Contacts of the helix formed by residues 72 - 82 (chain B) in PDB entry 3EJW
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 LEU 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 4.1 13.9 - - + +
47B GLN* 3.6 30.1 - - + +
48B VAL* 3.7 24.7 - - + -
51B ILE* 3.8 19.3 - - + -
64B VAL* 4.0 21.8 - - + -
66B SER* 3.5 26.9 - - - +
67B VAL* 5.2 0.4 - - + -
68B SER* 4.6 2.1 + - - +
69B PRO 5.4 0.2 - - - -
70B ASP 3.2 0.8 - - - -
71B GLY* 1.3 79.5 - - - +
73B CYS* 1.3 59.6 + - - +
74B PRO 3.5 1.3 - - - -
75B ALA* 3.3 6.2 + - - +
76B LEU* 2.9 41.0 + - + +
93B VAL* 4.3 6.7 - - + -
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Residues in contact with CYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO 3.7 22.4 - - - -
70B ASP* 3.0 16.5 + - + +
72B LEU* 1.3 77.6 - - - +
74B PRO* 1.3 69.2 - - + +
76B LEU* 3.2 1.4 + - - +
77B LYS* 2.8 34.8 + - + +
93B VAL* 4.7 1.8 - - - -
94B ASN* 4.0 8.1 - - - -
97B CYS* 2.0 50.3 - - - -
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Residues in contact with PRO 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.9 27.1 - - + -
36A TYR* 4.2 27.1 - - + +
37A ASP* 3.1 28.8 - - - +
38A GLY 5.0 1.1 - - - +
70B ASP 3.8 7.2 - - - +
71B GLY 4.1 7.0 - - - +
72B LEU 3.8 2.2 - - - -
73B CYS* 1.3 93.9 - - + +
75B ALA* 1.3 56.7 + - - +
77B LYS* 3.4 7.5 + - + +
78B ARG* 3.0 35.9 + - - +
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Residues in contact with ALA 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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48B VAL* 3.9 35.0 - - + -
51B ILE* 4.5 10.9 - - + +
52B ASN* 4.3 8.8 - - - +
71B GLY 5.5 0.2 + - - -
72B LEU 3.3 7.6 + - - +
74B PRO* 1.3 79.0 - - - +
76B LEU* 1.3 58.6 + - - +
78B ARG* 3.3 24.4 + - - +
79B ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 3.7 33.2 - - + -
62B LEU* 4.4 5.4 - - + -
64B VAL* 4.5 10.8 - - + -
72B LEU* 2.9 40.7 + - + +
73B CYS 3.8 2.7 - - - +
75B ALA* 1.3 74.1 - - - +
77B LYS* 1.3 60.8 + - - +
79B ALA* 3.2 4.7 + - - +
80B MET* 2.8 33.9 + - - +
86B VAL* 3.8 26.1 - - + +
93B VAL* 4.0 21.3 - - + -
97B CYS* 3.4 25.1 - - + +
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Residues in contact with LYS 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 CYS* 2.8 23.0 + - + +
74B PRO* 3.8 6.7 - - + +
76B LEU* 1.3 75.4 - - - +
78B ARG* 1.3 58.2 + - - +
80B MET* 3.2 21.3 + - + +
81B GLU* 3.0 34.1 + - - +
96B ASP* 2.9 43.4 + - - +
97B CYS* 3.8 16.8 - - - -
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 2.8 43.6 + - - +
38A GLY 4.6 2.2 + - - -
50A PHE* 3.8 19.2 - - - -
53A ASN* 5.5 8.5 - - - +
48B VAL* 6.0 0.8 - - - +
52B ASN* 4.3 15.4 + - - +
74B PRO* 3.0 13.1 + - - +
75B ALA* 3.6 36.4 - - - +
76B LEU 3.3 0.4 - - - -
77B LYS* 1.3 72.1 - - + +
79B ALA* 1.3 65.5 + - - +
81B GLU* 3.2 37.2 - - - +
82B ARG* 3.3 17.3 + - - +
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Residues in contact with ALA 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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51B ILE* 4.8 1.3 - - + -
55B VAL* 3.7 31.6 - - + -
62B LEU* 4.4 5.8 - - + -
75B ALA 2.9 14.0 + - - +
76B LEU* 3.2 11.6 + - - +
78B ARG* 1.3 77.0 - - - +
80B MET* 1.3 63.2 + - - +
82B ARG* 3.0 17.7 + - - +
84B VAL* 3.2 21.4 + - + +
86B VAL* 4.0 13.9 - - + -
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Residues in contact with MET 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 LEU 2.8 14.7 + - - +
77B LYS* 3.2 16.1 + - + +
79B ALA* 1.3 78.0 - - - +
81B GLU* 1.3 57.8 + - - +
83B GLY* 3.1 18.4 + - - -
84B VAL 3.5 12.4 + - - +
86B VAL* 3.4 25.1 - - + +
96B ASP 3.7 12.8 - - - +
97B CYS* 3.4 30.7 - - - +
98B ARG* 4.1 23.1 - - - +
99B SER* 4.6 3.4 - - - -
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Residues in contact with GLU 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 LYS* 3.0 15.3 + - - +
78B ARG* 3.2 37.6 - - - +
80B MET* 1.3 76.5 - - - +
82B ARG* 1.3 59.4 + - + +
83B GLY 3.3 1.5 + - - -
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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
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55B VAL* 3.5 38.7 + - - +
56B ASN* 4.2 18.5 + - - +
58B GLY* 6.0 1.0 - - - -
78B ARG* 3.3 15.6 + - - +
79B ALA* 3.0 10.6 + - - +
81B GLU* 1.3 79.1 - - + +
83B GLY* 1.3 59.8 + - - +
84B VAL* 3.7 7.4 + - + +
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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