Contacts of the helix formed by residues 38 - 51 (chain A) in PDB entry 1ORI
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A TYR* 1.3 64.6 + - - +
40A ALA* 3.4 7.0 - - - +
41A HIS* 3.6 26.8 + - - +
42A PHE* 2.9 47.1 + - - -
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Residues in contact with TYR 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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38A SER* 1.3 81.4 - - - +
40A ALA* 1.3 57.5 + - - +
41A HIS 3.1 0.2 - - - -
42A PHE* 4.8 5.8 - - - -
43A GLY* 2.9 32.7 + - - +
44A ILE 3.4 1.9 + - - -
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Residues in contact with ALA 40 (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 SER 3.4 3.6 - - - +
39A TYR* 1.3 76.9 - - - +
41A HIS* 1.3 62.0 + - + +
44A ILE* 2.9 31.1 - - + +
45A HIS* 4.8 0.7 + - - -
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Residues in contact with HIS 41 (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 SER* 3.5 25.2 + - - +
39A TYR 3.1 1.6 - - - -
40A ALA* 1.3 83.8 - - + +
42A PHE* 1.3 59.4 + - + +
43A GLY 3.4 0.2 + - - -
44A ILE* 3.5 1.6 - - - +
45A HIS* 2.7 35.0 - - - -
102A SER* 3.5 28.7 + - - -
103A SER* 3.2 31.9 + - - -
104A ILE* 4.6 8.3 - - + -
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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 SER* 2.9 36.0 + - - -
39A TYR* 4.8 4.3 - - - -
41A HIS* 1.3 79.9 - - + +
43A GLY* 1.3 70.2 + - - +
45A HIS* 3.7 7.8 + - - +
46A GLU* 3.2 34.4 + - + +
104A ILE* 5.4 7.4 - - + +
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Residues in contact with GLY 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 TYR* 2.9 20.3 + - - -
42A PHE* 1.3 88.4 - - - +
44A ILE* 1.3 64.7 + - - +
45A HIS 3.1 1.6 - - - -
46A GLU* 3.0 18.2 + - - +
47A GLU* 3.1 12.4 + - - +
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Residues in contact with ILE 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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39A TYR 3.4 5.5 + - - -
40A ALA* 2.9 32.3 - - - +
41A HIS 3.5 6.1 - - - +
43A GLY* 1.3 72.1 - - - +
45A HIS* 1.3 71.7 + - + +
47A GLU* 3.4 15.6 + - - +
48A MET* 2.9 49.6 + - + +
293A HIS* 6.5 0.2 - - + -
354A SAH 4.8 7.0 - - + -
700A UNL 4.3 22.0 - - - -
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Residues in contact with HIS 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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40A ALA 4.9 0.4 + - - -
41A HIS* 2.7 29.6 + - - -
42A PHE* 3.7 8.3 + - - +
43A GLY 3.1 0.4 - - - -
44A ILE* 1.3 84.5 - - + +
46A GLU* 1.3 60.4 + - - +
48A MET* 3.3 5.3 + - - +
49A LEU* 2.8 40.1 + - + +
80A GLY* 3.7 16.2 - - - -
81A THR* 4.0 24.2 + - + +
102A SER* 5.0 1.6 + - - -
104A ILE* 3.9 25.8 - - + +
354A SAH 3.4 49.5 + - + +
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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* 3.2 26.8 + - + +
43A GLY* 3.0 12.1 + - - +
45A HIS* 1.3 78.5 - - - +
47A GLU* 1.3 57.4 + - - +
49A LEU* 4.2 6.7 - - - +
50A LYS* 2.4 69.6 + - + +
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Residues in contact with GLU 47 (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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43A GLY 3.1 10.2 + - - +
44A ILE* 3.4 20.0 - - - +
45A HIS 3.1 0.2 - - - -
46A GLU* 1.3 79.9 - - - +
48A MET* 1.3 62.0 + - - +
50A LYS* 3.3 7.2 + - - +
51A ASP* 3.1 21.9 + - - +
148A TYR* 4.3 8.8 + - - -
291A TYR* 5.0 4.7 + - - +
293A HIS* 3.9 38.8 - - + +
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Residues in contact with MET 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 ILE* 2.9 34.5 + - + +
45A HIS* 3.8 6.1 - - - +
47A GLU* 1.3 74.8 - - + +
49A LEU* 1.3 61.7 + - - +
51A ASP* 3.3 13.0 - - - +
54A ARG* 2.8 34.9 + - - +
55A THR* 3.2 4.7 + - - -
144A GLU* 3.4 22.4 - - + +
293A HIS* 4.0 26.0 - - + +
354A SAH 3.6 33.4 - - - +
700A UNL 3.1 32.8 - - - -
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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 HIS* 2.8 27.8 + - + +
46A GLU* 4.2 5.6 - - - +
48A MET* 1.3 70.7 - - - +
50A LYS* 1.3 65.2 + - + +
51A ASP 3.1 2.1 + - - -
52A GLU* 4.5 4.9 + - - +
54A ARG* 4.3 3.4 - - - +
55A THR* 3.6 20.1 + - + +
81A THR* 4.0 25.6 - - + +
83A ILE* 3.8 41.7 - - + -
354A SAH 3.9 10.1 - - - +
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Residues in contact with LYS 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* 2.4 63.5 + - + +
47A GLU* 3.7 6.7 - - - +
48A MET 3.3 0.2 - - - -
49A LEU* 1.3 76.8 - - + +
51A ASP* 1.3 57.7 + - - +
52A GLU* 3.0 21.5 + - - +
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Residues in contact with ASP 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 GLU 3.1 12.4 + - - +
48A MET* 3.3 13.1 - - - +
49A LEU 3.1 1.0 - - - -
50A LYS* 1.3 73.2 - - - +
52A GLU* 1.3 58.6 + - - +
53A VAL* 3.7 8.8 + - - +
54A ARG* 3.4 24.7 + - + +
55A THR* 3.0 29.8 + - - -
291A TYR* 4.8 4.3 - - + +
292A THR* 3.7 12.2 - - - -
293A HIS* 2.6 50.7 + - + +
294A TRP* 4.4 0.5 - - - -
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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