Contacts of the helix formed by residues 65 - 81 (chain A) in PDB entry 1DNC
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 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A CYS 4.0 0.2 - - - +
59A VAL 3.3 22.0 - - - +
60A ASN 3.7 14.1 - - - +
61A VAL* 4.1 0.7 - - - -
62A GLY 3.5 26.2 - - - +
64A VAL* 1.4 88.7 - - + +
66A LYS* 1.3 59.0 + - - +
68A VAL* 3.4 1.6 + - + -
69A MET* 3.1 26.5 + - - +
103A ARG* 3.7 25.6 - - + +
107A VAL* 4.4 7.2 - - + -
181A PHE* 3.6 26.5 - - + -
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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
----------------------------------------------------------
62A GLY 3.0 21.3 + - - +
63A CSD 3.6 8.3 - - - +
65A PRO* 1.3 77.2 - - - +
67A LYS* 1.3 61.8 + - - +
69A MET* 3.1 7.6 + - - +
70A TRP* 2.8 27.5 + - + +
181A PHE* 3.7 15.0 - - + -
197A TYR* 4.5 1.0 - - - -
201A GLU* 2.7 46.0 + - + +
202A MET* 4.5 15.7 - - + -
205A ILE* 4.2 6.8 - - + +
372A PHE* 3.9 22.3 - - + -
499A FAD 2.8 49.1 + - + -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A CSD 2.9 17.9 + - - +
64A VAL* 3.3 5.4 + - - +
66A LYS* 1.3 77.8 - - + +
68A VAL* 1.3 66.8 + - + +
70A TRP* 3.2 31.7 + - + +
71A ASN* 2.9 42.6 + - - +
372A PHE* 3.7 39.3 - - + -
441A ASP* 4.8 4.6 + - - -
442A GLU* 4.9 9.1 + - - -
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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
----------------------------------------------------------
64A VAL 3.2 15.8 + - - +
65A PRO 3.7 6.7 - - - +
66A LYS 3.3 0.4 - - - -
67A LYS* 1.3 75.4 - - + +
69A MET* 1.3 61.4 + - - +
71A ASN* 3.3 13.6 + - + +
72A THR* 2.8 26.6 + - - +
99A ILE* 4.5 19.7 - - + -
103A ARG* 3.9 31.0 - - + +
106A TYR* 4.1 28.5 - - + -
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Residues in contact with MET 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO 3.1 13.9 + - - +
66A LYS* 3.1 9.5 + - - +
68A VAL* 1.3 75.7 - - - +
70A TRP* 1.3 59.3 + - - +
72A THR* 3.4 7.6 + - - +
73A ALA* 3.0 26.2 + - - +
94A PHE* 5.1 0.4 - - + -
96A TRP* 4.0 34.5 - - + -
99A ILE* 4.2 27.8 - - + -
103A ARG* 3.5 33.9 - - - +
180A PHE* 4.4 5.4 - - + -
181A PHE* 4.4 10.3 - - + -
205A ILE* 3.9 24.1 - - + +
209A LEU* 4.0 15.7 - - + +
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Residues in contact with TRP 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 14.9 + - + +
67A LYS* 3.2 33.2 + - - +
69A MET* 1.3 74.3 - - - +
71A ASN* 1.3 79.3 + - - +
73A ALA* 3.0 3.6 + - - +
74A VAL* 2.9 53.7 + - + +
205A ILE* 4.2 13.6 - - + +
372A PHE* 3.1 44.6 + + + -
373A SER 2.9 27.1 + - - -
374A HIS* 3.4 21.9 - + - -
376A PRO* 4.0 15.9 - - + -
441A ASP* 3.8 25.8 - - - -
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Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 2.9 37.6 + - - +
68A VAL* 3.6 12.7 - - + +
70A TRP* 1.3 93.1 - - - +
72A THR* 1.3 61.6 + - - +
74A VAL* 3.5 9.9 + - - +
75A HIS* 3.2 29.6 + - + -
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL 2.8 15.7 + - - -
69A MET* 3.5 11.9 - - - -
71A ASN* 1.3 76.8 - - - +
73A ALA* 1.3 63.6 + - - +
75A HIS* 3.2 23.4 + - + +
76A SER* 3.3 4.7 + - - -
94A PHE* 3.6 36.8 - - + -
99A ILE* 3.5 29.8 - - + +
209A LEU* 3.9 12.4 - - + +
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Residues in contact with ALA 73 (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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69A MET 3.0 13.8 + - - +
70A TRP* 3.0 9.4 + - - +
72A THR* 1.3 74.4 - - - +
74A VAL* 1.3 62.9 + - - +
76A SER* 3.0 20.3 + - - -
77A GLU* 3.2 9.9 + - - +
205A ILE* 4.1 15.0 - - + +
