Contacts of the helix formed by residues 70 - 87 (chain B) in PDB entry 3URZ
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 GLU 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ASN* 5.3 8.1 - - - +
68B ASN 4.7 6.8 - - - +
69B SER* 1.3 77.4 - - - +
71B ILE* 1.3 62.0 - - - +
72B SER 3.4 0.3 + - - -
73B SER* 3.7 15.9 + - - -
74B LYS* 4.3 9.5 + - - +
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Residues in contact with ILE 71 (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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34B ILE* 4.2 35.0 - - + -
39B ASN* 3.5 38.7 - - + +
42B ALA* 4.4 4.5 - - + -
43B VAL* 3.4 33.4 - - + -
65B VAL* 4.7 7.6 - - + -
69B SER* 3.1 17.7 - - - +
70B GLU* 1.3 78.6 - - - +
72B SER* 1.3 68.4 + - - +
74B LYS* 2.9 22.9 + - + +
75B LEU* 3.1 25.0 + - + +
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Residues in contact with SER 72 (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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61B TYR* 3.6 13.3 + - - -
65B VAL* 4.0 13.2 - - - -
66B ASP 3.5 16.4 - - - -
67B LYS* 3.5 21.9 + - - +
69B SER 3.3 16.4 + - - -
71B ILE* 1.3 79.2 - - - +
73B SER* 1.3 57.5 + - - +
75B LEU* 3.4 2.5 + - - +
76B ALA* 3.0 28.9 + - - +
102B LYS* 3.0 17.8 + - - -
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER 5.0 1.9 + - - -
70B GLU* 3.7 10.2 + - - -
71B ILE 3.1 0.8 + - - -
72B SER* 1.3 75.2 - - - +
74B LYS* 1.3 60.8 + - - +
77B THR* 2.7 35.0 + - - -
99B LEU* 3.3 16.4 - - - +
102B LYS* 3.5 29.5 - - - +
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Residues in contact with LYS 74 (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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39B ASN* 5.8 4.3 - - + -
43B VAL* 3.9 30.7 - - + -
70B GLU 4.6 9.0 - - - +
71B ILE* 2.9 17.7 + - + +
73B SER* 1.3 78.3 - - - +
75B LEU* 1.3 62.3 + - - +
77B THR* 3.4 6.9 + - - -
78B GLU* 3.2 28.0 + - - +
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Residues in contact with LEU 75 (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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30B VAL* 4.9 2.0 - - + -
34B ILE* 4.6 9.2 - - + -
42B ALA 4.6 2.2 - - - +
43B VAL* 4.3 16.6 - - + +
46B PHE* 3.4 62.3 - - + -
60B TYR* 4.8 1.8 - - + -
61B TYR* 4.2 7.2 - - + -
65B VAL* 3.6 36.6 - - + -
71B ILE* 3.1 31.7 + - + +
72B SER 3.7 5.8 - - - +
74B LYS* 1.3 75.2 - - - +
76B ALA* 1.3 64.2 + - - +
78B GLU 3.3 1.6 + - - -
79B LEU* 3.2 19.2 + - - +
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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
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61B TYR* 3.8 24.6 - - + +
72B SER 3.0 17.4 + - - +
73B SER* 3.8 5.6 - - - +
75B LEU* 1.3 76.0 - - - +
77B THR* 1.3 57.3 + - - +
79B LEU* 3.3 4.4 + - - +
80B ALA* 3.0 27.7 + - - +
95B PHE* 3.8 20.1 - - + +
98B GLU* 5.0 2.9 - - + -
99B LEU* 3.9 20.4 - - + -
102B LYS* 4.6 2.2 - - - +
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Residues in contact with THR 77 (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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73B SER 2.7 22.7 + - - -
74B LYS* 3.6 8.1 - - - -
75B LEU 3.2 0.4 - - - -
76B ALA* 1.3 74.3 - - - +
78B GLU* 1.3 66.7 + - - +
80B ALA* 3.5 2.4 + - - +
81B LEU* 3.1 30.0 + - + +
96B TYR* 5.1 8.2 + - + -
99B LEU* 3.5 23.4 - - + +
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Residues in contact with GLU 78 (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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43B VAL* 3.6 15.8 - - + +
46B PHE* 4.1 10.3 - - + -
47B ARG* 2.9 52.3 + - + +
50B ILE* 3.5 24.5 - - + +
74B LYS 3.2 15.2 + - - +
75B LEU 3.3 7.4 + - - +
77B THR* 1.3 80.9 - - - +
79B LEU* 1.3 60.4 + - - +
81B LEU* 3.6 16.5 + - - +
82B ALA* 3.2 18.5 + - - +
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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
