Contacts of the helix formed by residues 37 - 53 (chain A) in PDB entry 4BSN
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 HIS 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASN* 3.0 17.9 + - + +
34A CYS 3.1 15.9 - - - +
35A LEU 3.4 1.6 - - - +
36A TYR* 1.3 80.3 - - - +
38A GLY* 1.3 64.2 + - - +
39A GLU* 4.6 0.4 - - + +
40A GLY* 3.7 17.9 - - - +
41A ALA* 3.2 9.5 + - - +
44A ARG* 5.6 2.9 - - - +
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Residues in contact with GLY 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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37A HIS* 1.3 73.0 - - - +
39A GLU* 1.3 64.1 + - - +
41A ALA* 3.5 13.7 + - - +
42A GLN* 3.9 5.5 + - - +
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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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37A HIS* 4.6 0.2 - - - +
38A GLY* 1.3 72.1 - - - +
40A GLY* 1.3 66.3 + - - +
41A ALA 3.2 0.3 + - - -
42A GLN* 2.9 27.9 + - - +
43A GLN* 3.0 48.3 + - - +
44A ARG* 4.9 1.6 - - - +
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Residues in contact with GLY 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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33A ASN 4.5 0.2 - - - -
34A CYS* 3.4 9.7 - - - +
37A HIS* 3.7 19.5 - - - +
38A GLY 3.3 0.6 - - - -
39A GLU* 1.3 80.8 - - - +
41A ALA* 1.3 60.1 + - - +
44A ARG* 3.1 56.3 + - - +
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Residues in contact with ALA 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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34A CYS* 3.3 25.7 + - - +
37A HIS 3.2 13.9 + - - +
38A GLY* 3.5 8.1 - - - +
39A GLU 3.1 0.6 - - - -
40A GLY* 1.3 77.7 - - - +
42A GLN* 1.3 62.8 + - - +
45A MET* 3.1 26.7 + - - +
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Residues in contact with GLN 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 GLY 3.9 5.9 + - - +
39A GLU* 2.9 39.5 + - - +
41A ALA* 1.3 76.2 - - - +
43A GLN* 1.3 79.2 + - - +
45A MET* 3.4 5.1 + - - +
46A ALA* 3.1 28.0 + - + +
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Residues in contact with GLN 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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6A THR* 4.6 7.1 + - - +
9A ALA 5.2 0.4 - - - -
10A ASP* 3.5 35.4 - - - +
39A GLU* 3.0 36.0 + - - +
42A GLN* 1.3 89.3 + - - +
44A ARG* 1.3 86.1 + - - +
46A ALA* 3.5 6.3 + - - +
47A GLN* 3.0 25.5 + - + +
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Residues in contact with ARG 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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9A ALA* 4.6 19.8 - - - +
30A ASN* 4.2 24.8 - - + +
33A ASN* 4.6 18.4 - - - +
34A CYS* 3.7 13.9 - - + -
37A HIS* 5.6 2.6 - - - +
39A GLU* 4.9 1.6 - - - +
40A GLY* 3.1 39.1 + - - +
43A GLN* 1.3 110.5 + - - +
45A MET* 1.3 55.5 + - - +
47A GLN* 3.0 8.8 + - + -
48A GLU* 2.6 51.3 + - + +
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Residues in contact with MET 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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34A CYS* 5.2 0.6 - - - +
41A ALA 3.1 21.5 + - - +
42A GLN* 3.6 6.7 - - - +
44A ARG* 1.3 77.8 - - - +
46A ALA* 1.3 61.9 + - - +
48A GLU* 3.1 10.3 + - - +
49A VAL* 3.1 27.9 + - - +
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Residues in contact with ALA 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 GLN* 3.1 22.1 + - + +
43A GLN* 3.6 7.4 - - - +
45A MET* 1.3 76.7 - - - +
47A GLN* 1.3 61.1 + - - +
49A VAL* 3.2 17.4 - - + +
50A LEU* 3.1 28.5 - - + +
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Residues in contact with GLN 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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10A ASP 5.2 4.0 - - - +
13A ALA* 4.1 36.6 + - + +
14A ARG* 4.4 9.6 + - - +
17A LEU* 5.9 0.8 - - - +
43A GLN* 3.0 17.3 + - + +
44A ARG* 3.0 18.6 + - + +
46A ALA* 1.3 78.0 - - - +
48A GLU* 1.3 63.8 + - - +
50A LEU* 3.4 18.1 + - - +
51A THR* 3.0 57.1 + - + +
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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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30A ASN* 5.2 7.4 - - - +
31A VAL* 5.2 10.6 - - + +
34A CYS* 6.2 2.9 - - - -
44A ARG* 2.6 43.5 + - + +
45A MET* 3.1 9.2 + - - +
47A GLN* 1.3 85.9 - - - +
49A VAL* 1.3 60.1 + - + +
51A THR* 2.7 18.8 + - - +
52A HIS* 2.9 19.0 + - - +
78A TYR* 2.6 49.4 + - + -
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Residues in contact with VAL 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 MET 3.1 13.1 + - - +
46A ALA* 3.2 23.1 - - + +
48A GLU* 1.3 76.2 - - + +
50A LEU* 1.3 66.1 + - + +
52A HIS* 3.8 8.6 - - + +
53A LEU* 3.1 32.8 + - + +
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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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46A ALA* 3.1 29.0 + - + +
47A GLN* 3.6 20.4 - - - +
48A GLU 3.2 0.2 - - - -
49A VAL* 1.3 81.6 - - + +
51A THR* 1.3 61.5 + - - +
53A LEU* 3.6 27.5 + - + +
54A LYS* 3.9 6.2 + - - +
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Residues in contact with THR 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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13A ALA 5.4 1.3 - - - +
17A LEU* 4.6 20.2 - - + -
47A GLN* 3.0 39.4 + - + +
48A GLU* 2.7 24.6 + - - +
50A LEU* 1.3 75.0 - - - +
52A HIS* 1.3 62.2 + - - +
54A LYS* 3.4 20.0 + - - +
55A GLU 4.4 5.4 + - - +
78A TYR* 2.7 20.5 + - - +
82A ILE* 5.4 0.8 - - - +
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Residues in contact with HIS 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 2.9 17.6 + - - +
49A VAL* 3.8 9.2 - - + +
50A LEU 3.3 0.2 - - - -
51A THR* 1.3 76.0 + - - +
53A LEU* 1.3 65.2 + - + +
54A LYS 3.3 0.7 + - - -
55A GLU* 4.4 8.6 + - - +
82A ILE* 3.8 30.4 - - + +
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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 VAL* 3.1 25.2 + - + +
50A LEU* 3.7 23.6 - - + +
51A THR 3.2 0.6 - - - -
52A HIS* 1.3 77.8 - - + +
54A LYS* 1.3 67.3 + - - +
90A ARG* 5.4 0.7 + - - -
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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