208A ALA* 3.7 16.3 - - + +
209A LEU* 4.0 10.7 - - - +
374A HIS* 3.6 26.2 - - + +
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Residues in contact with VAL 74 (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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70A TRP* 2.9 56.3 + - + +
71A ASN* 3.6 8.7 - - - +
73A ALA* 1.3 76.8 - - - +
75A HIS* 1.3 62.8 + - + +
77A GLU* 3.3 13.0 + - - +
78A PHE* 3.1 52.7 + - + -
374A HIS* 4.1 9.0 - - + +
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Residues in contact with HIS 75 (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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71A ASN* 3.2 21.6 + - + +
72A THR* 3.3 14.6 - - + +
73A ALA 3.2 0.2 - - - -
74A VAL* 1.3 77.2 - - + +
76A SER* 1.3 58.0 + - - +
78A PHE* 3.4 9.2 + + - +
79A MET* 3.0 29.7 + - - +
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR 3.3 6.0 + - - -
73A ALA* 3.0 17.9 + - - -
75A HIS* 1.3 78.8 - - - +
77A GLU* 1.3 58.6 + - - +
79A MET* 3.2 39.1 + - - +
80A HIS* 3.3 17.8 + - - -
208A ALA* 2.6 32.4 + - - -
209A LEU* 4.4 7.9 - - - +
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Residues in contact with GLU 77 (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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73A ALA 3.2 10.8 + - - +
74A VAL* 3.3 12.8 + - - +
76A SER* 1.3 75.4 - - - +
78A PHE* 1.3 70.2 + - + +
80A HIS* 3.1 31.9 + - + +
81A ASP* 3.5 3.5 + - - -
208A ALA* 4.4 10.9 - - + +
374A HIS* 2.6 49.3 + - - +
413A ARG* 3.8 37.0 + - - +
438A LEU* 5.5 5.9 - - - +
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Residues in contact with PHE 78 (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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74A VAL* 3.1 38.4 + - + +
75A HIS* 3.8 8.7 - + - +
77A GLU* 1.3 82.3 - - + +
79A MET* 1.3 64.9 - - - +
81A ASP* 3.1 15.9 + - - +
82A HIS* 3.3 15.0 + - - -
407A TYR* 3.9 30.6 + + - +
413A ARG* 4.4 9.4 - - - -
438A LEU* 4.8 20.4 - - + -
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Residues in contact with MET 79 (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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75A HIS 3.0 13.7 + - - +
76A SER* 3.3 39.7 - - - +
78A PHE* 1.3 75.8 - - - +
80A HIS* 1.3 74.5 + - + +
82A HIS* 3.5 23.5 + - - +
83A ALA 5.0 0.2 + - - -
89A SER* 5.9 0.3 - - - -
90A CYS* 3.7 38.2 + - + +
92A GLY* 4.4 28.7 - - - +
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Residues in contact with HIS 80 (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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76A SER* 3.3 25.6 + - - -
77A GLU* 3.2 22.4 - - + +
78A PHE 3.1 0.4 - - - -
79A MET* 1.3 94.1 - - + +
81A ASP* 1.3 63.9 + - - +
82A HIS 3.4 0.7 + - - -
83A ALA* 4.8 4.3 + - - +
84A ASP* 4.8 5.4 + - - +
208A ALA* 5.0 5.2 + - - -
413A ARG* 4.4 16.5 - - + +
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Residues in contact with ASP 81 (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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77A GLU 3.8 3.4 - - - +
78A PHE* 3.1 7.8 + - - +
80A HIS* 1.3 79.9 - - - +
82A HIS* 1.3 62.7 + - - +
83A ALA 3.4 1.6 - - - -
84A ASP* 3.2 21.0 + - - +
85A TYR* 3.2 16.3 + - + -
407A TYR* 2.7 34.8 + - - +
408A HIS* 4.4 0.5 - - - -
411A THR* 4.0 20.6 - - + -
413A ARG* 2.8 53.7 + - - +
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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
------------------------------------------------------------
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