Contacts of the helix formed by residues 37 - 49 (chain A) in PDB entry 2GUT
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A MET* 5.1 1.6 - - - -
35A SER 3.7 1.2 - - - -
36A LYS* 1.3 86.2 - - - +
38A SER* 1.3 64.1 + - - +
39A LYS* 3.3 10.6 + - - +
40A ASP* 3.0 9.8 + - - +
41A MET* 2.7 43.9 + - - +
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Residues in contact with SER 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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20A VAL* 5.4 0.2 - - - -
23A ILE* 3.5 2.6 - - - +
24A GLU* 3.1 47.5 + - - -
27A MET* 3.3 25.3 - - - +
37A SER* 1.3 77.8 + - - +
39A LYS* 1.3 60.6 + - - -
41A MET* 2.8 6.0 + - - +
42A GLU* 2.6 50.9 + - - +
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Residues in contact with LYS 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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16A ARG* 5.3 13.4 + - - +
20A VAL* 4.7 17.8 - - + +
37A SER* 3.3 8.1 + - - +
38A SER* 1.3 77.7 - - - +
40A ASP* 1.3 59.9 + - - +
42A GLU* 3.1 12.3 + - - +
43A SER* 3.1 28.1 + - - -
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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
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36A LYS* 3.0 51.6 + - + +
37A SER* 3.0 15.2 + - - +
39A LYS* 1.3 78.5 - - - +
41A MET* 1.3 65.3 + - - +
43A SER* 2.6 23.6 + - - -
44A HIS* 3.1 11.4 + - - +
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Residues in contact with MET 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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23A ILE* 5.1 8.1 - - + -
27A MET* 3.5 31.9 - - + -
32A VAL* 5.8 0.2 - - + -
35A SER* 3.4 38.4 - - - +
37A SER* 2.7 35.8 + - - +
38A SER* 2.8 10.0 + - - +
40A ASP* 1.3 73.3 - - - +
42A GLU* 1.3 61.1 + - - +
44A HIS* 3.4 7.0 + - - +
45A VAL* 2.9 29.9 + - - +
62A LEU* 5.0 14.4 - - + -
66A PHE* 4.5 13.9 - - + -
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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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16A ARG* 5.4 4.2 - - + -
20A VAL* 2.9 51.4 - - + +
23A ILE* 3.2 43.1 - - + +
38A SER* 2.6 61.0 + - - +
39A LYS* 3.1 5.6 - - - +
41A MET* 1.3 69.8 - - - +
43A SER* 1.3 66.6 + - - +
45A VAL* 3.2 10.7 + - - +
46A PHE* 3.1 23.3 + - - +
55A TYR* 4.0 10.0 - - - +
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Residues in contact with SER 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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16A ARG* 4.8 18.8 - - - +
39A LYS 3.1 14.8 + - - -
40A ASP* 2.6 31.8 + - - -
42A GLU* 1.3 77.8 - - - +
44A HIS* 1.3 60.5 + - - +
46A PHE* 3.4 6.1 + - - +
47A LEU* 3.2 34.8 + - - +
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Residues in contact with HIS 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 12.9 + - - +
41A MET* 3.6 6.9 + - - +
42A GLU 3.2 0.2 - - - -
43A SER* 1.3 80.3 + - - +
45A VAL* 1.3 63.0 + - - +
47A LEU* 3.4 9.0 + - + -
48A LYS* 2.8 66.2 + - + +
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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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23A ILE* 6.2 0.9 - - + -
41A MET 2.9 21.3 + - - +
42A GLU* 3.2 8.3 + - - +
44A HIS* 1.3 79.7 - - + +
46A PHE* 1.3 52.0 + - - +
48A LYS* 3.2 7.6 + - - +
49A ALA* 2.7 36.0 + - - +
55A TYR* 3.4 23.6 - - + +
58A LEU* 3.6 34.7 - - + +
59A VAL* 3.9 13.5 - - + +
62A LEU* 5.4 12.6 - - + -
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Residues in contact with PHE 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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10A TRP* 3.2 57.2 - + - -
11A ARG* 3.5 35.4 - - + -
16A ARG* 4.2 32.3 - - + -
42A GLU 3.1 12.0 + - - +
43A SER* 3.6 11.0 - - - +
45A VAL* 1.3 75.8 - - - +
47A LEU* 1.3 62.8 + - + +
49A ALA* 2.8 32.8 + - - +
55A TYR* 3.8 15.0 - + + -
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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 SER* 3.2 24.6 + - - +
44A HIS* 4.0 8.1 - - + +
46A PHE* 1.3 84.1 - - + +
48A LYS* 1.3 59.2 + - - +
49A ALA 3.9 4.6 - - - +
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Residues in contact with LYS 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 HIS* 2.8 50.1 + - + +
45A VAL* 3.5 7.6 - - - +
47A LEU* 1.3 75.7 - - - +
49A ALA* 1.3 61.3 + - - +
50A LYS* 5.1 2.6 - - - +
54A GLU* 2.9 15.0 - - - +
58A LEU* 4.4 20.4 - - + -
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Residues in contact with ALA 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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10A TRP* 4.0 6.1 - - + -
45A VAL* 2.7 17.2 + - + +
46A PHE 2.8 15.2 + - - +
47A LEU 3.9 4.5 - - - +
48A LYS* 1.3 82.8 - - - +
50A LYS* 1.3 63.0 + - - +
51A THR 4.0 3.4 - - - +
54A GLU* 3.3 11.4 - - + -
55A TYR* 3.3 39.9 - - + +
58A LEU* 5.3 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