Contacts of the helix formed by residues 73 - 88 (chain B) in PDB entry 4DWN
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 GLY 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B CYS* 3.2 13.8 - - - -
69B LEU 3.6 3.2 + - - -
70B GLN 4.0 3.4 + - - -
71B ARG 3.5 3.4 + - - -
72B SER* 1.3 80.3 - - - +
74B GLU* 1.3 67.2 + - - -
75B ARG 3.3 2.7 - - - -
76B ASP* 3.1 7.0 + - - +
77B CYS* 3.1 18.0 + - - -
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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
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5B THR* 3.4 16.8 + - - +
6B TYR* 2.8 51.5 + - + +
7B CYS* 3.0 17.5 + - - -
73B GLY* 1.3 68.0 - - - -
75B ARG* 1.3 67.3 + - - +
77B CYS 3.8 0.2 - - - -
78B GLN* 2.9 31.5 + - - +
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO* 3.9 26.6 - - + +
41B GLN 3.7 20.2 + - - +
42B ILE* 3.4 24.7 + - + +
73B GLY 3.3 0.8 - - - -
74B GLU* 1.3 78.0 - - - +
76B ASP* 1.3 93.0 + - - +
78B GLN* 3.4 9.4 + - - +
79B GLU* 3.0 35.6 + - + +
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.4 30.0 - - + +
68B HIS* 5.3 1.0 + - - -
69B LEU* 4.0 18.1 - - + +
72B SER* 3.4 41.5 - - - +
73B GLY 3.1 6.3 + - - +
75B ARG* 1.3 114.8 + - - +
77B CYS* 1.3 63.9 + - - +
79B GLU* 3.3 2.6 + - - +
80B PHE* 3.2 21.0 + - - +
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Residues in contact with CYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.7 8.3 - - - +
7B CYS* 2.2 63.3 - - - +
10B LEU* 3.9 19.3 - - + -
69B LEU* 3.4 19.3 - - - -
70B GLN* 3.9 9.4 - - - -
73B GLY 3.1 5.5 + - - -
74B GLU 3.8 2.0 - - - +
76B ASP* 1.3 75.8 - - - +
78B GLN* 1.3 63.9 + - - +
80B PHE* 3.3 10.4 + - - +
81B TYR* 3.2 19.9 - - - -
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Residues in contact with GLN 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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6B TYR* 3.8 42.3 - - + +
74B GLU* 2.9 23.0 + - + +
75B ARG* 3.6 8.5 - - - +
77B CYS* 1.3 77.2 - - - +
79B GLU* 1.3 81.2 + - - +
81B TYR* 3.1 14.7 + - - +
82B ARG* 3.3 9.4 + - + +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 5.8 0.2 - - - +
35B LEU* 3.8 11.9 - - + +
40B PRO* 4.0 26.9 - - + +
42B ILE* 3.7 32.1 - - + -
75B ARG* 3.0 22.7 + - + +
76B ASP 3.3 1.5 + - - +
77B CYS 3.3 0.2 - - - -
78B GLN* 1.3 93.6 + - + +
80B PHE* 1.3 66.0 + - - +
82B ARG* 3.1 30.7 + - - +
83B ALA* 3.1 18.0 + - - +
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Residues in contact with PHE 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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10B LEU* 3.8 19.7 - - + -
17B LEU* 3.7 27.4 - - + -
23B LEU* 5.0 4.7 - - + -
31B ILE* 4.0 29.8 - - + -
35B LEU* 4.0 9.8 - - + +
62B LEU* 5.3 3.4 - - + -
65B LEU* 5.0 5.8 - - + -
66B LEU* 3.6 20.0 - - + -
69B LEU* 3.7 31.0 - - + -
76B ASP 3.2 9.3 + - - +
77B CYS 3.5 10.1 - - - +
78B GLN 3.2 0.4 - - - -
79B GLU* 1.3 75.1 - - - +
81B TYR* 1.3 69.4 + + - +
83B ALA* 3.2 5.3 + - - +
84B LEU* 2.9 51.9 + - + +
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Residues in contact with TYR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.6 46.2 - + + -
