Contacts of the helix formed by residues 44 - 58 (chain A) in PDB entry 4OE5
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 SER 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A THR* 2.6 40.1 + - - -
42A GLN 3.3 1.2 + - - -
43A GLY* 1.3 80.1 - - - +
45A PRO* 1.3 68.2 - - - +
46A GLU* 3.4 21.2 + - - -
47A ARG* 3.2 16.3 + - - +
48A ASP* 2.9 27.6 + - - -
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Residues in contact with PRO 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLY 3.7 3.3 - - - +
44A SER* 1.3 88.4 - - - +
46A GLU* 1.3 66.1 + - - +
48A ASP* 3.3 11.0 + - + +
49A ALA* 2.8 30.1 + - - +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.8 31.6 - - + +
39A ALA* 3.8 8.8 + - - +
40A PHE* 3.2 47.4 + - + +
41A THR* 4.5 0.3 + - - -
44A SER* 3.4 17.8 + - - +
45A PRO* 1.3 89.4 - - - +
47A ARG* 1.3 59.8 + - - +
49A ALA* 3.7 6.7 - - - +
50A LEU* 2.9 29.8 + - - +
140A ARG* 5.7 1.8 - - - -
141A ALA* 5.4 0.7 - - - +
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.0 35.9 + - + +
41A THR* 3.5 12.0 - - - +
42A GLN* 3.5 42.6 - - - +
43A GLY 4.5 1.3 - - - +
44A SER* 3.2 18.9 + - - +
46A GLU* 1.3 80.3 - - - +
48A ASP* 1.3 61.6 + - - +
50A LEU* 3.1 2.2 + - - +
51A GLN* 2.8 55.1 + - + +
384A PHE* 3.3 53.1 - - + +
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Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLY* 4.1 19.0 + - - +
44A SER 2.9 19.3 + - - +
45A PRO* 3.4 11.8 - - + +
47A ARG* 1.3 76.3 - - - +
49A ALA* 1.3 61.3 + - - +
51A GLN* 3.4 7.9 + - - +
52A LYS* 3.1 21.8 + - - +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PRO 2.8 20.3 + - - +
46A GLU* 3.7 8.1 - - - +
48A ASP* 1.3 72.2 - - - +
50A LEU* 1.3 57.0 + - - +
52A LYS* 3.3 8.7 + - - +
53A ALA* 3.0 22.5 + - - +
141A ALA* 3.5 22.8 - - + +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 4.1 15.3 - - + -
46A GLU 2.9 18.1 + - - +
47A ARG 3.1 3.8 + - - +
49A ALA* 1.3 74.0 - - - +
51A GLN* 1.3 61.4 + - + +
53A ALA* 3.1 0.9 + - - -
54A LEU* 2.8 46.0 + - + +
141A ALA* 3.8 15.9 - - + +
144A LEU* 3.8 11.9 - - + -
145A ALA* 3.7 31.9 - - - +
148A MET* 3.9 13.5 - - - -
155A VAL* 3.7 30.1 - - + -
384A PHE* 4.1 13.9 - - + -
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Residues in contact with GLN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 2.8 51.5 + - + +
48A ASP* 3.7 7.9 - - - +
50A LEU* 1.3 75.6 - - - +
52A LYS* 1.3 57.1 + - - +
54A LEU* 3.5 8.2 + - - +
55A LYS* 3.1 28.2 + - - +
381A ALA 4.8 3.1 - - - +
384A PHE* 3.4 29.9 - - + -
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Residues in contact with LYS 52 (chain A).
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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48A ASP 3.1 12.9 + - - +
49A ALA* 3.3 12.3 - - - +
50A LEU 3.1 0.2 - - - -
51A GLN* 1.3 74.9 - - - +
53A ALA* 1.3 65.6 + - - +
55A LYS* 3.4 6.8 + - - +
56A ASP* 3.2 30.9 + - - +
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA 3.0 15.8 + - - +
50A LEU 3.7 2.0 - - - +
52A LYS* 1.3 75.2 - - - +
54A LEU* 1.3 63.1 + - - +
56A ASP* 3.4 18.5 + - - +
57A LEU* 3.4 18.9 + - - +
141A ALA* 3.4 33.9 - - + +
142A GLU* 4.2 5.4 - - + +
145A ALA* 3.6 9.0 - - + -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 2.8 41.1 + - + +
51A GLN* 3.7 8.7 - - - +
53A ALA* 1.3 74.3 - - - +
55A LYS* 1.3 64.6 + - - +
57A LEU* 3.2 14.3 + - - +
58A LYS* 3.3 10.2 + - - +
145A ALA* 3.8 19.1 - - + +
148A MET* 4.1 16.8 - - + -
149A VAL* 3.7 29.1 - - + +
381A ALA* 4.1 22.9 - - + +
384A PHE* 3.9 23.6 - - + -
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Residues in contact with LYS 55 (chain A).
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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51A GLN 3.1 17.1 + - - +
52A LYS* 3.8 7.0 - - - +
54A LEU* 1.3 75.6 - - - +
56A ASP* 1.3 61.7 + - - +
58A LYS* 3.0 31.5 + - + +
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Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LYS* 3.2 19.2 + - - +
53A ALA* 3.6 11.9 - - - +
54A LEU 3.3 0.4 - - - -
55A LYS* 1.3 78.5 - - - +
57A LEU* 1.3 65.5 + - + +
58A LYS 3.7 1.4 + - - +
60A ARG* 3.7 15.6 - - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA 3.5 10.3 - - - +
54A LEU* 3.2 8.4 + - - +
55A LYS 3.1 0.6 - - - -
56A ASP* 1.3 81.0 - - + +
58A LYS* 1.3 65.6 + - - +
59A GLY 3.2 1.4 + - - -
60A ARG* 3.1 21.6 + - + +
89A HIS* 3.5 11.7 + - - -
145A ALA* 3.4 42.2 - - + +
146A LYS* 3.8 31.6 - - + +
149A VAL* 3.8 23.1 - - + -
240A LEU* 4.3 14.1 - - + -
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU 3.3 7.8 + - - +
55A LYS* 3.0 23.9 + - - +
56A ASP 4.3 0.9 - - - +
57A LEU* 1.3 73.5 - - - +
59A GLY* 1.3 63.5 + - - +
60A ARG* 3.2 4.7 + - - +
89A HIS* 4.6 3.4 - - - -
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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