Contacts of the helix formed by residues 32 - 48 (chain A) in PDB entry 5DTQ
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 ASP 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.7 1.1 - - + +
25A PRO 3.6 11.7 - - - +
26A VAL* 4.0 16.8 - - + +
27A TYR* 3.5 17.0 - - - +
30A HIS 5.5 0.7 - - - +
31A HIS* 1.3 76.4 + - - +
33A ALA* 1.4 62.5 + - - +
34A ALA* 3.2 22.7 + - - +
35A HIS* 3.1 44.0 + - - +
36A GLU* 3.4 7.3 + - - +
65A THR* 5.4 3.2 + - - -
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Residues in contact with ALA 33 (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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20A TYR* 4.2 14.8 - - + -
24A LEU* 4.1 7.4 - - + +
25A PRO* 2.9 40.0 + - + +
27A TYR* 3.4 27.2 - - - +
32A ASP* 1.4 69.2 - - - +
34A ALA* 1.4 59.0 + - - +
36A GLU* 3.3 5.0 + - - +
37A ILE* 2.9 32.3 + - - +
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Residues in contact with ALA 34 (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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24A LEU* 3.7 26.2 - - + +
32A ASP* 3.2 13.7 + - - +
33A ALA* 1.4 77.6 - - - +
35A HIS* 1.3 56.6 + - - +
37A ILE* 3.2 5.1 + - - +
38A ILE* 3.0 33.7 + - - +
65A THR* 3.8 32.3 - - + +
71A MET* 3.9 11.1 - - + +
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Residues in contact with HIS 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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30A HIS 4.0 11.9 + - - -
31A HIS* 4.7 2.2 - - + -
32A ASP* 3.1 42.2 + - - +
33A ALA 3.4 0.2 - - - -
34A ALA* 1.3 72.5 - - - +
36A GLU* 1.3 60.7 + - - +
38A ILE* 3.4 10.5 + - + +
39A GLU* 2.9 48.5 + - - +
63A TYR* 4.8 9.1 + - - -
65A THR* 4.0 25.8 + - + +
128B TYR 5.7 2.5 - - - -
130B PRO* 4.1 36.5 - - + +
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Residues in contact with GLU 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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20A TYR* 2.7 26.8 + - - -
27A TYR* 2.7 33.0 + - + -
32A ASP 3.4 7.7 + - - +
33A ALA 3.3 11.6 + - - +
34A ALA 3.2 0.2 - - - -
35A HIS* 1.3 78.5 - - - +
37A ILE* 1.4 50.0 + - - +
39A GLU* 3.7 5.9 - - - -
40A THR* 2.6 40.8 + - - +
109A HIS* 3.8 7.6 - - + -
113A GLN* 3.0 26.6 + - + +
116A ASN* 3.8 10.7 + - - +
117A HIS* 2.9 27.0 + - - -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.9 27.8 - - + -
9A LEU* 4.0 11.0 - - + -
20A TYR* 3.7 45.1 - - + -
24A LEU* 3.9 12.3 - - + -
33A ALA 2.9 18.1 + - - +
34A ALA 3.2 7.2 + - - +
36A GLU* 1.4 74.4 - - - +
38A ILE* 1.3 61.7 + - - +
40A THR* 3.3 3.2 + - - -
41A ILE* 3.1 42.3 + - + +
71A MET* 4.1 4.3 - - + -
74A LEU* 4.0 9.9 - - + -
75A CYS* 3.9 17.3 - - - -
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Residues in contact with ILE 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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34A ALA 3.0 23.3 + - - +
35A HIS* 3.8 10.3 - - + +
36A GLU 3.4 0.2 - - - -
37A ILE* 1.3 76.5 - - - +
39A GLU* 1.3 58.6 + - + +
41A ILE* 3.6 4.9 + - - +
42A ARG* 3.1 59.9 + - - +
60A LEU* 4.1 6.4 - - + +
63A TYR* 3.5 50.3 - - + +
65A THR* 3.9 13.0 - - + -
71A MET* 4.5 3.6 - - - -
74A LEU* 3.7 25.8 - - + -
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Residues in contact with GLU 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 HIS* 2.9 34.4 + - - +
36A GLU* 5.0 1.6 - - - -
38A ILE* 1.3 76.3 - - + +
40A THR* 1.4 59.4 + - - +
42A ARG* 3.6 10.6 + - - +
43A TRP* 3.0 33.8 + - - -
109A HIS* 3.9 22.2 + - + +
308B LYS* 3.4 44.7 + - - +
309B PRO* 3.8 22.2 - - + +
310B VAL* 6.0 0.7 - - + +
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Residues in contact with THR 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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9A LEU* 4.3 13.0 - - + -
20A TYR* 4.5 0.9 + - - -
36A GLU 2.6 25.5 + - - -
37A ILE* 3.3 5.5 + - - -
39A GLU* 1.4 73.3 - - - +
41A ILE* 1.4 59.6 + - - +
