Contacts of the helix formed by residues 71 - 89 (chain A) in PDB entry 4DUQ
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 ASP 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.7 2.2 - - - -
27A PHE 4.1 8.3 - - - +
28A LYS* 4.1 24.9 - - + +
65A ASN* 5.0 8.1 + - - -
67A ASP* 5.3 1.4 - - - +
69A GLN 4.0 0.6 - - - -
70A VAL* 1.3 75.8 - - - +
72A PHE* 1.3 58.9 + - - +
73A GLN* 3.2 13.3 + - - +
74A GLU* 2.9 45.8 + - - +
75A TYR* 2.9 26.0 + - - +
102A CA 4.5 0.2 - - - -
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Residues in contact with PHE 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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13A VAL* 4.1 10.5 - - + -
16A PHE* 3.6 42.0 - + + -
27A PHE 4.3 1.4 + - - +
71A ASP* 1.3 76.0 - - - +
73A GLN* 1.3 69.3 + - - +
75A TYR* 3.1 27.9 + + - +
76A ALA* 3.0 17.4 + - + +
79A LEU* 4.5 3.6 - - + -
83B THR* 3.5 44.9 - - + -
84B VAL* 3.7 19.7 - - + -
87B ASN* 3.3 43.3 - - + +
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Residues in contact with GLN 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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71A ASP* 3.2 10.5 + - - +
72A PHE* 1.3 87.4 - - - +
74A GLU* 1.3 65.5 + - + +
76A ALA* 3.2 17.8 + - - +
77A VAL* 3.9 6.6 + - - +
84B VAL* 3.0 38.9 - - - +
87B ASN* 5.0 2.6 - - - +
88B ASP* 4.2 11.7 + - - -
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Residues in contact with GLU 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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62A LEU* 3.3 30.6 - - - +
63A ASP* 4.0 0.2 - - - -
64A GLU* 3.0 25.9 + - + +
65A ASN* 3.1 12.6 + - - +
69A GLN 3.1 4.5 - - - +
70A VAL* 3.3 8.8 - - + -
71A ASP* 2.9 39.9 + - - +
73A GLN* 1.3 79.2 - - + +
75A TYR* 1.3 61.3 + - - +
77A VAL* 3.2 25.1 + - - +
78A PHE 3.7 1.9 + - - -
102A CA 2.4 30.7 - - - -
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Residues in contact with TYR 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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12A LEU* 2.7 32.1 + - - -
15A THR* 3.9 9.9 - - - +
16A PHE* 3.5 43.9 + + + -
29A LEU* 4.3 9.9 - - + -
34A MET* 5.1 2.0 - - + -
37A LEU* 4.3 18.8 - - + -
70A VAL* 3.5 10.9 - - + +
71A ASP 2.9 12.9 + - - +
72A PHE* 3.4 23.6 - + - +
74A GLU* 1.3 75.5 - - - +
76A ALA* 1.3 63.5 + - - +
78A PHE* 3.0 30.4 + + + +
79A LEU* 2.9 53.2 + - + +
5B LEU* 4.4 7.1 - - + +
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Residues in contact with ALA 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 PHE* 3.0 8.8 + - + +
73A GLN 3.2 13.4 + - - +
75A TYR* 1.3 76.1 - - - +
77A VAL* 1.3 62.4 + - + +
79A LEU* 4.1 13.7 - - + -
80A ALA* 3.0 19.2 + - - +
80B ALA* 3.4 24.1 - - + +
84B VAL* 3.4 30.7 - - + -
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Residues in contact with VAL 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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61A SER 5.9 2.0 - - - +
62A LEU* 4.3 13.2 - - + -
64A GLU* 6.3 2.9 - - + -
73A GLN 4.4 7.2 - - - +
74A GLU* 3.2 14.5 + - - +
75A TYR 3.1 0.6 - - - -
76A ALA* 1.3 77.2 - - + +
78A PHE* 1.3 62.6 + - - +
80A ALA* 3.3 8.4 + - - +
81A LEU* 3.1 22.0 + - + +
102B 15P 5.4 0.2 - - - +
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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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34A MET* 4.5 11.7 - - + -
37A LEU* 4.5 7.9 - - + -
38A LEU* 3.7 26.5 - - + -
42A LEU* 3.8 16.8 - - + -
45A PHE* 6.1 0.4 - + - -
58A LEU* 3.8 35.7 - - + -
62A LEU* 3.8 22.6 - - + +
74A GLU 3.7 0.8 + - - -
75A TYR* 3.0 31.0 + + - +
77A VAL* 1.3 80.4 - - - +
79A LEU* 1.3 60.8 + - - +
81A LEU* 3.2 15.7 + - + +
82A ILE* 2.9 51.7 + - + +
5B LEU* 5.8 0.2 - - + -
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Residues in contact with LEU 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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12A LEU* 4.2 28.0 - - + -
72A PHE* 4.5 1.6 - - + -
75A TYR* 2.9 61.1 + - + +
76A ALA* 3.5 16.8 - - + +
77A VAL 3.2 0.2 - - - -
78A PHE* 1.3 76.5 - - - +
80A ALA* 1.3 62.5 + - - +
82A ILE* 3.4 17.6 + - + +
