Contacts of the helix formed by residues 61 - 76 (chain A) in PDB entry 4DQ0
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ASP* 3.0 15.4 + - - +
60A LYS* 1.3 77.4 - - - +
62A ALA* 1.3 62.7 + - - +
63A MET* 2.8 26.6 + - - +
64A SER* 2.9 23.2 + - - +
65A ILE* 3.2 24.2 + - - +
137B ASP* 4.9 10.5 + - - -
142B PRO* 5.7 2.2 - - - +
143B CYS 3.2 27.6 + - - +
144B THR* 5.2 2.4 - - - +
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Residues in contact with ALA 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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60A LYS 3.3 7.0 + - - +
61A ASN* 1.3 72.2 + - - +
63A MET* 1.3 57.4 + - + +
65A ILE* 3.4 2.6 + - - +
66A ALA* 2.8 30.1 + - - +
84A VAL* 4.0 25.5 - - + +
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Residues in contact with MET 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 2.8 18.4 + - - +
62A ALA* 1.3 71.0 - - + +
64A SER* 1.3 60.3 + - - +
66A ALA* 3.2 7.7 + - - +
67A ASN* 2.8 28.8 + - - +
137B ASP* 5.6 5.8 - - - +
138B THR 5.6 4.0 - - - +
139B ALA* 5.5 9.0 - - - +
142B PRO* 4.7 25.4 - - + -
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY 3.4 23.6 - - - -
41A ASN* 4.4 3.3 - - - +
59A ASP* 4.6 1.3 + - - -
61A ASN* 2.9 30.3 + - - +
63A MET* 1.3 74.6 - - - +
65A ILE* 1.3 59.4 + - - +
67A ASN* 3.1 8.8 + - - +
68A VAL* 2.8 34.9 + - - +
144B THR* 3.3 28.7 - - - +
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Residues in contact with ILE 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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39A CYS* 3.7 29.8 - - - -
57A ALA 4.0 6.7 - - - +
59A ASP* 3.9 13.5 - - + +
61A ASN 3.2 12.7 + - - +
62A ALA 3.7 3.6 - - - +
64A SER* 1.3 80.1 - - - +
66A ALA* 1.3 56.9 + - - +
68A VAL* 3.3 5.9 + - + +
69A GLU* 2.9 29.7 + - + +
82A THR* 3.3 27.1 - - + +
83A ARG* 3.8 19.7 - - - +
84A VAL* 3.6 32.1 - - + -
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Residues in contact with ALA 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 ALA 2.8 21.3 + - - +
63A MET* 3.2 8.0 + - - +
65A ILE* 1.3 72.9 - - - +
67A ASN* 1.3 58.4 + - - +
69A GLU* 3.3 8.8 + - - +
70A ARG* 2.9 28.8 + - - +
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Residues in contact with ASN 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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13A TYR 5.2 1.4 + - - -
15A LEU* 4.1 18.6 - - - +
41A ASN* 4.8 6.1 + - - +
63A MET 2.8 14.4 + - - +
64A SER* 3.1 12.3 + - - +
66A ALA* 1.3 72.9 - - - +
68A VAL* 1.3 67.3 + - + +
70A ARG* 2.8 38.6 + - - +
71A ILE* 3.0 47.3 + - - +
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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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39A CYS* 5.2 1.6 - - - -
40A GLY 4.9 2.0 - - - +
41A ASN 3.5 25.8 - - - +
42A GLY* 4.0 12.6 - - - -
45A SER* 5.5 0.7 - - - -
46A LEU* 4.6 10.7 - - + +
57A ALA* 5.2 4.3 - - + -
64A SER 2.8 27.5 + - - +
65A ILE* 3.7 11.7 - - + +
67A ASN* 1.3 73.0 - - - +
69A GLU* 1.3 52.8 + - - +
71A ILE* 3.3 8.1 + - + +
72A LYS* 2.8 33.5 + - - +
80A LEU* 3.9 22.7 - - + -
82A THR* 3.8 20.9 - - + -
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Residues in contact with GLU 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 ILE* 2.9 18.8 + - + +
66A ALA* 3.5 8.5 - - - +
67A ASN 3.3 0.2 - - - -
68A VAL* 1.3 76.6 - - - +
70A ARG* 1.3 61.6 + - - +
72A LYS* 3.3 29.5 + - - +
73A SER* 3.1 21.5 + - - -
82A THR* 2.9 41.7 + - - +
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Residues in contact with ARG 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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13A TYR* 4.2 17.0 + - - +
66A ALA 2.9 14.3 + - - +
67A ASN* 2.8 35.1 + - - +
69A GLU* 1.3 75.9 - - - +
71A ILE* 1.3 77.3 + - - +
73A SER* 3.2 15.8 + - - -
74A ILE* 3.2 35.9 + - + +
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Residues in contact with ILE 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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9A PHE* 4.5 1.1 - - + -
13A TYR* 3.7 55.4 - - + -
15A LEU* 4.3 3.1 - - + -
41A ASN 5.7 0.7 - - - +
46A LEU* 3.8 35.4 - - + -
67A ASN* 3.0 36.5 + - - +
68A VAL* 3.8 4.3 - - - +
70A ARG* 1.3 90.9 - - - +
72A LYS* 1.3 62.6 - - - +
74A ILE* 3.3 7.3 + - - +
75A GLU* 3.0 30.4 + - + +
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Residues in contact with LYS 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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46A LEU* 5.0 0.2 - - - +
68A VAL 2.8 18.5 + - - +
69A GLU* 3.4 34.4 + - - +
70A ARG 3.2 0.2 - - - -
71A ILE* 1.3 77.9 - - - +
73A SER* 1.3 58.1 + - - +
75A GLU 3.7 0.2 - - - -
76A ASN* 2.9 25.1 + - - -
77A LEU* 3.2 44.2 + - + +
78A ASP* 4.7 6.6 + - - +
80A LEU* 2.6 41.8 + - + +
81A HIS* 4.2 15.6 + - - +
82A THR* 5.5 0.2 - - + -
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Residues in contact with SER 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 GLU 3.1 12.0 + - - -
70A ARG* 3.2 10.7 + - - -
72A LYS* 1.3 80.0 - - - +
74A ILE* 1.3 64.3 + - - +
76A ASN* 3.4 21.2 + - - +
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Residues in contact with ILE 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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12A LYS* 5.5 2.9 - - - +
13A TYR* 3.5 29.2 - - + +
70A ARG* 3.2 39.7 + - + +
71A ILE* 3.3 7.6 + - - +
73A SER* 1.3 78.9 - - - +
75A GLU* 1.3 65.4 + - - +
76A ASN* 3.5 7.6 + - - +
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Residues in contact with GLU 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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4A ARG* 3.5 30.1 + - - +
8A TYR* 2.9 32.4 + - - -
9A PHE* 4.0 10.5 - - + -
12A LYS* 3.4 6.6 + - - -
13A TYR* 2.2 35.3 + - - +
71A ILE* 3.0 29.6 + - + +
74A ILE* 1.3 77.4 - - - +
76A ASN* 1.3 71.3 + - - +
77A LEU* 3.2 20.8 + - + +
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Residues in contact with ASN 76 (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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72A LYS 2.9 8.4 + - - -
73A SER* 3.4 14.0 + - - +
74A ILE 3.3 8.6 - - - +
75A GLU* 1.3 79.3 - - - +
77A LEU* 1.3 59.9 + - - +
78A ASP* 3.1 25.8 + - - +
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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