Contacts of the helix formed by residues 45 - 55 (chain F) in PDB entry 5M73
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 THR 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F PRO* 4.5 1.1 - - - -
43F ASN 3.7 9.2 - - - +
44F PRO* 1.3 76.1 - - - +
46F ALA* 1.3 64.4 + - - +
47F THR* 3.4 11.8 + - - -
48F GLU* 2.5 43.3 + - - +
49F ILE* 3.1 27.7 + - - +
76F VAL 5.1 1.6 - - - -
77F GLN* 3.2 41.1 - - + +
79F ARG 5.3 0.4 - - - -
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Residues in contact with ALA 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F PRO* 4.1 8.7 - - + +
45F THR* 1.3 74.0 - - - +
47F THR* 1.3 58.5 + - - +
49F ILE* 3.4 12.7 + - - +
50F GLN* 3.0 29.8 + - - +
62F LEU* 4.1 12.0 - - + +
63F GLU 5.4 0.4 - - - +
64F LYS* 5.5 1.6 - - - -
79F ARG 3.9 5.0 + - - +
80F GLY* 3.5 36.3 - - - -
81F ARG 4.1 4.7 - - - +
82F VAL* 4.2 11.3 - - + +
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Residues in contact with THR 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F THR* 3.1 10.8 + - - -
46F ALA* 1.3 78.2 - - - +
48F GLU* 1.3 60.2 + - + +
50F GLN* 3.3 8.5 + - - +
51F ASP* 3.0 41.4 + - - +
62F LEU* 4.2 13.8 - - + +
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Residues in contact with GLU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F GLU 5.2 1.2 - - - +
43F ASN 4.0 3.5 - - - +
44F PRO* 3.7 9.4 - - - +
45F THR* 2.5 48.1 + - - +
47F THR* 1.3 76.1 - - + +
49F ILE* 1.3 67.8 + - - +
51F ASP* 3.1 8.3 + - - +
52F VAL* 3.0 29.7 + - - +
112F ILE* 3.8 33.4 - - + +
115F LEU* 5.1 9.4 - - + -
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Residues in contact with ILE 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ILE* 4.1 31.4 - - + +
19F TYR 4.6 0.4 - - - -
20F PRO* 4.1 24.5 - - + -
23F LEU* 4.2 23.3 - - + -
44F PRO* 5.1 2.0 - - + -
45F THR 3.1 15.8 + - - +
46F ALA* 3.6 11.7 - - - +
48F GLU* 1.3 74.8 - - - +
50F GLN* 1.3 61.0 + - - +
52F VAL* 3.1 10.6 - - - +
53F CYS* 2.8 37.8 + - + -
82F VAL* 3.8 22.0 - - + -
104F VAL* 6.2 1.1 - - + -
108F ALA* 4.7 9.2 - - + -
112F ILE* 4.4 6.7 - - + +
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Residues in contact with GLN 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ALA 3.0 17.4 + - - +
47F THR* 3.6 8.0 + - - +
49F ILE* 1.3 77.7 - - - +
51F ASP* 1.3 79.2 + - - +
53F CYS* 3.5 10.3 - - - -
54F SER* 2.9 25.0 + - - -
58F LEU* 3.9 18.0 - - + +
60F VAL* 5.6 2.9 - - + -
61F PHE* 5.5 0.9 - - - -
62F LEU* 3.2 44.7 + - + +
82F VAL* 4.7 3.3 - - + +
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Residues in contact with ASP 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F THR* 3.0 28.9 + - - +
48F GLU* 3.1 6.2 + - - +
50F GLN* 1.3 90.2 + - - +
52F VAL* 1.3 61.0 + - - +
54F SER* 2.9 24.6 + - - -
55F ALA* 4.0 2.9 + - - +
115F LEU* 3.5 28.2 - - + +
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Residues in contact with VAL 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F GLU 3.0 10.7 + - - +
49F ILE* 3.1 23.3 - - - +
51F ASP* 1.3 76.6 - - - +
53F CYS* 1.3 62.1 + - + +
54F SER 3.5 0.2 + - - -
55F ALA* 3.7 16.2 + - - +
56F VAL* 4.4 3.6 + - - +
107F TYR* 5.3 5.5 - - - -
108F ALA* 3.9 26.5 - - + +
111F MET* 3.7 37.8 - - + +
112F ILE* 3.8 15.9 - - + +
115F LEU* 3.5 26.0 - - + -
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Residues in contact with CYS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ILE* 2.8 41.0 + - + +
50F GLN* 3.5 13.9 - - - -
52F VAL* 1.3 78.2 - - + +
54F SER* 1.3 65.5 + - - +
55F ALA 3.1 0.2 - - - -
56F VAL* 3.0 31.9 + - + +
57F GLY 3.7 1.0 + - - -
58F LEU* 3.2 27.6 - - + +
60F VAL* 4.2 12.6 - - + -
82F VAL* 4.8 2.7 - - - -
84F VAL* 6.0 0.4 - - - -
104F VAL* 5.1 15.0 - - + -
107F TYR* 6.2 1.8 - - - -
108F ALA* 6.0 2.0 - - + -
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Residues in contact with SER 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLN* 2.9 20.5 + - - -
51F ASP* 2.9 14.1 + - - -
52F VAL 3.2 0.2 - - - -
53F CYS* 1.3 76.4 - - - +
55F ALA* 1.3 65.2 + - - +
57F GLY* 3.2 10.4 + - - -
58F LEU* 3.4 33.4 + - - +
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Residues in contact with ALA 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ASP 4.0 2.2 + - - +
52F VAL* 3.7 12.2 + - - +
53F CYS 3.1 0.6 - - - -
54F SER* 1.3 83.2 + - - +
56F VAL* 1.3 57.3 + - - +
57F GLY 3.2 3.7 + - - -
107F TYR* 5.7 4.0 - - - +
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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