83A THR* 2.7 31.1 + - - +
5B LEU* 5.0 0.9 - - + -
9B LEU* 5.3 1.1 - - + -
80B ALA* 4.5 8.5 - - + -
83B THR* 3.9 29.6 - - + -
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Residues in contact with ALA 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 ALA 3.0 12.4 + - - +
77A VAL* 3.7 9.6 - - + +
79A LEU* 1.3 76.8 - - - +
81A LEU* 1.3 63.4 + - - +
83A THR* 3.6 2.4 - - - -
84A VAL* 3.0 28.1 + - - +
76B ALA* 3.9 28.1 - - - +
77B VAL* 4.5 6.7 - - + +
80B ALA* 4.1 5.8 - - + +
102B 15P 3.7 20.2 - - - -
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Residues in contact with LEU 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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58A LEU* 5.5 6.1 - - + -
62A LEU* 6.4 1.1 - - + -
77A VAL* 3.1 14.1 + - + +
78A PHE* 3.5 25.6 - - + +
80A ALA* 1.3 77.2 - - - +
82A ILE* 1.3 58.9 + - + +
84A VAL* 3.2 4.3 + - + +
85A MET* 2.9 56.1 + - + +
102B 15P 3.8 22.6 + - + +
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Residues in contact with ILE 82 (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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42A LEU* 4.0 17.9 - - + -
45A PHE* 3.8 26.1 - - + -
75A TYR* 5.8 0.2 - - + -
78A PHE* 2.9 60.2 + - + +
79A LEU* 3.5 20.0 - - + +
81A LEU* 1.3 77.6 - - + +
83A THR* 1.3 56.2 + - - +
85A MET* 3.7 12.0 - - - +
86A SER* 2.7 37.6 + - - -
5B LEU* 4.4 7.6 - - + -
9B LEU* 3.8 27.6 - - + -
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Residues in contact with THR 83 (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 LEU* 5.7 0.2 - - - +
79A LEU* 2.7 24.4 + - - +
80A ALA* 3.6 5.1 - - - -
82A ILE* 1.3 73.8 - - - +
84A VAL* 1.3 64.5 + - - +
86A SER* 3.2 7.5 + - - -
87A ASN* 3.1 16.8 + - - +
9B LEU* 3.6 19.3 - - + +
12B LEU* 3.9 31.9 - - + +
13B VAL* 4.1 2.7 - - + +
72B PHE* 3.6 27.9 - - + -
75B TYR* 5.1 2.2 - - + -
76B ALA* 4.0 16.6 + - + -
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Residues in contact with VAL 84 (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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80A ALA 3.0 14.6 + - - +
81A LEU* 3.6 9.0 - - + +
83A THR* 1.3 76.4 - - - +
85A MET* 1.3 64.7 + - + +
87A ASN* 3.2 4.0 + - - +
88A ASP* 3.0 38.8 + - - +
72B PHE* 3.9 15.7 - - + -
73B GLN* 4.2 14.4 - - + +
76B ALA* 3.9 17.3 - - + -
102B 15P 3.7 28.9 - - - +
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Residues in contact with MET 85 (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 PHE* 3.3 40.4 - - + -
81A LEU* 2.9 48.7 + - + +
82A ILE* 3.7 8.3 - - - +
83A THR 3.3 0.2 - - - -
84A VAL* 1.3 78.5 - - + +
86A SER* 1.3 58.1 + - - +
88A ASP* 4.7 0.2 - - - -
89A PHE* 2.9 54.9 + - + +
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Residues in contact with SER 86 (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 PHE* 3.8 11.2 - - - -
82A ILE 2.7 22.1 + - - -
83A THR* 3.2 6.3 + - - -
85A MET* 1.3 77.6 - - - +
87A ASN* 1.3 63.6 + - - +
89A PHE 4.0 11.8 - - - -
9B LEU* 3.6 30.8 - - - +
10B ALA* 5.3 1.1 - - - -
13B VAL* 3.9 16.3 - - - +
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Residues in contact with ASN 87 (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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83A THR 3.1 4.9 + - - -
84A VAL* 3.2 8.0 + - - +
86A SER* 1.3 80.3 - - - +
88A ASP* 1.3 73.0 + - - +
89A PHE 4.9 0.3 - - - -
13B VAL* 3.2 17.8 - - + +
17B HIS* 2.7 32.5 + - - -
72B PHE* 3.6 46.6 - - + +
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Residues in contact with ASP 88 (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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84A VAL* 3.0 31.3 + - - +
87A ASN* 1.3 92.5 + - - +
89A PHE* 1.3 94.0 + - + +
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Residues in contact with PHE 89 (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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85A MET* 2.9 38.8 + - + +
86A SER* 4.0 12.1 - - - -
87A ASN 3.4 0.9 - - - -
88A ASP* 1.3 105.8 - - + +
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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