Contacts of the helix formed by residues 57 - 72 (chain A) in PDB entry 1D0L
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 ASN 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASP 5.4 0.8 + - - +
54A PHE* 3.1 25.7 + - - +
55A ALA 3.4 1.0 + - - -
56A ASN* 1.3 76.2 - - - +
58A PRO* 1.3 67.2 - - - +
59A ASN* 2.9 43.0 + - - +
60A ALA* 3.2 9.1 + - + +
61A GLN* 3.2 24.4 + - - +
183A PHE* 3.0 29.0 + - - +
184A ASN* 3.4 23.0 + - - +
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Residues in contact with PRO 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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56A ASN 3.4 9.8 - - - +
57A ASN* 1.3 88.6 - - - +
59A ASN* 1.3 63.8 + - - +
61A GLN* 3.3 8.5 + - + +
62A GLN* 2.9 43.6 + - - +
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Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASN* 2.9 12.6 + - - +
58A PRO* 1.3 79.4 - - - +
60A ALA* 1.3 60.2 + - - +
62A GLN* 3.4 14.8 + - - +
63A PHE* 3.0 29.5 + - - +
182A SER 4.5 4.7 + - - +
183A PHE* 3.1 39.5 + - + -
186A PRO* 6.3 1.6 - - - +
189A ALA* 6.4 0.9 - - - -
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Residues in contact with ALA 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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50A MET* 3.9 13.0 - - + -
54A PHE* 3.9 11.7 - - + +
57A ASN* 3.2 24.2 + - + +
59A ASN* 1.3 78.5 - - - +
61A GLN* 1.3 58.0 + - - +
63A PHE* 3.3 2.8 + - - +
64A ILE* 3.0 34.8 + - - +
82A LEU* 5.1 1.3 - - + -
183A PHE* 3.7 34.9 - - + -
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Residues in contact with GLN 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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48A MET 4.6 2.9 + - - +
49A GLN* 3.9 17.4 + - - +
50A MET* 3.7 28.3 - - - +
55A ALA 3.5 22.0 + - - +
56A ASN 5.7 0.4 - - - -
57A ASN 3.2 14.6 + - - +
58A PRO* 3.6 9.4 - - + +
59A ASN 3.3 0.2 - - - -
60A ALA* 1.3 74.2 - - - +
62A GLN* 1.3 64.8 + - + +
64A ILE* 3.4 4.5 + - - +
65A ASP* 3.1 28.8 + - - +
75A ARG* 3.2 37.3 + - - +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 2.9 31.8 + - - +
59A ASN* 3.8 13.4 + - - +
60A ALA 3.3 0.2 - - - -
61A GLN* 1.3 76.9 - - + +
63A PHE* 1.3 62.8 + - - +
65A ASP* 3.2 12.2 + - - +
66A LYS* 3.0 22.7 + - - +
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Residues in contact with PHE 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 ASN 3.0 18.9 + - - +
60A ALA 3.5 4.5 - - - +
62A GLN* 1.3 77.7 - - - +
64A ILE* 1.3 63.7 + - - +
66A LYS* 3.2 15.9 + - + +
67A MET* 3.0 51.3 + - + +
78A LEU* 5.0 0.9 - - + -
82A LEU* 4.5 9.6 - - + -
183A PHE* 3.5 24.5 - + + -
193A SER* 3.2 40.2 - - - +
196A LEU* 3.6 26.0 - - + -
197A GLU* 3.7 16.8 - - + -
200A LEU* 3.7 17.5 - - + -
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Residues in contact with ILE 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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50A MET* 4.0 29.4 - - + -
60A ALA 3.0 19.4 + - - +
61A GLN* 3.7 12.1 - - - +
63A PHE* 1.3 75.0 - - - +
65A ASP* 1.3 65.1 + - - +
67A MET* 3.2 3.3 + - - +
68A VAL* 3.0 29.9 + - + +
75A ARG* 3.7 39.7 - - + +
78A LEU* 3.8 26.5 - - + -
79A GLN* 4.1 17.3 - - + -
82A LEU* 3.7 21.3 - - + -
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Residues in contact with ASP 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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61A GLN* 3.1 20.6 + - - +
62A GLN* 3.2 13.0 + - - +
64A ILE* 1.3 75.7 - - - +
66A LYS* 1.3 58.3 + - - +
68A VAL* 3.4 6.4 + - - +
69A ASN* 3.0 31.1 + - - +
75A ARG* 2.9 28.1 + - - -
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Residues in contact with LYS 66 (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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62A GLN 3.0 12.4 + - - +
63A PHE* 3.5 21.5 - - + +
65A ASP* 1.3 74.5 - - - +
67A MET* 1.3 63.9 + - - +
69A ASN* 4.7 3.6 - - - -
70A LYS* 2.8 59.2 + - + +
193A SER* 5.5 5.5 + - - +
194A GLY* 6.0 0.8 - - - -
197A GLU* 3.6 35.7 + - - +
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Residues in contact with MET 67 (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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63A PHE* 3.0 51.2 + - + +
64A ILE 3.2 0.4 + - - +
66A LYS* 1.3 77.4 - - - +
68A VAL* 1.3 58.4 + - - +
71A HIS* 3.0 42.6 + - + +
72A GLY 3.3 4.9 + - - -
73A PHE* 3.3 41.5 + - + -
78A LEU* 3.5 24.7 - - + -
197A GLU* 3.8 39.3 - - - +
200A LEU* 4.2 8.7 - - + -
201A LEU* 4.4 0.9 - - + -
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Residues in contact with VAL 68 (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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64A ILE* 3.0 24.4 + - + +
65A ASP* 3.7 7.2 - - - +
67A MET* 1.3 74.6 - - - +
69A ASN* 1.3 62.0 + - + +
72A GLY* 2.8 29.6 + - - -
73A PHE* 3.4 29.2 - - + +
75A ARG* 3.8 32.3 - - + +
78A LEU* 5.2 0.4 - - + -
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Residues in contact with ASN 69 (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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65A ASP 3.0 16.2 + - - +
66A LYS* 4.0 3.4 - - - +
68A VAL* 1.3 82.7 - - + +
70A LYS* 1.3 67.1 + - - +
72A GLY* 4.3 1.4 + - - -
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Residues in contact with LYS 70 (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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66A LYS* 2.8 45.6 + - + +
69A ASN* 1.3 81.2 - - - +
71A HIS* 1.3 77.1 + - + +
197A GLU* 2.8 32.8 + - - +
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Residues in contact with HIS 71 (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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66A LYS 5.4 0.2 - - - -
67A MET* 3.0 42.0 + - + +
70A LYS* 1.3 108.6 + - + +
72A GLY* 1.3 59.6 + - - +
73A PHE* 3.3 15.5 - - + -
197A GLU* 2.8 26.1 + - - -
201A LEU* 3.7 29.2 - - + +
204A ARG* 3.0 25.3 + - - +
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Residues in contact with GLY 72 (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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68A VAL* 2.8 21.1 + - - -
69A ASN 4.3 1.4 + - - -
70A LYS 3.7 1.0 - - - -
71A HIS* 1.3 73.2 - - - +
73A PHE* 1.3 66.2 + - - +
74A ASP 3.7 0.9 + - - -
204A ARG* 4.3 3.4 + - - -
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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