Contacts of the helix formed by residues 44 - 54 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A ILE* 4.6 25.1 - - + +
821A ILE* 5.9 0.9 - - + -
824A LYS* 3.4 26.0 - - + +
37D ARG* 3.2 4.7 + - - -
42D ASN 3.8 0.8 + - - -
43D PRO* 1.4 74.9 - - - +
45D GLU* 1.4 62.8 + - - +
46D ALA* 3.7 6.4 - - + +
47D GLU* 2.7 52.7 + - - +
48D LEU* 3.1 16.6 + - - +
82D GLU* 4.2 5.2 - - - +
114D GLU* 3.3 16.4 - - - +
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A LYS* 4.6 2.9 - - - +
827A ARG* 4.0 34.0 - - - +
37D ARG* 2.6 46.0 + - - +
44D THR* 1.4 71.2 - - - +
46D ALA* 1.3 56.3 + - - +
48D LEU* 3.4 15.2 - - + +
49D GLN* 3.1 34.5 + - + +
114D GLU* 2.8 26.3 + - + +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR* 3.7 7.2 - - - +
45D GLU* 1.3 71.7 - - - +
47D GLU* 1.4 59.7 + - + +
49D GLN* 3.0 9.9 + - - +
50D ASP* 2.9 37.9 + - - +
114D GLU* 2.8 15.7 + - - +
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PRO* 3.7 11.7 - - + +
44D THR* 2.7 57.1 + - - +
46D ALA* 1.4 71.1 - - + +
48D LEU* 1.3 57.6 + - - +
50D ASP* 3.4 12.4 + - - +
51D MET* 2.9 41.3 + - + +
75D LYS* 5.1 5.5 - - - +
78D ASP* 5.4 16.7 - - + +
82D GLU* 4.5 10.5 - - - +
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LYS* 5.5 6.5 - - - +
32D LEU* 3.5 27.1 - - + -
33D GLY* 3.4 43.1 - - - +
36D MET* 3.8 10.5 - - - -
37D ARG* 4.0 2.9 - - - +
43D PRO* 4.7 4.5 - - + +
44D THR 3.1 13.3 + - - +
45D GLU* 3.4 24.9 - - + +
47D GLU* 1.3 76.2 - - - +
49D GLN* 1.3 75.2 + - - +
51D MET* 3.6 8.0 + - - +
52D ILE* 3.2 26.7 + - + +
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Residues in contact with GLN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LYS* 2.7 31.4 + - - +
45D GLU* 3.1 18.4 + - + +
46D ALA* 3.0 10.9 + - - +
48D LEU* 1.3 98.7 + - - +
50D ASP* 1.3 56.8 + - - +
52D ILE* 3.3 11.7 + - - +
53D ASN* 2.8 37.3 + - + +
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Residues in contact with ASP 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA* 2.9 23.8 + - - +
47D GLU* 3.6 14.1 - - - +
49D GLN* 1.3 78.5 - - - +
51D MET* 1.4 55.3 + - - +
53D ASN* 3.1 7.1 + - - +
54D GLU* 3.0 36.1 + - - +
75D LYS* 5.2 10.5 - - - +
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Residues in contact with MET 51 (chain D).
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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32D LEU* 5.2 4.3 - - + -
36D MET* 3.4 39.7 - - + +
43D PRO* 5.3 3.4 - - - -
47D GLU* 2.9 26.1 + - + +
48D LEU* 3.7 6.3 - - - +
50D ASP* 1.4 74.5 - - - +
52D ILE* 1.4 62.0 + - + +
54D GLU* 3.4 21.9 - - - +
55D VAL* 3.7 9.9 - - - +
71D MET* 3.4 47.9 - - + +
72D MET* 4.2 3.4 - - - +
74D ARG* 6.0 0.2 - - - +
75D LYS* 3.8 28.7 - - + -
79D THR* 4.0 20.2 - - + -
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Residues in contact with ILE 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D THR* 3.7 37.0 - - + +
30D LYS* 4.5 8.5 - - + +
32D LEU* 3.4 25.4 - - + -
48D LEU* 3.2 15.5 + - + +
49D GLN* 3.7 21.3 - - - +
51D MET* 1.4 75.0 - - - +
53D ASN* 1.3 59.7 + - - +
55D VAL* 2.9 34.6 - - - +
57D ALA* 4.4 20.7 - - + +
58D ASP 5.4 0.2 + - - -
63D ILE* 6.5 0.4 - - + -
71D MET* 6.0 0.9 - - - -
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Residues in contact with ASN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D GLN 2.8 21.7 + - - +
50D ASP* 3.1 7.4 + - - +
52D ILE* 1.3 74.7 - - - +
54D GLU* 1.3 59.1 + - - +
55D VAL 3.2 8.0 + - - +
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Residues in contact with GLU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ASP* 3.0 20.8 + - - +
51D MET* 3.4 12.3 - - - +
53D ASN* 1.3 75.9 - - - +
55D VAL* 1.3 53.9 + - - +
74D ARG* 2.7 65.1 + - - +
75D LYS* 3.1 37.4 + - - +
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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