ILE* 5.2 2.5 - - + +
31L GLU* 5.8 8.3 - - + -
48L PHE 3.0 17.7 + - - +
49L ARG* 4.1 5.6 - - - +
51L LEU* 1.3 73.2 - - - +
53L ALA* 1.3 54.0 + - - +
55L VAL* 4.7 2.2 - - - +
56L ALA* 2.6 38.0 + - - +
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Residues in contact with ALA 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L ARG 2.9 18.8 + - - +
50L GLU* 4.0 4.7 - - - +
52L LEU* 1.3 76.1 - - - +
54L GLY* 1.3 58.1 + - - +
56L ALA* 3.4 6.0 - - - +
57L THR* 2.9 32.6 + - - -
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Residues in contact with GLY 54 (chain L).
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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50L GLU 2.9 17.0 + - - -
51L LEU* 3.1 5.3 + - - -
53L ALA* 1.3 79.3 - - - +
55L VAL* 1.3 60.1 + - - +
57L THR* 4.4 1.3 - - - -
58L ASN* 3.3 23.6 + - - +
90L TYR* 5.3 8.3 - - - -
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Residues in contact with VAL 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L LEU* 6.4 1.8 - - + -
51L LEU 2.9 17.5 + - - +
52L LEU* 4.8 1.8 - - - +
54L GLY* 1.3 71.2 - - - -
56L ALA* 1.3 64.3 + - - +
58L ASN* 3.4 17.5 - - - +
86L ARG* 5.1 15.5 - - + +
87L ILE* 5.8 2.9 - - + -
90L TYR* 5.1 13.7 - - + +
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Residues in contact with ALA 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L ILE* 4.1 25.8 - - + -
52L LEU 2.6 24.8 + - - +
53L ALA* 3.4 8.3 - - - +
54L GLY 3.2 0.2 - - - -
55L VAL* 1.3 80.8 - - - +
57L THR* 1.3 62.5 + - - +
58L ASN 3.2 4.1 + - - +
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Residues in contact with THR 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L ALA 2.9 16.5 + - - -
54L GLY 4.9 1.1 - - - -
56L ALA* 1.3 77.3 - - - +
58L ASN* 1.3 58.0 + - - +
59L THR* 4.5 5.0 - - - -
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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