Contacts of the helix formed by residues 45 - 59 (chain A) in PDB entry 1DNY
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A HIS* 1.3 75.8 - - - +
46A LEU* 1.3 65.7 + - - +
47A LYS 2.8 7.8 + - - -
48A ALA* 3.3 13.7 + - - +
49A MET* 3.0 21.1 + - - +
65A LEU* 4.9 6.0 - - - +
68A LEU* 5.1 1.6 - - - +
69A PHE* 3.4 32.4 - - - -
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Residues in contact with LEU 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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44A HIS* 3.6 10.2 - - + +
45A SER* 1.3 78.5 - - - +
47A LYS* 1.3 58.1 + - + +
49A MET* 3.9 14.8 - - + -
50A ALA* 3.0 26.6 + - + +
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Residues in contact with LYS 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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26A VAL* 2.7 44.0 - - + +
27A LEU* 3.4 26.0 - - + -
28A GLY* 5.8 0.4 - - - -
42A GLY* 5.8 4.0 - - - -
43A GLY* 4.2 23.8 + - - +
44A HIS* 5.1 2.0 - - + +
45A SER* 2.8 3.3 + - - +
46A LEU* 1.3 77.7 - - + +
48A ALA* 1.3 70.2 + - - +
49A MET 3.0 0.7 - - - -
50A ALA* 2.6 22.1 + - - +
51A VAL 3.0 0.9 + - - -
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Residues in contact with ALA 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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27A LEU* 3.8 1.8 - - - +
38A PHE* 3.1 35.0 + - + -
45A SER* 3.3 12.5 + - - +
47A LYS* 1.3 76.9 - - - +
49A MET* 1.3 65.6 + - - +
51A VAL* 2.6 33.5 + - - +
52A ALA 2.9 3.5 + - - -
68A LEU* 2.8 29.5 - - + +
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Residues in contact with MET 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 SER 3.0 14.6 + - - +
46A LEU* 3.6 18.2 - - + +
47A LYS 3.0 0.2 - - - -
48A ALA* 1.3 75.9 - - - +
50A ALA* 1.3 67.7 + - - +
52A ALA* 2.6 26.7 + - + +
53A ALA* 2.9 26.4 + - + +
63A LEU 5.3 0.7 - - - +
65A LEU* 3.0 52.9 - - + -
68A LEU* 3.6 4.1 - - - +
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Residues in contact with ALA 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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22A ILE* 4.2 2.8 - - - +
26A VAL* 2.9 39.5 - - + +
46A LEU* 3.0 16.1 + - + +
47A LYS 2.6 7.0 + - - +
49A MET* 1.3 70.9 - - - +
51A VAL* 1.3 59.5 + - - -
53A ALA* 2.9 12.7 + - - +
54A GLN* 2.8 19.6 + - - +
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Residues in contact with VAL 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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19A LEU* 3.4 20.4 - - + -
22A ILE* 3.1 37.7 - - + +
23A TRP* 3.3 25.4 - - + +
26A VAL* 4.2 0.9 - - + -
27A LEU* 4.1 13.2 - - + -
38A PHE* 3.7 12.3 - - + -
47A LYS 3.0 9.2 + - - +
48A ALA* 2.6 30.3 + - - +
50A ALA* 1.3 71.6 - - - +
52A ALA* 1.3 52.6 + - - +
54A GLN* 2.7 28.2 + - - +
55A VAL* 2.9 8.9 + - - +
77A LEU* 5.0 0.4 - - + -
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Residues in contact with ALA 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 ALA 2.9 4.4 + - - -
49A MET* 2.6 29.8 + - - +
51A VAL* 1.3 72.8 - - - +
53A ALA* 1.3 61.1 + - - +
55A VAL* 3.0 14.0 + - - +
56A HIS* 3.0 12.0 + - - +
63A LEU* 3.3 38.3 - - + +
64A PRO 4.8 0.9 - - - +
68A LEU* 3.3 25.0 - - + +
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Residues in contact with ALA 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 MET* 2.9 27.3 + - + +
50A ALA* 3.1 15.7 - - - +
52A ALA* 1.3 73.8 - - - +
54A GLN* 1.3 65.1 + - - +
56A HIS* 2.9 18.6 + - - +
57A ARG* 2.9 24.3 + - + +
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Residues in contact with GLN 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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18A LYS* 3.0 21.4 + - + -
19A LEU* 6.0 0.4 - - + -
22A ILE* 3.3 49.1 - - + +
25A ARG* 5.6 5.9 - - - +
26A VAL* 5.1 3.6 - - - +
50A ALA 2.8 7.8 + - - +
51A VAL 2.7 13.3 + - - +
53A ALA* 1.3 78.9 - - - +
55A VAL* 1.3 55.4 + - + +
57A ARG* 4.8 2.2 - - - +
58A GLU* 2.3 69.8 + - + +
59A TYR* 5.0 0.2 - - - -
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Residues in contact with VAL 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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19A LEU* 4.2 13.9 - - + -
51A VAL 3.1 16.6 - - - +
52A ALA* 3.2 17.9 - - - +
54A GLN* 1.3 80.4 - - - +
56A HIS* 1.3 48.0 + - - +
59A TYR* 2.5 54.3 + - + +
61A VAL* 3.4 8.8 - - + +
63A LEU* 3.6 20.6 - - + -
77A LEU* 3.9 9.2 - - + -
81A VAL* 3.0 43.3 - - + -
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Residues in contact with HIS 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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52A ALA 3.0 10.7 + - - +
53A ALA* 2.9 13.1 + - - +
55A VAL* 1.3 74.7 - - - +
57A ARG* 1.3 64.9 + - + +
59A TYR 2.3 26.5 - - - +
60A GLN* 4.0 11.7 + - + +
61A VAL 4.3 16.3 + - - +
62A GLU* 6.0 0.6 - - - -
63A LEU* 5.8 2.3 + - + +
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Residues in contact with ARG 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 ALA* 2.9 18.3 + - + +
54A GLN* 5.6 1.3 - - - +
56A HIS* 1.3 79.9 - - + +
58A GLU* 1.3 84.2 + - - +
59A TYR* 3.2 1.0 + - - -
60A GLN* 5.9 0.5 - - - +
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Residues in contact with GLU 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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18A LYS* 3.4 36.9 + - + +
54A GLN* 2.3 56.3 + - - +
57A ARG* 1.3 89.3 - - - +
59A TYR* 1.3 90.4 + - + +
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Residues in contact with TYR 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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14A ALA 4.7 0.2 + - - -
15A VAL* 4.0 24.4 + - + +
18A LYS* 3.3 29.7 - - + +
19A LEU* 4.8 3.2 - - + +
55A VAL* 2.5 59.9 + - + +
56A HIS* 2.3 29.8 - - - +
57A ARG 4.5 0.4 - - - -
58A GLU* 1.3 108.3 - - + +
60A GLN* 1.3 60.2 + - - +
61A VAL* 3.1 14.3 + - + +
81A VAL* 3.2 17.0 - - + -
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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