Contacts of the helix formed by residues 51 - 64 (chain A) in PDB entry 2D9U
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 PRO 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LEU 3.5 8.7 - - - +
50A ASP* 1.3 82.0 - - + +
52A ARG* 1.3 83.7 + - + +
53A LEU 3.1 2.2 - - - -
54A LEU* 2.7 26.8 + - + +
55A LEU* 2.9 25.6 + - + +
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Residues in contact with ARG 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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15A CYS* 5.3 0.7 - - - -
50A ASP* 3.4 26.6 + - + +
51A PRO* 1.3 87.7 - - + +
53A LEU* 1.3 69.3 + - + +
55A LEU* 3.3 13.9 + - + +
56A ALA* 2.9 24.3 + - - +
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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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13A ALA* 3.4 32.8 - - + +
14A GLU 3.1 27.8 - - - +
15A CYS* 3.5 20.0 - - - -
16A ILE* 3.4 26.0 - - + +
30A VAL* 5.1 2.9 - - + -
48A ILE* 4.5 13.2 - - + -
49A LEU 6.0 0.2 - - - +
50A ASP* 3.8 31.6 - - + +
51A PRO 2.9 1.0 + - - -
52A ARG* 1.3 82.4 - - + +
54A LEU* 1.3 65.8 + - - +
56A ALA* 3.2 14.4 + - - +
57A PHE 3.4 3.5 + - - -
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Residues in contact with LEU 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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16A ILE* 3.5 8.5 - - + +
28A TYR* 3.8 36.3 - - + +
45A GLU* 4.4 18.6 - - + +
48A ILE* 3.6 31.0 - - + +
50A ASP 4.0 2.7 + - - +
51A PRO* 2.7 18.9 + - + +
53A LEU* 1.3 74.6 - - - +
55A LEU* 1.3 64.8 + - + +
57A PHE* 3.0 7.0 + - + +
58A GLN* 2.8 43.8 + - + +
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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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51A PRO* 2.9 28.1 + - + +
52A ARG* 3.5 15.5 - - + +
54A LEU* 1.3 77.8 - - + +
56A ALA* 1.3 66.2 + - - +
57A PHE 2.8 1.6 + - - -
58A GLN* 2.9 34.5 + - - +
59A LYS* 2.9 23.2 + - + +
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Residues in contact with ALA 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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15A CYS* 3.3 27.1 - - - -
16A ILE 5.5 2.0 - - - +
52A ARG 2.9 11.5 + - - +
53A LEU 3.2 11.7 - - - +
55A LEU* 1.3 75.4 - - - +
57A PHE* 1.3 59.3 + - - +
59A LYS* 3.8 9.2 - - - +
60A LYS* 3.3 24.5 + - - +
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Residues in contact with PHE 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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16A ILE* 3.8 32.9 + - + -
17A LEU 3.2 23.3 - - - -
18A SER* 3.5 23.8 - - - -
19A LYS* 3.5 33.0 - - + -
28A TYR* 4.0 16.4 - + + -
53A LEU 3.4 3.3 + - - +
54A LEU* 3.0 9.8 + - + +
55A LEU 2.8 0.4 + - - -
56A ALA* 1.3 76.2 - - - +
58A GLN* 1.3 58.0 - - + +
59A LYS 2.9 1.6 - - - -
60A LYS* 2.6 43.8 + - + +
61A GLU* 2.9 28.3 + - + -
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Residues in contact with GLN 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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45A GLU* 5.8 1.8 + - - -
54A LEU* 2.8 39.6 + - + +
55A LEU* 2.9 32.2 + - - +
57A PHE* 1.3 72.6 - - + +
59A LYS* 1.3 62.6 + - + +
61A GLU* 3.3 24.1 - - - +
62A HIS* 3.9 2.9 + - - +
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Residues in contact with LYS 59 (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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55A LEU* 2.9 21.0 + - + +
56A ALA* 3.8 7.9 - - - +
57A PHE 2.7 4.4 + - - -
58A GLN* 1.3 74.1 - - + +
60A LYS* 1.3 64.6 - - + +
62A HIS* 3.3 21.5 + - - +
63A GLU* 3.5 4.2 - - - +
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Residues in contact with LYS 60 (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 ILE 5.8 2.2 - - - +
17A LEU 5.7 1.6 - - - +
56A ALA 3.3 18.6 - - - +
57A PHE* 2.6 30.3 + - + +
59A LYS* 1.3 71.6 - - + +
61A GLU* 1.3 67.3 + - - +
63A GLU* 2.7 38.4 + - + +
64A LYS* 3.8 2.0 + - - +
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Residues in contact with GLU 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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19A LYS* 2.5 43.4 + - - +
57A PHE* 2.9 33.0 + - + +
58A GLN* 3.3 18.4 - - - +
60A LYS* 1.3 75.1 - - - +
62A HIS* 1.3 65.9 + - - +
64A LYS* 2.8 40.6 + - - +
65A GLU* 3.3 4.8 + - - +
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Residues in contact with HIS 62 (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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58A GLN 3.9 3.1 + - - +
59A LYS 3.3 15.9 + - - +
60A LYS 2.8 0.8 + - - -
61A GLU* 1.3 77.3 - - - +
63A GLU* 1.3 80.8 + - - +
65A GLU* 2.7 43.7 + - - +
68A ASN* 5.2 9.0 - - - -
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Residues in contact with GLU 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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59A LYS 3.5 5.9 - - - +
60A LYS* 2.7 51.8 + - + +
62A HIS* 1.3 87.2 - - - +
64A LYS* 1.3 63.7 + - + +
65A GLU 3.1 8.1 - - - +
66A VAL* 4.9 2.6 - - - +
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Residues in contact with LYS 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 LYS 5.0 1.1 - - - +
61A GLU* 2.8 34.3 + - - +
63A GLU* 1.3 76.7 - - + +
65A GLU* 1.3 60.9 + - - +
66A VAL* 3.9 8.3 + - - +
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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