Contacts of the helix formed by residues 43 - 57 (chain E) in PDB entry 1UDI
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 PRO 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E ALA 3.6 6.7 - - - +
42E ASN* 1.3 91.4 - - - +
44E LEU* 1.3 68.5 + - + +
45E THR 3.3 0.3 + - - -
46E ALA* 3.4 8.3 + - + +
47E HIS* 3.0 40.8 + - + +
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Residues in contact with LEU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ASN* 2.9 16.2 + - - +
43E PRO* 1.3 85.6 - - + +
45E THR* 1.3 61.0 + - - +
47E HIS* 3.8 19.3 + - + +
48E LEU* 3.2 20.3 + - - +
164E GLY* 6.0 0.5 - - - -
167E ARG* 3.8 31.2 + - - +
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Residues in contact with THR 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E GLU* 2.7 30.7 + - - +
40E LEU* 3.9 20.6 - - + +
42E ASN* 3.0 6.9 + - - +
44E LEU* 1.3 77.3 - - - +
46E ALA* 1.3 65.9 + - - +
47E HIS 3.2 0.2 - - - -
48E LEU* 3.0 8.9 + - + +
49E LEU* 2.9 40.2 + - + +
167E ARG* 2.8 27.6 + - - +
168E PHE* 4.3 15.6 - - + -
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Residues in contact with ALA 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU 4.6 4.4 + - - +
42E ASN 3.5 4.5 + - - +
43E PRO* 3.4 13.9 + - + +
45E THR* 1.3 80.4 - - - +
47E HIS* 1.3 65.9 + - + +
49E LEU* 3.3 8.3 + - - +
50E ALA* 3.0 26.8 + - - +
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Residues in contact with HIS 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E PRO* 3.0 31.6 + - + +
44E LEU* 4.1 18.6 - - + +
45E THR 3.2 0.6 - - - -
46E ALA* 1.3 80.7 - - + +
48E LEU* 1.3 60.7 + - - +
50E ALA* 3.2 9.0 + - - +
51E GLU* 2.8 30.5 + - - +
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Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU 3.2 15.0 + - - +
45E THR* 3.0 12.9 + - - +
47E HIS* 1.3 72.5 - - - +
49E LEU* 1.3 73.5 + - + +
51E GLU* 3.1 6.1 + - - +
52E TYR* 2.9 22.4 + - + +
163E ILE* 3.3 38.8 - - + +
164E GLY* 3.6 27.8 - - - +
165E TRP* 3.7 35.2 - - + +
167E ARG* 4.9 1.1 - - - +
168E PHE* 3.9 27.4 - - + -
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Residues in contact with LEU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E PHE* 4.0 21.1 - - + -
26E PHE* 3.4 38.8 - - + -
40E LEU* 5.1 2.0 - - + -
45E THR* 2.9 42.6 + - + +
46E ALA* 3.7 9.6 - - - +
48E LEU* 1.3 84.9 - - + +
50E ALA* 1.3 60.8 + - - +
52E TYR* 3.2 8.5 + - + +
53E ASN* 2.4 41.1 + - - +
165E TRP* 5.1 9.2 - - + -
168E PHE* 5.7 1.1 - - + -
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Residues in contact with ALA 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E ALA 3.0 14.5 + - - +
47E HIS* 3.3 14.6 - - - +
48E LEU 3.1 0.2 - - - -
49E LEU* 1.3 77.2 - - - +
51E GLU* 1.3 57.4 + - - +
53E ASN* 3.2 1.3 + - - +
54E ARG* 3.0 54.2 + - - +
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Residues in contact with GLU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E HIS 2.8 16.2 + - - +
48E LEU* 3.5 6.5 - - - +
50E ALA* 1.3 73.3 - - - +
52E TYR* 1.3 64.5 + - - +
54E ARG* 4.6 10.7 - - - +
55E ARG* 2.7 72.1 + - - +
163E ILE* 3.7 26.0 - - + +
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Residues in contact with TYR 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E VAL* 5.7 0.2 - - + -
26E PHE* 3.6 29.6 - + - -
48E LEU 2.9 12.9 + - - +
49E LEU* 3.4 10.1 - - + +
50E ALA 3.2 0.2 - - - -
51E GLU* 1.3 77.5 - - - +
53E ASN* 1.3 76.6 + - - +
55E ARG* 3.1 20.6 + - - +
56E CYS* 3.2 34.4 + - - -
61E VAL* 4.4 7.4 - - + +
65E ARG* 2.6 51.0 + - - +
68E VAL* 4.3 4.1 - - + +
151E THR* 3.8 33.0 - - + -
160E HIS* 5.5 2.9 - + - -
163E ILE* 4.9 9.4 - - + +
165E TRP* 4.4 15.5 - + + -
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Residues in contact with ASN 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E VAL* 5.5 4.2 - - - +
26E PHE* 5.7 0.6 - - - -
49E LEU* 2.4 37.6 + - - +
50E ALA* 4.4 0.4 - - - +
52E TYR* 1.3 94.8 - - - +
54E ARG* 1.3 91.0 + - - +
55E ARG 3.4 0.2 + - - -
56E CYS* 3.6 11.1 + - - +
57E GLN* 3.2 22.5 + - - +
65E ARG* 4.1 12.5 + - - +
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Residues in contact with ARG 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E ALA* 3.0 44.6 + - - +
51E GLU* 4.1 15.7 - - - +
53E ASN* 1.3 103.7 - - - +
55E ARG* 1.3 61.9 + - + +
57E GLN* 3.2 41.9 - - - +
58E THR* 3.7 9.7 + - - +
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Residues in contact with ARG 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E GLU* 2.7 47.7 + - - +
52E TYR* 3.1 6.6 + - - +
54E ARG* 1.3 76.3 - - - +
56E CYS* 1.3 56.7 + - - +
57E GLN 3.0 6.1 + - - -
58E THR* 3.2 4.6 + - - +
59E GLU* 2.9 59.6 + - + +
61E VAL* 4.3 0.7 - - + -
159E SER* 4.3 13.9 + - - -
160E HIS* 3.7 28.2 - - + +
163E ILE* 3.7 25.9 - - - +
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Residues in contact with CYS 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E TYR* 3.2 50.4 + - - +
53E ASN* 3.6 7.4 + - - +
54E ARG 3.6 0.4 - - - -
55E ARG* 1.3 74.5 - - - +
57E GLN* 1.3 60.6 + - + +
58E THR 3.5 0.2 - - - -
59E GLU 3.5 16.3 - - - +
61E VAL* 4.1 17.0 - - + -
65E ARG* 4.6 13.9 - - - +
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Residues in contact with GLN 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ASN 3.2 14.9 + - - +
54E ARG* 3.2 48.8 - - - +
55E ARG 3.0 0.6 - - - -
56E CYS* 1.3 80.4 - - + +
58E THR* 1.3 66.2 + - + +
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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