Contacts of the helix formed by residues 38 - 55 (chain A) in PDB entry 1OE4
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 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLU 3.7 3.6 - - - +
37A SER* 1.3 83.8 - - - +
39A ALA* 1.3 53.9 + - - +
40A ASP 3.4 1.3 - - - -
41A SER* 3.2 10.2 + - - +
42A PHE* 2.8 35.7 + - - +
84A CYS* 3.7 13.7 - - - +
86A SER* 3.3 40.8 - - - +
87A LYS* 3.9 9.6 - - + +
215A VAL* 3.4 27.4 - - + +
216A LEU* 4.0 12.1 - - + -
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Residues in contact with ALA 39 (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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37A SER* 3.2 13.6 + - - +
38A PRO* 1.3 74.8 - - - +
40A ASP* 1.3 59.8 + - - +
42A PHE* 3.2 4.5 + - - +
43A LEU* 3.0 35.1 + - - +
80A VAL* 3.8 23.3 - - + +
81A GLN* 3.7 25.4 - - - +
84A CYS* 3.4 20.5 + - - +
85A LYS* 5.4 0.2 - - - -
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Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 4.5 3.9 + - - +
38A PRO 3.4 0.6 - - - -
39A ALA* 1.3 78.4 - - - +
41A SER* 1.3 62.7 + - - +
43A LEU* 3.4 7.9 + - - +
44A LYS* 3.1 31.5 + - + +
81A GLN* 3.0 27.9 + - - -
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER 5.1 2.2 + - - -
38A PRO* 3.2 14.8 + - - +
40A ASP* 1.3 78.2 - - - +
42A PHE* 1.3 62.6 + - - +
44A LYS* 3.3 10.0 + - - +
45A VAL* 3.1 25.3 + - - +
215A VAL* 4.1 23.5 - - - +
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Residues in contact with PHE 42 (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 PRO 2.8 18.1 + - - +
39A ALA* 3.6 6.3 - - - +
41A SER* 1.3 76.9 - - - +
43A LEU* 1.3 63.3 + - - +
45A VAL* 3.1 15.1 + - + +
46A GLU* 3.1 42.8 + - + +
76A HIS* 4.7 1.1 - + - -
80A VAL* 4.0 19.7 - - + -
84A CYS* 4.7 1.8 - - - -
171A PHE* 3.9 19.7 - + - -
173A HIS* 3.5 33.2 - + - -
212A ALA* 3.9 20.6 - - + -
215A VAL* 4.1 14.1 - - + +
216A LEU* 3.8 40.2 - - + -
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Residues in contact with LEU 43 (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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39A ALA 3.0 19.0 + - - +
40A ASP* 3.8 6.7 - - - +
41A SER 3.4 0.2 - - - -
42A PHE* 1.3 75.0 - - - +
44A LYS* 1.3 58.0 + - + +
46A GLU* 3.2 15.4 + - - +
47A LEU* 2.8 37.8 + - + +
73A TRP* 3.6 28.8 - - + -
76A HIS* 4.2 4.7 - - - +
77A GLU* 3.8 26.7 - - + +
80A VAL* 3.8 30.1 - - + -
81A GLN* 3.4 29.8 - - - +
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Residues in contact with LYS 44 (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 ASP* 3.1 21.2 + - + +
41A SER* 3.5 11.9 - - - +
42A PHE 3.2 0.2 - - - -
43A LEU* 1.3 72.7 - - + +
45A VAL* 1.3 66.9 + - + +
47A LEU* 3.4 10.8 + - + +
48A GLU* 3.0 25.7 + - - +
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Residues in contact with VAL 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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41A SER 3.1 14.4 + - - +
42A PHE* 3.1 11.7 + - + +
44A LYS* 1.3 77.5 - - + +
46A GLU* 1.3 60.8 + - + +
48A GLU* 3.3 9.2 + - - +
49A LEU* 3.0 26.3 + - - +
173A HIS* 6.3 0.2 - - - +
208A ALA* 3.7 31.1 - - + +
211A GLN* 3.7 34.2 - - + +
212A ALA* 4.2 10.5 - - + +
215A VAL* 4.2 17.9 - - + -
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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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42A PHE* 3.1 37.9 + - + +
43A LEU* 3.2 13.5 + - - +
45A VAL* 1.3 80.6 - - + +
47A LEU* 1.3 57.5 + - - +
49A LEU* 3.3 12.3 + - + +
50A ASN* 2.9 33.3 + - - +
69A LEU* 3.5 17.6 - - + +
73A TRP* 4.3 10.3 - - + -
76A HIS* 2.4 41.5 + - - -
102A MET* 5.9 0.2 - - - +
173A HIS* 3.4 24.2 + - + -
