Contacts of the helix formed by residues 41 - 58 (chain B) in PDB entry 4DHX
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 GLY 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ILE 3.3 9.1 + - - -
39B GLU 3.2 6.2 + - - -
40B CYS* 1.3 77.7 - - - +
42B TRP* 1.3 64.9 + - - +
43B LYS 3.2 2.9 - - - -
44B ASP* 3.2 19.4 + - - +
45B GLN* 3.1 27.6 + - - +
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Residues in contact with TRP 42 (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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1180A MET* 3.7 32.3 - - + -
1183A PHE* 3.9 24.9 - + + -
1184A VAL* 4.0 8.5 - - + -
37B LEU* 3.0 40.8 + - + +
40B CYS* 3.3 16.1 - - - -
41B GLY* 1.3 77.1 - - - +
43B LYS* 1.3 67.2 + - - +
45B GLN* 3.3 15.9 + - - +
46B LEU* 3.3 46.5 + - + +
75B GLY* 2.9 38.2 + - - -
78B LEU* 3.6 32.1 - - + +
79B VAL* 3.7 13.1 - - + +
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Residues in contact with LYS 43 (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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1183A PHE* 3.8 28.9 - - + -
1187A THR* 3.8 29.8 - - + +
37B LEU 3.5 3.2 + - - -
38B ILE* 4.2 30.4 - - + +
41B GLY 3.2 0.6 - - - -
42B TRP* 1.3 87.1 - - + +
44B ASP* 1.3 66.4 + - - +
46B LEU* 3.2 7.7 + - + +
47B LYS* 3.1 45.5 + - - +
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Residues in contact with ASP 44 (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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38B ILE 5.2 3.5 - - - +
41B GLY* 3.2 20.3 + - - +
43B LYS* 1.3 78.9 - - - +
45B GLN* 1.3 57.6 + - + +
47B LYS* 3.3 27.1 + - - +
48B ALA* 3.0 28.8 + - - +
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Residues in contact with GLN 45 (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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40B CYS 5.9 0.4 + - - -
41B GLY 3.1 18.6 + - - +
42B TRP* 3.4 20.5 - - + +
43B LYS 3.2 0.2 - - - -
44B ASP* 1.3 74.1 - - + +
46B LEU* 1.3 65.6 + - + +
48B ALA* 3.4 6.5 + - - +
49B HIS* 3.1 23.6 + - - +
74B LYS* 4.6 10.0 + - - +
78B LEU* 3.4 42.5 - - + +
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Residues in contact with LEU 46 (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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1183A PHE 4.5 0.2 - - - +
1184A VAL* 3.9 25.1 - - + +
1187A THR* 4.0 22.4 - - + +
1188A CYS* 6.4 0.4 - - - -
42B TRP* 3.3 45.7 + - + +
43B LYS* 3.2 10.9 + - + +
45B GLN* 1.3 80.5 - - + +
47B LYS* 1.3 57.6 + - - +
49B HIS* 3.2 7.1 + - + +
50B CYS* 2.9 33.0 + - - -
71B ILE* 3.5 28.9 - - + +
75B GLY* 4.0 23.6 - - - -
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Residues in contact with LYS 47 (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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1187A THR* 3.7 14.6 - - + -
1191A GLU* 3.2 42.2 - - - +
43B LYS* 3.1 34.6 + - + +
44B ASP* 3.5 30.3 + - - +
46B LEU* 1.3 75.5 - - - +
48B ALA* 1.3 66.6 + - - +
50B CYS* 3.2 7.5 + - - +
51B LYS* 3.0 22.5 + - - +
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Residues in contact with ALA 48 (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 ASP 3.0 17.6 + - - +
45B GLN* 3.7 7.2 - - - +
47B LYS* 1.3 75.3 - - - +
49B HIS* 1.3 63.0 + - - +
51B LYS* 3.3 10.8 + - - +
52B GLU* 3.3 25.5 + - - +
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Residues in contact with HIS 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 GLN 3.1 14.0 + - - +
46B LEU* 3.5 10.5 - - - +
48B ALA* 1.3 74.5 - - - +
50B CYS* 1.3 65.5 + - - +
52B GLU* 3.3 11.6 + - + +
53B VAL* 3.1 35.8 + - + +
70B GLU* 3.8 26.3 + - + +
71B ILE* 3.6 22.2 + - + +
