Contacts of the helix formed by residues 34 - 48 (chain A) in PDB entry 5JEI
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 GLY 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PRO 3.2 13.9 - - - -
16A TYR 3.3 6.5 - - - -
18A MET* 4.3 0.7 - - - -
33A GLU* 1.3 77.4 - - - +
35A TYR* 1.3 66.7 + - - -
37A VAL* 3.2 1.7 + - - +
38A ASP* 3.0 25.8 + - - -
254A TRP* 3.4 26.3 - - - -
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Residues in contact with TYR 35 (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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15A PRO 2.9 14.5 + - - +
16A TYR* 4.2 6.1 - + - -
34A GLY* 1.3 72.0 - - - +
36A CYS* 1.3 69.6 + - - +
38A ASP* 3.4 3.4 + - - +
39A LEU* 2.9 33.8 + - + +
106A PHE* 3.5 40.8 + + - -
107A MET* 3.4 25.3 - - + +
247A LEU* 3.7 23.9 + - + +
250A LEU* 3.6 41.3 - - + +
251A LYS* 3.6 10.8 - - + -
254A TRP* 3.4 19.1 - - + +
255A TRP* 3.8 22.7 - + + -
306A TOE 5.3 0.9 - - - -
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Residues in contact with CYS 36 (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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16A TYR* 2.8 38.5 + - - +
17A VAL* 3.9 14.1 - - + -
35A TYR* 1.3 82.9 - - - +
37A VAL* 1.3 61.2 + - - +
39A LEU* 3.7 5.4 - - - -
40A ALA* 2.8 30.1 + - - +
53A LEU* 5.6 0.7 - - - +
87A ILE* 3.7 18.2 - - + +
88A ALA* 3.7 32.5 - - - -
106A PHE* 4.3 9.4 - - - -
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Residues in contact with VAL 37 (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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16A TYR 4.1 1.3 - - - +
17A VAL* 4.0 15.7 - - + -
29A ASN* 4.9 2.9 - - + +
32A TYR* 3.7 29.4 - - + +
33A GLU* 3.5 31.6 - - - +
34A GLY 3.2 10.0 + - - +
36A CYS* 1.3 77.6 - - - +
38A ASP* 1.3 67.3 + - - +
40A ALA* 3.4 5.5 + - - +
41A ALA* 3.2 21.5 + - - +
51A TYR* 4.5 3.1 + - - +
53A LEU* 4.2 21.9 - - + +
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Residues in contact with ASP 38 (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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33A GLU* 5.9 0.3 - - - -
34A GLY 3.0 14.0 + - - +
35A TYR 3.6 7.9 - - - +
37A VAL* 1.3 81.0 - - - +
39A LEU* 1.3 61.5 + - - +
41A ALA* 3.3 7.9 + - - +
42A GLU* 3.2 27.5 + - + +
250A LEU* 3.7 24.4 - - + +
253A LYS* 2.9 21.0 + - - -
254A TRP* 2.8 27.0 + - - -
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Residues in contact with LEU 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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35A TYR* 2.9 29.4 + - + +
36A CYS* 3.8 7.0 - - - +
37A VAL 3.3 0.4 - - - -
38A ASP* 1.3 77.2 - - - +
40A ALA* 1.3 56.8 + - - +
42A GLU* 3.1 3.1 + - + -
43A ILE* 2.8 43.8 + - + +
87A ILE* 4.5 4.3 - - + -
106A PHE* 3.9 38.6 - - + -
222A ILE* 4.1 17.5 - - + -
238A VAL* 5.6 2.2 - - + -
241A LEU* 3.9 19.5 - - + -
246A LEU* 5.1 0.2 - - + -
247A LEU* 3.7 26.2 - - + -
250A LEU* 4.1 8.0 - - + +
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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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36A CYS 2.8 18.9 + - - +
37A VAL 3.7 5.4 - - - +
39A LEU* 1.3 77.2 - - - +
41A ALA* 1.3 57.6 + - - +
