Contacts of the helix formed by residues 51 - 65 (chain A) in PDB entry 2RGI
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A VAL* 1.3 67.1 - - - +
52A GLU* 1.3 63.9 + - - +
53A GLU* 3.6 7.6 + - - +
54A GLY* 2.9 26.3 + - - -
55A LEU* 3.0 25.9 + - - +
85A MET* 2.8 35.4 + - + +
91A GLN* 3.6 18.8 - - - +
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Residues in contact with GLU 52 (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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45A PHE 3.7 22.5 - - - +
46A VAL* 3.9 13.8 - - + +
47A GLY* 2.7 41.5 + - - +
48A GLU* 4.9 3.8 - - - +
50A VAL* 2.9 9.5 + - - +
51A ASP* 1.3 72.0 - - - +
53A GLU* 1.3 58.4 + - - +
55A LEU* 3.4 1.2 + - - +
56A LYS* 2.9 37.6 + - + +
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Residues in contact with GLU 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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51A ASP* 3.2 6.1 + - - +
52A GLU* 1.3 79.8 - - - +
54A GLY* 1.3 61.8 + - - +
56A LYS* 3.4 19.3 + - - +
57A LYS* 2.9 69.5 + - + +
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Residues in contact with GLY 54 (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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51A ASP* 2.9 21.9 + - - -
53A GLU* 1.3 78.9 - - - +
55A LEU* 1.3 55.6 + - - +
57A LYS* 3.6 5.1 + - - +
58A LEU* 2.9 28.8 + - - +
85A MET* 3.5 17.4 - - - +
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Residues in contact with LEU 55 (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 PHE* 3.8 43.1 - - + +
50A VAL* 3.8 27.4 - - + -
51A ASP 3.0 20.9 + - - +
52A GLU 3.7 3.1 - - - +
54A GLY* 1.3 74.8 - - - +
56A LYS* 1.3 60.3 + - - +
58A LEU* 3.6 3.3 - - + +
59A MET* 2.9 37.1 + - - +
82A ILE* 3.9 27.1 - - + -
85A MET* 3.7 38.1 - - + +
86A SER* 4.3 4.5 - - - -
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Residues in contact with LYS 56 (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 PHE* 5.4 1.2 + - - +
52A GLU* 2.9 24.4 + - + +
53A GLU* 3.5 20.6 + - - +
55A LEU* 1.3 74.9 - - - +
57A LYS* 1.3 79.1 + - + +
59A MET* 3.4 5.5 + - - +
60A GLY* 2.9 25.3 + - - -
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Residues in contact with LYS 57 (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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53A GLU* 2.9 46.0 + - + +
54A GLY* 3.9 5.4 - - - +
56A LYS* 1.3 99.8 - - + +
58A LEU* 1.3 65.8 + - - +
60A GLY* 3.3 2.4 + - - +
61A SER* 2.9 23.6 + - - -
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Residues in contact with LEU 58 (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 LEU* 4.3 2.2 - - + -
54A GLY 2.9 19.5 + - - +
55A LEU* 3.2 5.4 + - + +
57A LYS* 1.3 76.6 - - - +
59A MET* 1.3 68.2 + - + +
61A SER* 2.4 26.2 + - - +
62A LEU* 3.2 24.7 + - + +
78A PHE* 4.2 21.3 - - + -
81A LEU* 3.8 23.6 - - + -
82A ILE* 3.9 26.5 - - + -
85A MET* 3.3 28.3 - - + -
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Residues in contact with MET 59 (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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35A LYS* 3.6 35.7 - - + +
38A LEU* 3.7 29.2 - - + -
39A HIS* 3.5 48.5 - - + +
45A PHE* 3.8 26.2 - - + -
55A LEU 2.9 20.3 + - - +
56A LYS* 3.7 5.6 - - - +
58A LEU* 1.3 80.1 - - + +
60A GLY* 1.3 61.6 + - - +
62A LEU* 3.2 22.8 + - - +
63A ASP 3.3 8.3 + - - -
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Residues in contact with GLY 60 (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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56A LYS 2.9 15.9 + - - -
57A LYS* 3.3 4.5 + - - -
59A MET* 1.3 76.2 - - - +
61A SER* 1.3 57.0 + - - +
63A ASP* 3.0 32.9 - - - +
64A GLU* 3.1 7.1 + - - +
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Residues in contact with SER 61 (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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31A LYS* 4.9 2.1 + - - +
57A LYS 2.9 13.3 + - - -
58A LEU* 2.4 31.3 + - - +
60A GLY* 1.3 73.9 - - - +
62A LEU* 1.3 67.4 + - - +
64A GLU* 3.3 8.3 + - - -
65A ASN* 3.0 33.2 + - - +
78A PHE* 5.0 4.7 - - - -
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Residues in contact with LEU 62 (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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31A LYS* 3.8 40.5 - - + +
32A GLY* 5.2 0.7 - - - -
34A MET* 4.2 8.1 - - + -
35A LYS* 3.8 26.5 - - + +
38A LEU* 3.6 31.2 - - + -
58A LEU* 3.6 18.4 - - + +
59A MET* 3.2 13.1 + - - +
61A SER* 1.3 82.3 + - - +
63A ASP* 1.3 61.7 + - - +
65A ASN 3.2 3.5 + - - -
66A SER* 3.1 25.3 + - - -
78A PHE* 3.9 28.9 - - + -
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Residues in contact with ASP 63 (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 LYS* 3.6 32.3 + - - +
59A MET 3.3 1.4 + - - -
60A GLY* 3.0 20.2 + - - +
62A LEU* 1.3 73.6 - - - +
64A GLU* 1.3 66.7 + - - +
65A ASN 3.0 2.8 + - - -
66A SER* 3.3 19.8 + - - -
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Residues in contact with GLU 64 (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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60A GLY 3.1 7.8 + - - +
61A SER* 3.3 14.5 + - - +
63A ASP* 1.3 80.1 - - - +
65A ASN* 1.3 72.8 + - - +
66A SER 4.0 0.5 + - - -
67A ASP* 5.4 0.3 - - - +
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Residues in contact with ASN 65 (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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31A LYS* 3.1 35.1 + - + +
61A SER* 3.0 22.9 + - - +
62A LEU 3.3 3.8 - - - -
63A ASP 3.0 1.0 - - - -
64A GLU* 1.3 98.5 + - - +
66A SER* 1.3 61.6 + - - +
67A ASP* 3.3 8.3 - - - -
68A GLN* 3.0 41.3 + - - +
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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