74B LYS* 4.1 38.6 + - + +
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Residues in contact with CYS 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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1187A THR* 4.9 1.8 - - - -
1188A CYS* 3.7 42.8 - - - -
1191A GLU* 4.1 23.1 - - + +
46B LEU 2.9 18.1 + - - +
47B LYS 3.2 10.1 + - - +
49B HIS* 1.3 74.7 - - - +
51B LYS* 1.3 65.6 + - - +
53B VAL* 3.2 3.0 + - - +
54B ILE* 2.9 32.5 + - + +
67B LEU* 4.3 9.8 - - + +
71B ILE* 4.2 14.3 - - - +
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Residues in contact with LYS 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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1191A GLU* 5.5 2.0 + - - +
47B LYS 3.0 12.0 + - - +
48B ALA* 3.5 13.2 - - - +
50B CYS* 1.3 76.9 - - - +
52B GLU* 1.3 68.8 + - - +
54B ILE* 3.7 9.6 - - - +
55B LYS* 3.0 36.5 + - + +
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Residues in contact with GLU 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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48B ALA 3.3 12.7 + - - +
49B HIS* 3.3 15.6 + - + +
50B CYS 3.2 0.4 - - - -
51B LYS* 1.3 89.5 - - - +
53B VAL* 1.3 60.5 + - + +
55B LYS* 3.4 32.8 + - - +
56B GLU* 2.9 40.6 + - + +
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Residues in contact with VAL 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 HIS* 3.1 26.4 + - + +
50B CYS 3.2 3.8 + - - +
52B GLU* 1.3 73.0 - - - +
54B ILE* 1.3 61.1 + - - +
56B GLU* 3.7 5.1 - - - +
57B LYS* 2.9 47.1 + - + +
62B VAL* 4.5 3.4 - - + -
66B ASP* 5.3 1.1 - - + +
67B LEU* 3.4 26.0 - - + +
70B GLU* 3.6 27.1 - - + -
71B ILE* 3.4 19.5 - - + -
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Residues in contact with ILE 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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1191A GLU* 4.3 13.7 - - + +
1192A LEU* 4.2 18.4 - - + -
1195A ALA* 4.0 24.7 - - + -
50B CYS 2.9 24.2 + - - +
51B LYS* 3.7 8.1 - - - +
53B VAL* 1.3 76.9 - - - +
55B LYS* 1.3 59.2 + - - +
58B GLY* 2.8 31.6 + - - +
59B LEU* 3.8 27.6 - - + +
62B VAL* 4.6 7.9 - - + -
67B LEU* 4.1 19.7 - - + -
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Residues in contact with LYS 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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51B LYS* 3.0 25.3 + - + +
52B GLU* 3.7 35.1 + - - +
54B ILE* 1.3 78.6 - - - +
56B GLU* 1.3 69.8 + - - +
58B GLY* 4.5 2.6 + - - -
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Residues in contact with GLU 56 (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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52B GLU* 2.9 32.7 + - + +
53B VAL* 3.7 6.7 - - - +
54B ILE 3.1 0.4 - - - -
55B LYS* 1.3 90.0 + - + +
57B LYS* 1.3 71.8 + - + +
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Residues in contact with LYS 57 (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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53B VAL* 2.9 34.2 + - + +
56B GLU* 1.3 85.1 - - + +
58B GLY* 1.3 60.4 + - - +
61B HIS* 3.5 27.3 - - + +
62B VAL* 4.0 23.1 - - + +
66B ASP* 6.1 2.0 - - + -
70B GLU* 5.1 12.9 + - - -
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Residues in contact with GLY 58 (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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54B ILE 2.8 22.0 + - - -
55B LYS 4.4 2.9 - - - -
56B GLU 3.6 0.6 - - - -
57B LYS* 1.3 74.5 - - - +
59B LEU* 1.3 62.0 + - - -
60B GLU* 3.1 4.0 - - - -
61B HIS* 3.0 6.2 + - - -
62B VAL* 2.8 30.4 + - - +
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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