Contacts of the helix formed by residues 54 - 68 (chain B) in PDB entry 6B0Z
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 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B ARG* 2.6 36.8 + - - +
52B THR* 3.2 1.5 - - - -
53B ASN* 1.3 73.5 - - - +
55B GLN* 1.3 63.2 + - - +
56B VAL 3.2 2.7 - - - -
57B THR* 2.6 41.6 + - - +
58B LYS* 3.5 17.8 + - - +
92B TRP* 3.8 29.8 - - + +
93B LYS* 4.3 15.4 + - - +
95B PRO* 5.3 0.3 - - - +
98B THR* 4.3 11.4 + - - +
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 3.5 27.6 - - - +
39A LEU 3.6 19.5 - - - +
40A HIS* 3.3 32.1 - - + +
52B THR 3.1 17.7 + - - +
53B ASN 3.1 3.7 + - - +
54B ASP* 1.3 78.5 - - - +
56B VAL* 1.3 57.8 + - - +
58B LYS* 3.2 31.5 + - - +
59B ASP* 2.7 51.1 + - - +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 4.5 2.4 + - - +
41A SER* 5.8 5.6 - - - +
42B TYR* 4.1 13.6 - - + -
43B ASP 3.6 37.5 - - - +
44B LEU* 3.7 9.2 - - + -
48B ASN* 3.9 12.1 - - - +
49B ARG* 3.8 22.0 - - + -
52B THR* 3.3 24.1 + - + +
54B ASP 4.6 0.4 - - - -
55B GLN* 1.3 78.2 - - - +
57B THR* 1.3 60.1 + - - +
59B ASP* 3.8 7.2 - - - +
60B ALA* 2.9 28.1 + - - +
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Residues in contact with THR 57 (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 LEU* 4.0 12.1 - - + +
49B ARG* 3.4 18.4 - - - +
54B ASP* 2.6 34.5 + - - +
56B VAL* 1.3 79.2 - - - +
58B LYS* 1.3 61.9 + - - +
60B ALA* 3.3 4.4 + - - +
61B ALA* 3.1 21.5 + - - +
95B PRO* 3.7 34.3 - - + +
98B THR* 3.9 20.0 - - + +
99B ILE* 4.4 6.5 - - + +
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Residues in contact with LYS 58 (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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38A ASP* 5.5 4.4 + - - -
53B ASN 4.7 10.3 + - - -
54B ASP* 4.0 19.7 + - - +
55B GLN* 3.2 31.6 + - - +
57B THR* 1.3 76.7 - - - +
59B ASP* 1.3 59.5 + - - +
61B ALA* 3.3 3.3 + - - +
62B GLU* 2.9 28.2 + - - +
98B THR* 4.3 18.6 - - + -
102B ILE* 4.4 17.6 - - + +
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A HIS* 2.7 40.6 + - - +
42A TYR* 4.0 10.1 + - - +
67A HIS* 5.1 0.9 + - - -
42B TYR* 4.0 18.0 + - + -
55B GLN* 2.7 43.2 + - - +
56B VAL* 3.8 7.9 - - - +
57B THR 3.3 0.2 - - - -
58B LYS* 1.3 75.8 - - - +
60B ALA* 1.3 58.9 + - - +
62B GLU* 3.2 20.3 + - - +
63B ALA* 2.9 28.8 + - - +
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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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11B VAL* 4.2 0.5 - - - +
13B MET* 3.8 32.3 - - + -
42B TYR* 3.9 24.3 - - + -
44B LEU* 4.4 5.6 - - + -
56B VAL 2.9 18.2 + - - +
57B THR 3.5 5.6 - - - +
58B LYS 3.2 0.2 - - - -
59B ASP* 1.3 75.1 - - - +
61B ALA* 1.3 62.8 + - - +
63B ALA* 3.0 4.3 + - - +
64B ILE* 3.0 28.7 + - - +
99B ILE* 5.2 0.9 - - + -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B THR 3.1 9.8 + - - +
58B LYS 3.3 7.4 + - - +
60B ALA* 1.3 78.4 - - - +
62B GLU* 1.3 62.6 + - - +
64B ILE* 3.4 11.9 + - - +
65B LYS* 3.2 18.2 + - - +
98B THR* 5.8 0.2 - - + -
99B ILE* 4.0 25.7 - - + +
102B ILE* 3.7 32.2 - - + +
103B LEU* 3.7 12.6 - - + +
