Contacts of the helix formed by residues 59 - 73 (chain B) in PDB entry 6W6Y
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 ASN 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASN* 2.8 42.4 + - - +
55B LYS* 4.9 0.6 - - - +
57B THR 3.1 1.2 - - - -
58B ASN* 1.3 79.6 - - - +
60B ALA* 1.3 62.6 + - - +
61B MET 3.2 2.9 - - - -
62B GLN* 3.2 17.5 + - - +
63B VAL* 3.1 35.8 + - + +
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Residues in contact with ALA 60 (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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57B THR* 3.2 18.7 + - - +
58B ASN 3.3 2.2 + - - +
59B ASN* 1.3 77.2 - - - +
61B MET* 1.3 61.6 + - - +
63B VAL* 3.5 7.3 + - - +
64B GLU* 3.1 24.6 + - - +
86B HIS* 3.7 26.6 + - + +
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Residues in contact with MET 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 5.7 1.3 - - + -
37B ASN* 4.6 4.0 - - - -
45B HIS* 3.7 22.4 - - + +
50B ALA 4.7 0.7 - - - +
53B LEU* 4.0 20.9 - - + -
54B ASN* 3.4 23.6 - - - +
57B THR* 3.1 25.8 + - + +
59B ASN 3.2 0.2 - - - -
60B ALA* 1.3 75.2 - - - +
62B GLN* 1.3 55.0 + - - +
64B GLU* 3.4 5.1 + - - +
65B SER* 2.8 36.6 + - - +
84B SER 4.9 0.4 - - - +
85B GLY* 5.5 2.2 - - - +
86B HIS* 3.6 20.1 + - + -
88B LEU* 4.9 4.0 - - + -
92B CYS* 3.9 29.4 - - + -
94B HIS* 3.8 20.9 - - + +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU 2.9 23.4 + - - -
44B LYS* 3.8 12.1 - - - +
45B HIS* 2.8 38.6 + - - +
54B ASN* 2.8 14.3 + - - +
59B ASN* 3.2 30.9 + - - +
61B MET* 1.3 73.5 - - - +
63B VAL* 1.3 59.6 + - - +
65B SER* 4.0 0.8 - - - -
66B ASP* 2.9 58.6 + - - +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASN* 3.1 30.1 + - + +
60B ALA* 4.0 6.1 - - - +
62B GLN* 1.3 75.2 - - - +
64B GLU* 1.3 63.7 + - - +
66B ASP* 3.5 9.1 + - - +
67B ASP* 3.3 20.5 + - + +
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA 3.1 17.3 + - - +
61B MET* 3.7 6.9 - - - +
63B VAL* 1.3 79.4 - - - +
65B SER* 1.3 54.7 + - - +
67B ASP* 3.2 9.7 + - + +
68B TYR* 3.0 25.8 + - - +
83B LEU* 3.6 26.4 - - + +
84B SER* 2.8 37.9 + - - +
86B HIS* 2.8 28.1 + - + +
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.6 31.8 - - - +
45B HIS* 2.8 17.9 + - - -
61B MET* 2.8 23.6 + - - +
62B GLN* 3.2 4.9 + - - -
64B GLU* 1.3 73.5 - - - +
66B ASP* 1.3 69.0 + - - +
68B TYR* 3.2 3.1 + - - +
69B ILE* 3.0 29.0 + - - +
83B LEU* 4.1 14.9 - - - +
94B HIS* 4.1 9.0 - - - -
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Residues in contact with ASP 66 (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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42B TYR 5.1 1.4 - - - +
43B LEU 4.6 0.5 - - - +
44B LYS* 2.9 32.6 + - - +
62B GLN* 2.9 40.4 + - - +
63B VAL* 3.7 9.4 - - - +
64B GLU 3.3 0.2 - - - -
65B SER* 1.3 77.9 - - - +
67B ASP* 1.3 56.0 + - - +
69B ILE* 3.2 8.5 + - - +
70B ALA* 2.9 27.9 + - - +
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 3.3 10.2 + - + +
64B GLU* 3.2 12.0 + - - +
65B SER 3.2 0.6 - - - -
66B ASP* 1.3 75.0 - - - +
68B TYR* 1.3 67.1 + - - +
70B ALA* 3.3 11.6 + - - +
71B THR* 3.2 28.1 + - - -
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Residues in contact with TYR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.8 15.5 - - + -
64B GLU 3.0 13.1 + - - +
65B SER 3.5 7.0 - - - +
67B ASP* 1.3 77.9 + - - +
69B ILE* 1.3 63.5 + - + +
71B THR* 3.3 1.9 + - - -
72B ASN* 2.8 67.2 + - + +
73B GLY 3.8 18.2 + - - -
75B LEU* 3.6 23.1 - - + +
80B SER 5.0 0.5 + - - -
81B CYS* 3.7 27.4 - - + +
82B VAL 5.8 1.1 - - - -
83B LEU* 4.0 32.8 - - + -
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Residues in contact with ILE 69 (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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41B VAL 3.8 21.3 - - - +
42B TYR* 3.5 46.2 - - + +
43B LEU* 4.1 7.6 - - + -
65B SER 3.0 18.1 + - - +
66B ASP* 3.6 9.9 - - - +
68B TYR* 1.3 87.3 - - + +
70B ALA* 1.3 60.7 + - - +
73B GLY* 2.9 46.3 + - - +
74B PRO* 3.9 2.7 - - + -
75B LEU 4.7 0.2 - - - +
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Residues in contact with ALA 70 (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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66B ASP 2.9 13.1 + - - +
67B ASP* 3.3 18.6 - - - +
69B ILE* 1.3 78.5 - - - +
71B THR* 1.3 60.5 + - - +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 3.2 19.0 + - - -
68B TYR* 4.6 0.9 - - - -
70B ALA* 1.3 80.6 - - - +
72B ASN* 1.3 79.7 + - - +
73B GLY 3.7 0.4 - - - -
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 2.8 66.0 + - + +
71B THR* 1.3 92.0 - - - +
73B GLY* 1.3 62.1 + - - +
74B PRO 4.7 2.3 - - - +
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Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 3.8 10.4 + - - -
69B ILE* 2.9 34.0 + - - +
70B ALA 5.0 0.2 + - - -
71B THR 3.7 1.0 - - - -
72B ASN* 1.3 80.9 - - - +
74B PRO* 1.3 78.4 - - - +
75B LEU 3.8 0.3 + - - -
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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