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46B PHE* 3.9 13.9 - - + -
50B ILE* 4.0 15.9 - - + -
54B ILE* 4.0 25.8 - - + -
57B THR* 4.0 2.2 - - + -
58B GLU* 4.0 21.5 - - - +
61B TYR* 3.8 25.4 - - + -
75B LEU 3.2 13.3 + - - +
76B ALA 3.7 7.0 - - - +
77B THR 3.3 0.2 - - - -
78B GLU* 1.3 71.7 - - - +
80B ALA* 1.3 66.3 + - - +
82B ALA* 3.3 2.0 + - - +
83B TYR* 3.0 36.0 + - + -
95B PHE* 3.6 37.7 - - + -
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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
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76B ALA 3.0 16.5 + - - +
77B THR* 3.8 4.7 - - - +
79B LEU* 1.3 75.4 - - - +
81B LEU* 1.3 62.5 + - - +
83B TYR* 3.5 0.6 + - - -
84B LYS* 3.1 23.4 + - - +
92B ALA* 3.8 12.6 - - - +
95B PHE* 3.7 20.3 - - + +
96B TYR* 3.6 41.8 - - + +
99B LEU* 4.7 0.2 - - + -
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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
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77B THR* 3.1 22.2 + - + +
78B GLU* 3.8 18.6 - - - +
80B ALA* 1.3 77.6 - - - +
82B ALA* 1.3 60.9 + - - +
84B LYS* 3.4 31.8 + - - +
85B LYS* 3.1 53.9 + - + +
96B TYR* 3.9 9.8 + - - +
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Residues in contact with ALA 82 (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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50B ILE* 3.3 35.2 - - + -
54B ILE* 3.6 10.5 - - + -
78B GLU 3.2 15.2 + - - +
79B LEU 3.3 1.5 + - - +
81B LEU* 1.3 75.2 - - - +
83B TYR* 1.3 65.0 + - - +
85B LYS* 3.4 11.2 + - - +
86B ASN* 3.1 29.3 + - - +
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Residues in contact with TYR 83 (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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54B ILE* 3.5 35.7 + - + +
55B ASP* 4.2 3.6 + - - -
58B GLU* 2.4 37.6 + - - +
79B LEU* 3.0 35.1 + - + +
82B ALA* 1.3 73.2 - - - +
84B LYS* 1.3 63.2 + - - +
86B ASN* 3.3 3.9 + - - +
87B ARG 3.1 3.5 + - - -
88B ASN* 2.9 51.1 + - + +
91B LYS* 3.4 22.4 - - + -
92B ALA* 3.6 20.9 - - - +
95B PHE* 3.9 21.8 - + - -
300B PG4 3.9 24.2 + - - -
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Residues in contact with LYS 84 (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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80B ALA 3.1 13.8 + - - +
81B LEU* 3.5 26.3 - - - +
82B ALA 3.3 0.2 - - - -
83B TYR* 1.3 75.0 - - - +
85B LYS* 1.3 65.1 + - + +
87B ARG* 3.1 16.8 + - - +
89B TYR* 4.1 11.0 - - + -
92B ALA* 3.8 7.3 - - + +
96B TYR* 3.5 23.4 + - + +
112B ALA* 6.2 0.6 - - - +
115B GLU* 4.8 10.2 + - - +
116B MSE 3.7 39.0 - - + -
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Residues in contact with LYS 85 (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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81B LEU* 3.1 59.7 + - + +
82B ALA* 3.4 10.6 + - - +
84B LYS* 1.3 79.1 - - + +
86B ASN* 1.3 64.4 + - - +
87B ARG* 3.2 17.5 + - - +
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Residues in contact with ASN 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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54B ILE* 3.8 18.8 - - - +
82B ALA* 3.1 15.7 + - - +
83B TYR* 3.6 9.6 - - - +
84B LYS 3.2 0.2 - - - -
85B LYS* 1.3 78.0 - - - +
87B ARG* 1.3 69.5 + - - +
88B ASN 4.2 1.3 - - - +
300B PG4 3.6 48.3 + - - +
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Residues in contact with ARG 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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83B TYR 3.1 0.2 + - - -
84B LYS 3.1 13.9 + - - +
85B LYS 4.0 13.4 + - - +
86B ASN* 1.3 81.1 + - - +
88B ASN* 1.3 59.5 + - - +
89B TYR* 3.3 46.8 + - + +
300B PG4 5.2 1.6 - - - -
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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
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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