Contacts of the helix formed by residues 46 - 56 (chain D) in PDB entry 4PE5
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 ASP 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D LEU* 5.5 0.4 - - - -
45D SER* 1.3 71.2 - - - +
47D GLU* 1.3 64.5 + - - +
48D VAL* 3.2 3.4 - - + +
49D ALA* 4.0 19.0 - - + +
50D ILE* 3.2 22.1 + - - +
289D LEU* 5.4 3.7 - - - +
290D PRO* 5.3 2.6 - - + +
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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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41D LEU* 4.9 7.6 - - + -
45D SER 3.3 6.9 + - - +
46D ASP* 1.3 71.2 - - - +
48D VAL* 1.3 60.8 + - - +
50D ILE* 3.6 6.0 - - - +
51D LYS* 2.9 33.8 + - - +
70D LEU* 4.0 19.2 - - + +
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Residues in contact with VAL 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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46D ASP* 3.2 2.8 - - + -
47D GLU* 1.3 79.1 - - - +
49D ALA* 1.3 58.4 + - - +
51D LYS* 3.9 3.2 - - - +
52D ASP* 2.9 32.0 + - - +
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Residues in contact with ALA 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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46D ASP* 3.6 20.6 + - + +
47D GLU 3.5 0.4 - - - -
48D VAL* 1.3 78.3 - - - +
50D ILE* 1.3 57.4 + - - +
52D ASP* 3.6 6.6 + - - +
53D ALA* 2.9 30.8 + - - +
290D PRO* 3.8 15.1 - - + +
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Residues in contact with ILE 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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39D VAL* 6.5 0.4 - - + -
41D LEU* 5.0 7.6 - - + -
46D ASP 3.2 18.8 + - - +
47D GLU* 3.6 7.9 - - - +
48D VAL 3.2 0.2 - - - -
49D ALA* 1.3 76.5 - - - +
51D LYS* 1.3 58.2 + - - +
53D ALA* 2.9 19.4 + - - +
54D HIS* 2.9 17.4 + - - +
70D LEU* 4.5 12.3 - - + -
289D LEU* 6.0 3.1 - - + -
290D PRO* 3.8 23.4 - - + +
293D VAL* 5.3 13.9 - - + +
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Residues in contact with LYS 51 (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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47D GLU 2.9 20.6 + - - +
48D VAL* 4.2 2.7 - - - +
50D ILE* 1.3 73.9 - - - +
52D ASP* 1.3 57.8 + - - +
54D HIS* 4.1 7.0 - - - -
55D GLU* 2.9 36.3 + - + +
70D LEU* 4.6 16.8 - - + -
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Residues in contact with ASP 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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48D VAL 2.9 20.8 + - - +
49D ALA* 3.7 7.2 - - - +
51D LYS* 1.3 77.2 - - - +
53D ALA* 1.3 56.9 + - - +
54D HIS 3.2 1.7 + - - -
55D GLU* 5.4 0.2 - - - -
56D LYS* 3.2 30.1 + - - +
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Residues in contact with ALA 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 ALA 2.9 17.3 + - - +
50D ILE 2.9 7.5 + - - +
52D ASP* 1.3 74.4 - - - +
54D HIS* 1.3 56.9 + - - +
56D LYS* 5.0 2.2 - - - -
57D ASP* 5.8 3.5 - - - +
290D PRO* 3.7 23.2 - - + +
291D ALA* 5.2 0.7 - - - +
294D ARG* 3.8 21.1 - - + +
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Residues in contact with HIS 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 ILE 2.9 15.1 + - - +
51D LYS* 4.0 7.6 - - - +
52D ASP 3.2 0.2 - - - -
53D ALA* 1.3 80.6 - - - +
55D GLU* 1.3 60.9 + - - +
56D LYS 3.6 1.1 - - - -
57D ASP* 4.9 8.7 - - - +
59D PHE* 5.1 7.8 - - - -
66D PRO* 6.1 0.7 - - - +
68D VAL* 5.3 12.3 - - + +
70D LEU* 5.9 2.5 - - + -
290D PRO 5.8 0.4 - - - +
293D VAL* 5.1 7.4 - - + -
294D ARG* 5.4 5.4 - - - +
297D ILE* 4.2 25.5 - - + +
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Residues in contact with GLU 55 (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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51D LYS* 2.9 19.5 + - + +
52D ASP* 5.4 0.2 - - - -
54D HIS* 1.3 76.9 - - + +
56D LYS* 1.3 66.2 + - - +
57D ASP 3.7 1.3 - - - -
58D ASP* 4.5 6.3 + - - +
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Residues in contact with LYS 56 (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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52D ASP* 3.2 21.4 + - - +
53D ALA* 5.3 1.3 - - - -
54D HIS 3.6 0.4 - - - -
55D GLU* 1.3 79.1 - - - +
57D ASP* 1.3 57.2 + - - +
58D ASP* 2.7 19.6 + - - +
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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