Contacts of the helix formed by residues 48 - 55 (chain B) in PDB entry 5DTM
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 ILE 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B PRO* 3.5 32.3 - - + -
13B VAL* 6.2 0.9 - - + -
44B VAL* 2.9 25.1 + - + +
45B CYS 3.1 12.7 - - - +
47B GLU* 1.4 83.8 - - + +
49B PRO* 1.4 69.0 - - + +
50B ASP* 4.3 4.3 - - + +
51B LEU* 3.0 33.0 + - + +
52B LYS 3.2 4.0 + - - -
82B ILE* 5.7 0.4 - - + -
85B ILE* 5.1 2.5 - - + -
89B TRP* 3.7 37.7 - - + -
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Residues in contact with PRO 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B CYS 4.2 4.2 - - - +
46B GLU 4.9 4.7 - - - +
47B GLU 3.4 12.1 - - - +
48B ILE* 1.4 83.1 - - + +
50B ASP* 1.3 64.6 + - - +
52B LYS* 3.2 8.0 + - + +
53B LEU* 3.1 27.5 + - + +
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE* 3.3 6.1 - - + +
49B PRO* 1.3 79.3 - - - +
51B LEU* 1.3 57.5 + - - +
53B LEU* 3.3 20.2 + - - +
54B ALA* 2.9 23.0 + - - +
85B ILE* 3.2 27.2 - - + +
88B LEU* 3.8 17.8 - - + +
89B TRP* 3.6 20.7 + - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 3.4 36.6 - - + +
45B CYS* 3.9 16.8 - - - -
48B ILE* 3.0 24.5 + - + +
50B ASP* 1.3 77.3 - - - +
52B LYS* 1.3 58.9 + - - +
54B ALA* 3.2 2.1 + - - +
55B MET* 2.9 29.7 + - - +
78B TYR* 3.9 14.8 - - + +
81B ALA* 3.5 42.0 - - + +
82B ILE* 3.6 20.0 - - + +
85B ILE* 3.8 10.4 - - + +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LYS* 6.2 2.0 - - - +
42B ARG 5.7 0.4 - - - -
45B CYS* 3.5 38.0 + - + +
46B GLU* 2.8 34.4 + - - +
48B ILE 3.2 2.4 + - - -
49B PRO* 3.2 11.9 + - + +
51B LEU* 1.3 75.6 - - - +
53B LEU* 1.4 62.4 + - - +
55B MET* 3.5 7.4 + - - +
57B ASN* 3.1 36.8 + - - +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PRO* 3.1 17.7 + - + +
50B ASP* 3.4 22.9 - - - +
52B LYS* 1.4 78.7 - - - +
54B ALA* 1.3 60.7 + - - +
55B MET 4.0 3.6 - - - +
57B ASN* 5.5 0.7 + - - -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASP 2.9 6.8 + - - +
51B LEU 3.2 3.3 + - - +
53B LEU* 1.3 75.7 - - - +
55B MET* 1.3 65.4 + - - +
56B GLU* 3.6 6.1 + - - +
81B ALA* 4.2 18.1 - - + +
84B SER* 4.5 9.6 - - - -
85B ILE* 3.5 29.8 - - + -
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Residues in contact with MET 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ILE* 4.1 13.5 - - + -
45B CYS* 4.0 22.9 - - - -
51B LEU 2.9 17.3 + - - +
52B LYS 3.5 5.3 + - - +
53B LEU 3.4 3.7 - - - +
54B ALA* 1.3 77.6 - - - +
56B GLU* 1.3 65.8 + - - +
57B ASN* 3.0 26.8 + - - +
59B VAL* 3.6 31.4 - - + -
60B LEU* 4.2 13.5 - - + -
74B LEU* 4.1 3.6 - - + +
77B LYS* 3.7 19.5 - - + +
78B TYR* 3.8 31.6 - - + +
81B ALA* 3.7 9.8 - - + +
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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