Contacts of the helix formed by residues 71 - 91 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.8 3.6 - - - -
27B PHE 4.1 8.5 - - - +
28B LYS* 4.2 22.3 - - + -
65B ASN* 4.3 13.9 + - - -
67B ASP* 5.0 1.2 - - - +
69B GLN 3.9 0.8 + - - -
70B VAL* 1.3 74.9 - - - +
72B PHE* 1.3 66.3 + - - +
73B GLN* 3.3 8.8 + - - +
74B GLU* 2.9 46.3 + - - +
75B TYR* 2.9 21.3 + - - +
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 3.6 41.7 - - + -
84A VAL* 3.9 17.5 - - + -
87A ASN* 3.6 46.0 - - + +
13B VAL* 3.9 13.5 - - + -
16B PHE* 3.5 53.8 - + + -
17B HIS* 6.0 0.2 - - + -
27B PHE 4.3 2.7 + - - +
71B ASP* 1.3 76.0 - - - +
73B GLN* 1.3 60.3 + - - +
75B TYR* 3.2 11.7 + + - +
76B ALA* 2.9 26.7 + - + -
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 4.2 17.3 - - + +
71B ASP* 3.3 8.0 + - - +
72B PHE* 1.3 78.5 - - - +
74B GLU* 1.3 62.6 + - + +
76B ALA* 3.2 2.1 + - - +
77B VAL* 3.1 29.4 + - + +
102B 15P 2.2 63.4 - - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.3 29.2 - - - +
63B ASP* 4.0 0.6 - - - -
64B GLU* 3.0 27.7 + - + +
65B ASN* 3.1 13.2 + - - +
69B GLN 3.0 5.0 - - - +
70B VAL* 3.2 10.5 - - + +
71B ASP* 2.9 38.4 + - - +
73B GLN* 1.3 76.3 - - + +
75B TYR* 1.3 57.5 + - - +
77B VAL* 3.5 8.5 + - - +
78B PHE* 3.0 26.2 + - - +
104B CA 2.4 31.2 - - - -
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.0 4.1 - - + +
83A THR* 5.1 0.7 - - + -
12B LEU* 2.8 34.2 + - + -
15B THR* 3.9 8.3 - - - +
16B PHE* 3.5 40.3 + + + -
29B LEU* 4.2 9.6 - - + -
34B MET* 5.2 1.6 - - + -
37B LEU* 4.1 22.7 - - + -
70B VAL* 3.6 10.6 - - + +
71B ASP 2.9 17.3 + - - +
72B PHE* 3.4 19.7 - + - +
74B GLU* 1.3 74.8 - - - +
76B ALA* 1.3 63.0 + - - +
78B PHE* 3.1 15.7 + + - +
79B LEU* 2.9 65.1 + - + +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 3.9 17.5 - - + +
83A THR* 4.0 22.0 + - + -
84A VAL* 3.9 24.7 - - + -
72B PHE* 2.9 20.4 + - + +
73B GLN 3.2 5.1 + - - +
75B TYR* 1.3 77.3 - - - +
77B VAL* 1.3 57.9 + - - +
79B LEU* 3.4 3.7 + - - +
80B ALA* 3.0 28.8 + - - +
102B 15P 5.1 0.7 - - - -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 4.5 5.2 - - + -
62B LEU* 5.8 2.2 - - + -
64B GLU* 6.5 1.1 - - + -
73B GLN* 3.1 16.3 + - + +
74B GLU* 3.7 9.9 - - - +
76B ALA* 1.3 73.5 - - - +
78B PHE* 1.4 67.4 + - - +
80B ALA* 3.2 7.7 + - - +
81B LEU* 2.9 39.6 + - + +
102B 15P 4.0 21.5 - - - -
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B MET* 4.4 17.3 - - + -
37B LEU* 5.0 3.1 - - + -
38B LEU* 3.8 25.4 - - + -
42B LEU* 3.7 24.7 - - + -
58B LEU* 4.0 22.0 - - + -
62B LEU* 3.7 36.7 - - + +
74B GLU 3.0 15.1 + - - +
75B TYR* 3.1 15.7 + + - +
77B VAL* 1.4 76.3 - - - +
79B LEU* 1.3 68.9 + - + +
81B LEU* 3.1 11.0 + - + +
82B ILE* 2.9 44.7 + - + +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.2 18.4 - - + -
9A LEU* 4.2 12.1 - - + -
12A LEU* 5.8 0.9 - - + -
12B LEU* 3.5 32.8 - - + -
42B LEU* 4.4 0.2 - - + -
75B TYR* 2.9 58.3 + - + +
76B ALA* 4.0 4.7 - - - +
78B PHE* 1.3 91.9 - - + +
80B ALA* 1.3 58.1 + - - +
82B ILE* 3.2 27.3 + - + +
83B THR* 2.8 34.7 + - - -
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 6.3 0.2 - - - -
76A ALA* 3.4 34.5 - - + +
79A LEU* 4.5 7.6 - - + -
80A ALA* 4.1 13.7 - - + +
76B ALA 3.0 17.9 + - - +
77B VAL* 3.2 5.1 + - - +
79B LEU* 1.3 76.3 - - - +
81B LEU* 1.3 61.6 + - + +
83B THR* 3.2 7.9 + - - -