43A ILE* 3.3 1.7 + - - +
44A ALA* 2.9 31.2 + - - +
49A PHE* 5.1 1.0 - - - -
51A TYR* 4.0 21.3 - - + -
53A LEU* 4.2 12.8 - - + -
87A ILE* 3.8 31.9 - - + +
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Residues in contact with ALA 41 (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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37A VAL 3.2 10.1 + - - +
38A ASP* 3.6 10.1 - - - +
39A LEU 3.2 0.4 - - - -
40A ALA* 1.3 79.0 - - - +
42A GLU* 1.3 65.3 + - - +
44A ALA* 3.5 1.6 + - - +
45A LYS* 3.0 28.4 + - - +
51A TYR* 3.2 23.0 + - - +
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Residues in contact with GLU 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 ASP* 3.2 16.0 + - + +
39A LEU* 3.1 7.9 + - - +
41A ALA* 1.3 79.2 - - - +
43A ILE* 1.3 65.4 + - - +
45A LYS* 3.3 25.1 + - - +
46A HIS* 3.0 35.8 + - - -
241A LEU* 3.9 22.8 - - + +
246A LEU* 4.1 27.2 - - + +
250A LEU* 5.2 1.1 - - + -
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Residues in contact with ILE 43 (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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39A LEU* 2.8 46.0 + - + +
40A ALA* 3.8 4.3 - - - +
42A GLU* 1.3 74.8 - - - +
44A ALA* 1.3 59.2 + - - +
46A HIS* 3.2 1.6 + - - +
47A CYS* 2.9 35.1 + - - -
49A PHE* 4.1 10.8 - - + -
85A ILE* 5.0 0.2 - - + -
87A ILE* 4.4 12.3 - - + -
222A ILE* 3.9 29.8 - - + -
234A VAL* 4.0 29.4 - - + -
237A ALA* 4.6 12.8 - - + -
238A VAL* 4.4 8.3 - - + -
241A LEU* 4.2 8.1 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.8 + - - +
41A ALA 3.7 2.9 - - - +
43A ILE* 1.3 76.8 - - - +
45A LYS* 1.3 58.1 + - - +
48A GLY* 2.8 26.5 + - - -
49A PHE* 3.1 44.5 + - + +
51A TYR* 3.4 26.9 - - + -
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Residues in contact with LYS 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 ALA 3.0 17.3 + - - +
42A GLU* 3.5 27.8 - - - +
43A ILE 3.3 0.2 - - - -
44A ALA* 1.3 78.6 - - - +
46A HIS* 1.3 82.9 + - - +
47A CYS 3.4 0.2 + - - -
48A GLY* 3.6 7.7 + - - -
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Residues in contact with HIS 46 (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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42A GLU* 3.0 30.1 + - - +
43A ILE 3.2 3.1 + - - +
45A LYS* 1.3 103.4 + - - +
47A CYS* 1.3 60.4 + - - +
48A GLY 3.5 0.2 - - - -
237A ALA* 4.1 19.3 - - + -
240A LYS* 3.7 36.0 - - + +
241A LEU* 3.7 27.0 - - + +
244A GLN* 4.5 8.6 + - - -
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Residues in contact with CYS 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 ILE* 2.9 24.8 + - - +
46A HIS* 1.3 77.0 - - - +
48A GLY* 1.3 62.9 + - - +
49A PHE* 3.5 21.4 + - + -
230A LEU* 5.2 1.8 - - + -
233A ALA* 3.6 46.0 - - + +
234A VAL* 3.9 10.1 - - - -
237A ALA* 3.9 12.1 - - - -
309A ETE 4.3 13.7 - - - +
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Residues in contact with GLY 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 ALA 2.8 9.6 + - - -
45A LYS* 3.6 6.8 + - - -
46A HIS 3.5 2.6 - - - -
47A CYS* 1.3 81.2 - - - +
49A PHE* 1.3 56.8 + - - +
309A ETE 4.5 6.4 - - - +
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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