43A TRP* 3.3 2.8 + - - +
44A VAL* 2.9 33.6 + - - +
109A HIS* 3.0 19.0 + - - -
113A GLN* 3.2 15.9 + - - +
205A TRP* 4.7 1.6 - - + -
208A TRP* 3.6 32.1 - - + -
209A TYR* 3.4 17.4 - - + +
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Residues in contact with ILE 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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9A LEU* 3.8 25.6 - - + -
37A ILE* 3.1 30.3 + - + +
38A ILE* 3.9 4.7 - - - +
40A THR* 1.4 73.1 - - - +
42A ARG* 1.3 57.9 + - - +
44A VAL* 3.4 2.8 + - - +
45A CYS* 3.0 35.6 + - - -
55A MET* 4.1 11.9 - - - -
60A LEU* 3.9 27.1 - - + -
74A LEU* 4.0 25.8 - - + +
78A TYR* 3.7 43.7 - - + -
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Residues in contact with ARG 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 ILE* 3.1 41.7 + - - +
39A GLU* 3.8 11.6 - - - +
40A THR 3.3 0.2 - - - -
41A ILE* 1.3 76.2 - - - +
43A TRP* 1.3 56.2 + - - +
45A CYS* 3.4 6.8 + - - +
46A GLU* 3.0 30.2 + - - +
60A LEU* 3.2 49.7 + - + +
63A TYR* 4.4 6.1 + - - -
243B PHE* 5.6 4.2 - - - -
309B PRO* 3.4 39.8 + - + +
310B VAL* 5.2 5.9 - - - +
311B SER* 5.6 7.7 + - - -
401B 5F6 6.0 3.2 + - - -
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Residues in contact with TRP 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 GLU 3.0 24.3 + - - +
40A THR* 3.7 5.6 - - - +
42A ARG* 1.3 72.7 - - - +
44A VAL* 1.4 64.3 + - - +
46A GLU* 3.1 19.6 + - + +
47A GLU* 3.1 45.6 + - - +
103A SER* 4.3 2.2 - - - -
105A GLY* 3.4 30.7 + - - -
106A LEU* 3.9 28.3 - - + -
109A HIS* 3.5 34.2 + + + +
209A TYR* 5.1 0.7 - - + -
299B LEU* 3.6 37.9 - - + -
305B TRP 5.2 0.9 - - - -
307B GLY 3.3 22.6 + - - -
308B LYS* 5.0 0.6 - - - +
309B PRO* 3.4 24.5 - - + +
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Residues in contact with VAL 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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12A PRO* 3.7 29.4 - - + -
40A THR 2.9 23.3 + - - +
41A ILE 3.4 4.5 + - - +
43A TRP* 1.4 73.0 - - - +
45A CYS* 1.3 50.0 + - - +
47A GLU* 3.3 4.8 + - - +
48A ILE* 2.8 37.4 + - + +
51A LEU* 3.6 20.0 - - + -
78A TYR* 3.8 17.3 - - + +
208A TRP* 3.7 29.8 - - + -
209A TYR* 4.2 11.9 - - + -
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Residues in contact with CYS 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 ILE* 3.0 25.1 + - - +
42A ARG* 3.7 6.7 - - - +
44A VAL* 1.3 71.1 - - - +
46A GLU* 1.3 66.9 + - - +
48A ILE 3.2 19.3 - - - +
49A PRO* 4.3 1.7 - - - +
51A LEU* 3.8 18.8 - - - -
52A LYS* 4.1 22.2 - - + +
55A MET* 3.5 36.1 - - - -
60A LEU* 5.1 6.1 - - + -
78A TYR* 4.9 0.2 - - - -
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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 ARG 3.0 14.3 + - - +
43A TRP* 3.1 23.3 + - + +
45A CYS* 1.3 81.5 - - - +
47A GLU* 1.3 61.9 + - + +
48A ILE 3.6 2.1 + - - -
49A PRO* 4.5 5.9 - - - +
297B SER* 5.6 0.4 - - - -
299B LEU* 3.7 41.9 - - + +
300B LYS* 4.3 16.0 - - - +
309B PRO* 6.0 0.2 - - - +
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Residues in contact with GLU 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 TRP* 3.1 33.9 + - + +
44A VAL* 4.1 4.3 - - - +
46A GLU* 1.3 79.1 - - - +
48A ILE* 1.4 61.9 + - + +
49A PRO* 3.4 9.2 - - - +
103A SER* 3.2 31.1 + - - -
106A LEU* 3.6 27.5 - - + +
211A LYS* 4.0 18.9 + - - +
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Residues in contact with ILE 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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12A PRO* 3.5 33.7 - - + +
44A VAL* 2.8 23.3 + - + +
45A CYS 3.2 13.6 - - - +
47A GLU* 1.4 81.0 - - + +
49A PRO* 1.3 66.8 - - + +
50A ASP* 4.1 7.0 - - + +
51A LEU* 3.2 36.9 + - + +
52A LYS 3.7 0.3 + - - -
82A ILE* 5.2 2.2 - - + -
85A ILE* 4.7 2.9 - - + -
89A TRP* 3.8 38.6 - - + -
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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