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Residues in contact with GLU 62 (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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66A LYS* 3.1 34.8 - - - +
67A HIS* 5.3 2.6 + - - -
58B LYS 2.9 13.8 + - - +
59B ASP* 3.3 24.9 - - - +
60B ALA 3.2 0.2 - - - -
61B ALA* 1.3 77.0 - - - +
63B ALA* 1.3 62.3 + - - +
65B LYS* 3.3 9.5 + - + +
66B LYS* 3.1 23.4 + - + +
102B ILE* 5.0 4.5 - - - +
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Residues in contact with ALA 63 (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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11B VAL* 3.7 12.3 - - + -
40B HIS* 4.9 0.9 - - + -
42B TYR* 3.3 39.7 - - + +
59B ASP 2.9 7.7 + - - +
60B ALA 3.0 8.2 + - - +
62B GLU* 1.3 77.1 - - - +
64B ILE* 1.3 58.0 + - - +
66B LYS* 3.2 6.1 + - - -
67B HIS* 2.9 42.3 + - + +
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Residues in contact with ILE 64 (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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11B VAL* 3.8 22.9 - - + -
13B MET* 3.7 32.1 - - + -
60B ALA 3.0 13.6 + - - +
61B ALA* 3.7 7.4 - - - +
63B ALA* 1.3 75.2 - - - +
65B LYS* 1.3 56.4 + - - +
68B ASN* 2.7 34.2 + - - +
69B VAL 4.5 0.7 - - - -
70B GLY* 4.1 8.3 - - - +
99B ILE* 4.2 9.0 - - + -
103B LEU* 3.7 26.5 - - + -
302B THR* 3.5 14.2 - - + +
303B VAL 4.1 15.0 - - - +
304B GLU* 4.1 15.9 - - + -
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Residues in contact with LYS 65 (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 ALA 3.2 12.1 + - - +
62B GLU* 3.3 12.3 + - + +
64B ILE* 1.3 77.7 - - - +
66B LYS* 1.3 61.6 + - - +
68B ASN* 3.7 13.3 + - - -
102B ILE* 3.8 27.4 + - + +
103B LEU* 3.9 20.1 - - + +
299B ASP* 5.4 2.1 - - - +
302B THR* 4.0 8.6 + - + +
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Residues in contact with LYS 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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62A GLU* 6.0 7.8 - - - -
62B GLU* 3.1 17.5 + - + +
63B ALA* 3.8 6.3 - - - +
64B ILE 3.2 0.2 - - - -
65B LYS* 1.3 79.3 - - - +
67B HIS* 1.3 89.1 + - + +
68B ASN* 3.9 8.0 + - - +
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Residues in contact with HIS 67 (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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55A GLN* 5.6 0.2 - - - -
59A ASP* 4.9 2.8 + - - -
9B SER* 3.1 25.5 + - - +
11B VAL* 4.0 12.8 - - + -
40B HIS* 3.1 41.1 + + - -
63B ALA* 2.9 28.3 + - + +
66B LYS* 1.3 109.4 + - + +
68B ASN* 1.3 69.6 + - - +
69B VAL 3.0 9.1 + - - +
343B ARG* 3.1 20.6 + - - -
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Residues in contact with ASN 68 (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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64B ILE 2.7 22.0 + - - -
65B LYS 3.7 10.5 + - - -
66B LYS 3.9 7.3 + - - +
67B HIS* 1.3 76.8 - - - +
69B VAL* 1.3 60.2 + - - +
299B ASP* 4.5 1.6 + - - -
301B LYS* 3.5 47.1 + - - +
302B THR* 2.9 26.9 + - - -
303B VAL 2.9 26.9 + - - +
342B HIS* 3.8 1.9 - - - -
343B ARG* 5.0 3.6 + - - -
346B LEU* 3.9 12.6 - - + +
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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