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Residues in contact with LEU 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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43A LEU* 2.8 27.9 + - + +
44A LYS* 3.9 10.3 - - + +
46A GLU* 1.3 72.1 - - - +
48A GLU* 1.3 61.1 + - - +
50A ASN* 3.4 15.1 + - + +
51A LEU* 3.2 21.7 + - - +
69A LEU 5.3 0.2 - - - +
73A TRP* 3.5 42.2 - - + +
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Residues in contact with GLU 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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44A LYS 3.0 18.3 + - - +
45A VAL* 3.6 6.7 - - - +
47A LEU* 1.3 72.9 - - - +
49A LEU* 1.3 66.1 + - - +
51A LEU* 3.2 12.7 + - + +
52A LYS* 3.1 48.3 + - - +
211A GLN* 3.4 30.3 + - - +
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Residues in contact with LEU 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 VAL* 3.0 14.0 + - + +
46A GLU* 3.5 13.5 - - + +
48A GLU* 1.3 74.4 - - - +
50A ASN* 1.3 65.8 + - - +
52A LYS* 3.2 7.6 + - + +
53A LEU* 2.9 42.2 + - + +
69A LEU* 6.2 1.6 - - + -
173A HIS* 5.9 7.2 - - + +
175A HIS 4.6 9.6 - - - +
177A PRO* 4.0 25.8 - - + -
204A ILE* 3.5 33.0 - - + +
205A CYS* 4.4 3.6 - - - -
208A ALA* 3.8 30.1 - - + -
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Residues in contact with ASN 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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46A GLU 2.9 18.1 + - - +
47A LEU* 3.6 23.5 - - + +
48A GLU 3.4 0.4 - - - -
49A LEU* 1.3 75.6 - - - +
51A LEU* 1.3 57.2 + - - +
53A LEU* 3.3 3.7 + - - +
54A SER* 2.9 32.3 + - - -
67A ASN* 3.1 27.7 + - - +
69A LEU* 3.3 41.3 + - - +
70A VAL* 4.3 8.9 - - + +
73A TRP* 4.5 1.4 - - - -
177A PRO* 4.4 9.0 - - - +
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Residues in contact with LEU 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 LEU 3.2 10.6 + - - +
48A GLU* 3.5 13.9 - - + +
49A LEU 3.2 0.4 - - - -
50A ASN* 1.3 77.6 - - - +
52A LYS* 1.3 63.1 + - + +
54A SER* 2.7 28.8 + - - +
55A ASN* 3.3 20.8 + - - +
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Residues in contact with LYS 52 (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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48A GLU* 3.1 47.0 + - - +
49A LEU* 3.2 9.9 + - - +
51A LEU* 1.3 80.7 - - + +
53A LEU* 1.3 61.2 + - - +
55A ASN* 3.5 16.0 + - - +
56A LEU* 3.9 14.8 + - - +
204A ILE* 4.0 33.4 - - + +
207A GLU* 3.9 21.8 + - - +
211A GLN* 5.3 1.2 - - - +
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Residues in contact with LEU 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 LEU* 2.9 33.2 + - + +
50A ASN* 3.8 4.7 - - - +
52A LYS* 1.3 73.3 - - - +
54A SER* 1.3 60.3 + - - +
56A LEU* 3.0 39.9 + - + +
58A PHE* 5.2 2.3 - - - -
67A ASN* 4.6 5.8 - - - +
177A PRO* 3.6 38.1 - - + -
178A LEU* 3.9 25.2 - - + +
201A LEU* 3.6 29.4 - - + -
204A ILE* 4.1 16.6 - - + -
205A CYS* 4.5 1.6 - - - -
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Residues in contact with SER 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 ASN 2.9 15.9 + - - -
51A LEU* 2.7 27.7 + - - +
53A LEU* 1.3 74.9 - - - +
55A ASN* 1.3 65.6 + - - +
56A LEU 3.4 5.2 + - - +
67A ASN* 6.1 0.2 - - - +
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Residues in contact with ASN 55 (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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51A LEU* 3.3 28.0 + - - +
52A LYS* 3.5 10.6 + - - +
53A LEU 3.1 1.0 - - - -
54A SER* 1.3 83.1 + - - +
56A LEU* 1.3 63.4 + - - +
57A VAL* 3.8 9.4 + - - +
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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