84B VAL* 3.1 28.0 + - - +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 4.7 12.6 - - + -
77B VAL* 2.9 35.1 + - + +
78B PHE* 3.4 13.5 - - + +
80B ALA* 1.3 75.3 - - - +
82B ILE* 1.3 62.2 + - + +
84B VAL* 3.3 12.3 + - + +
85B MET* 3.0 29.6 + - - +
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.8 19.5 - - + -
42B LEU* 3.6 24.9 - - + -
45B PHE* 4.0 21.6 - - + -
78B PHE* 2.9 38.0 + - + +
79B LEU* 3.2 38.3 + - + +
81B LEU* 1.3 80.5 - - + +
83B THR* 1.3 51.6 + - - +
85B MET* 3.0 24.3 + - - +
86B SER* 2.6 34.6 + - - -
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Residues in contact with THR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.3 27.0 - - - +
12A LEU* 3.8 13.9 - - + +
13A VAL* 3.6 15.7 - - + -
72A PHE* 3.6 22.4 - - + -
79A LEU* 3.9 18.4 - - + -
79B LEU 2.8 17.2 + - - -
80B ALA 3.7 4.5 - - - -
82B ILE* 1.3 74.2 - - - +
84B VAL* 1.3 57.0 + - - +
86B SER* 3.5 6.9 - - - -
87B ASN* 2.7 33.6 + - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.7 16.5 - - + -
73A GLN* 3.0 40.2 - - - +
76A ALA* 3.4 25.6 - - + -
80B ALA 3.1 18.6 + - - +
81B LEU* 3.4 14.8 - - + +
83B THR* 1.3 75.2 - - - +
85B MET* 1.3 57.3 + - + +
87B ASN* 3.3 1.7 + - - +
88B ASP* 2.9 41.6 + - - +
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Residues in contact with MET 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 4.7 11.4 - - + -
81B LEU* 3.0 15.7 + - - +
82B ILE* 3.2 34.8 - - + +
84B VAL* 1.3 79.4 - - + +
86B SER* 1.3 53.7 + - - +
88B ASP* 3.2 14.2 + - - +
89B PHE* 2.9 51.3 + - + -
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 5.0 7.1 + - - +
10A ALA* 5.0 5.9 + - - +
13A VAL* 3.8 17.6 - - - +
45B PHE* 4.3 19.0 - - - -
82B ILE 2.6 16.8 + - - -
83B THR* 3.5 10.3 - - - -
85B MET* 1.3 69.1 - - - +
87B ASN* 1.3 61.8 + - - +
89B PHE* 3.2 10.3 + - - +
90B PHE* 2.8 30.4 + - - +
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Residues in contact with ASN 87 (chain B).
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* 3.4 15.3 - - + +
17A HIS* 2.5 36.1 + - - -
72A PHE* 3.3 43.1 - - + +
73A GLN* 5.0 2.8 - - - +
83B THR 2.7 20.2 + - - +
84B VAL 3.6 4.5 - - - +
86B SER* 1.3 68.9 - - - +
88B ASP* 1.3 65.0 + - - +
90B PHE* 4.2 0.2 - - - -
91B GLN* 2.8 36.7 + - - +
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 4.2 14.2 + - - -
84B VAL* 2.9 30.9 + - - +
85B MET* 3.2 17.2 + - - +
87B ASN* 1.3 78.3 + - - +
89B PHE* 1.3 64.8 + - + +
91B GLN* 3.1 20.1 - - - +
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B SER 5.7 3.1 - - - -
45B PHE* 4.8 15.9 - + - -
85B MET* 2.9 46.9 + - + -
86B SER* 3.7 8.7 - - - +
88B ASP* 1.3 78.3 - - + +
90B PHE* 1.3 65.0 + - - +
91B GLN 3.5 2.4 + - - +
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Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.4 28.3 - - + -
14A THR* 4.3 23.1 - - + -
17A HIS* 4.4 8.1 - + + -
86B SER* 2.8 18.7 + - - +
87B ASN 3.7 3.4 - - - +
89B PHE* 1.3 79.6 - - - +
91B GLN* 1.3 90.9 + - + +
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A HIS* 3.5 45.0 + - + +
27A PHE* 3.5 23.8 - - + -
87B ASN* 2.8 27.7 + - - +
88B ASP* 3.1 15.7 - - - +
89B PHE 3.4 2.5 - - - +
90B PHE* 1.3 107.6 - - + +
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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
------------------------------------------------------------
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