9B ARG* 3.0 27.5 + - + +
10B LEU* 3.1 18.9 + - + -
13B ASP* 2.6 32.0 + - + +
77B CYS 3.2 21.5 + - - -
78B GLN 3.1 7.8 + - - +
80B PHE* 1.3 90.0 - + - +
82B ARG* 1.3 66.1 + - - +
84B LEU* 3.8 7.7 - - + +
85B TYR* 2.9 24.6 + - - +
92B HIS* 5.1 9.0 + + + +
95B LEU* 3.5 23.6 - - + -
97B SER* 4.6 2.0 - - - -
98B ARG* 5.7 2.0 - - - -
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 4.1 17.7 - - + +
78B GLN 3.3 6.7 + - - +
79B GLU* 3.1 32.7 + - - +
81B TYR* 1.3 78.4 - - - +
83B ALA* 1.3 61.7 + - - +
85B TYR* 3.2 6.4 + - - +
86B ILE* 3.1 48.2 + - + +
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Residues in contact with ALA 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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31B ILE* 3.8 28.0 - - + +
34B GLN* 3.9 32.1 - - + -
35B LEU* 4.4 5.6 - - + -
79B GLU 3.1 11.5 + - - +
80B PHE 3.4 9.0 - - - +
82B ARG* 1.3 77.2 - - - +
84B LEU* 1.3 58.4 + - - +
87B HIS* 2.9 35.9 + - - +
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Residues in contact with LEU 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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17B LEU* 4.0 19.5 - - + -
23B LEU* 3.9 11.4 - - + -
31B ILE* 3.8 20.1 - - + +
80B PHE* 2.9 36.4 + - + +
81B TYR* 3.8 10.8 - - + +
82B ARG 3.2 0.2 - - - -
83B ALA* 1.3 74.8 - - - +
85B TYR* 1.3 58.1 + - - +
88B ALA* 2.8 62.3 + - + +
91B LEU* 4.3 3.6 - - + -
92B HIS* 4.8 10.8 - - - +
95B LEU* 3.8 31.4 - - + -
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Residues in contact with TYR 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 TYR 2.9 17.3 + - - +
82B ARG* 3.2 7.8 + - - +
84B LEU* 1.3 75.6 - - - +
86B ILE* 1.3 70.6 + - + +
89B GLN* 3.2 60.3 + - - +
92B HIS* 3.5 37.0 + + + +
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Residues in contact with ILE 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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34B GLN* 3.9 28.7 - - - +
82B ARG* 3.1 44.7 + - + +
85B TYR* 1.3 88.2 - - + +
87B HIS* 1.3 89.0 + - + +
88B ALA 3.7 0.2 - - - -
89B GLN* 4.9 2.9 + - - +
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Residues in contact with HIS 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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27B GLN* 3.3 24.1 + - - +
30B ARG* 3.5 62.1 + - + +
31B ILE* 4.2 10.5 - - + -
34B GLN* 3.0 32.1 + - + -
83B ALA 2.9 25.6 + - - +
86B ILE* 1.3 96.9 + - + +
88B ALA* 1.3 59.2 + - - +
89B GLN 3.9 0.7 - - - -
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Residues in contact with ALA 88 (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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23B LEU* 3.7 25.1 - - + -
27B GLN* 3.5 22.4 - - + +
31B ILE* 5.0 1.1 - - + -
84B LEU* 2.8 30.5 + - + +
87B HIS* 1.3 74.6 - - - +
89B GLN* 1.3 64.8 + - - +
90B PRO* 3.2 6.3 - - - -
91B LEU* 3.0 17.4 + - + +
92B HIS* 3.3 7.8 + - - -
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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