Contacts of the helix formed by residues 44 - 54 (chain P) in PDB entry 2DFS
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 44 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820M ILE* 4.6 25.4 - - + +
821M ILE* 5.9 0.9 - - + -
824M LYS* 3.4 26.0 - - + +
37P ARG* 3.3 4.1 + - - -
42P ASN 3.7 0.6 + - - -
43P PRO* 1.4 75.2 - - - +
45P GLU* 1.3 63.0 + - - +
46P ALA* 3.7 5.7 - - - +
47P GLU* 2.7 52.6 + - - +
48P LEU 3.1 16.8 + - - -
82P GLU* 4.3 5.6 + - - +
114P GLU* 3.3 17.0 - - - +
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Residues in contact with GLU 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824M LYS* 4.5 2.9 - - - +
827M ARG* 3.6 36.7 - - - +
37P ARG* 2.6 45.3 + - - +
44P THR* 1.3 71.5 - - - +
46P ALA* 1.3 56.5 + - - +
48P LEU* 3.4 14.8 - - + +
49P GLN* 3.0 35.9 + - + +
114P GLU* 2.8 25.3 + - + +
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Residues in contact with ALA 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P THR* 3.7 7.2 - - - +
45P GLU* 1.3 69.6 - - - +
47P GLU* 1.4 60.4 + - + +
49P GLN* 3.0 9.0 + - - +
50P ASP* 2.9 38.8 + - - +
114P GLU* 2.8 17.4 + - - +
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Residues in contact with GLU 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P PRO* 3.6 11.5 - - + +
44P THR* 2.7 58.8 + - - +
46P ALA* 1.4 71.6 - - + +
48P LEU* 1.3 56.6 + - - +
50P ASP* 3.3 11.8 + - - +
51P MET* 2.9 39.6 + - + +
75P LYS* 5.2 4.8 - - - +
78P ASP* 5.4 16.6 - - + +
79P THR* 6.5 0.9 - - + -
82P GLU* 4.6 9.5 - - - +
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Residues in contact with LEU 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P THR 6.0 0.4 - - - +
30P LYS* 5.5 5.4 - - - +
32P LEU* 3.5 28.3 - - + -
33P GLY* 3.3 42.8 - - - +
36P MET* 3.8 9.9 - - - -
37P ARG* 4.0 3.1 - - - +
43P PRO* 4.7 4.1 - - + +
44P THR 3.1 13.9 + - - +
45P GLU* 3.4 24.7 - - + +
47P GLU* 1.3 75.7 - - - +
49P GLN* 1.3 77.4 + - - +
51P MET* 3.6 7.8 + - - +
52P ILE* 3.2 26.5 + - + +
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Residues in contact with GLN 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P LYS* 2.8 32.6 + - - +
45P GLU* 3.0 17.4 + - + +
46P ALA* 3.0 10.7 + - - +
48P LEU* 1.3 98.8 + - - +
50P ASP* 1.3 56.9 + - - +
52P ILE* 3.3 10.8 + - - +
53P ASN* 2.8 36.9 + - - +
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Residues in contact with ASP 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ALA* 2.9 24.5 + - - +
47P GLU* 3.3 13.0 + - - +
49P GLN* 1.3 76.7 - - - +
51P MET* 1.4 56.1 + - - +
53P ASN* 3.1 7.0 + - - +
54P GLU* 3.0 35.8 + - - +
75P LYS* 5.3 9.2 - - - +
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Residues in contact with MET 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P LEU* 5.2 2.7 - - + -
36P MET* 3.4 39.5 - - + +
43P PRO* 5.3 2.2 - - - -
47P GLU* 2.9 26.1 + - + +
48P LEU* 3.7 6.3 - - - +
50P ASP* 1.4 75.7 - - - +
52P ILE* 1.4 61.9 + - + +
54P GLU* 3.4 20.6 + - - +
55P VAL* 3.7 10.0 - - - +
71P MET* 3.4 48.2 - - + +
72P MET* 4.2 3.1 - - - +
74P ARG* 6.1 0.2 - - - +
75P LYS* 3.7 29.4 - - + -
79P THR* 3.9 22.2 - - + -
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Residues in contact with ILE 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P THR* 3.7 35.4 - - + +
30P LYS* 4.4 9.2 - - - +
32P LEU* 3.4 24.9 - - + -
48P LEU* 3.2 16.8 + - + +
49P GLN* 3.7 21.1 - - - +
51P MET* 1.4 75.7 - - - +
53P ASN* 1.3 58.8 + - - +
55P VAL* 2.9 34.3 - - - +
57P ALA* 4.5 20.4 - - + +
63P ILE* 6.5 0.2 - - + -
67P GLU* 6.0 0.2 - - - -
71P MET* 5.7 0.9 - - - -
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Residues in contact with ASN 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P GLN 2.8 21.9 + - - +
50P ASP* 3.1 7.5 + - - +
52P ILE* 1.3 74.1 - - - +
54P GLU* 1.3 57.7 + - - +
55P VAL 3.2 7.9 + - - +
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Residues in contact with GLU 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P ASP* 3.0 20.8 + - - +
51P MET* 3.4 12.5 - - - +
53P ASN* 1.3 76.1 - - - +
55P VAL* 1.3 55.0 + - - +
74P ARG* 2.7 62.8 + - - +
75P LYS* 3.0 38.9 + - - +
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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