Contacts of the helix formed by residues 54 - 68 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ARG* 2.7 34.6 + - - +
52A THR* 3.2 2.2 - - - -
53A ASN* 1.3 72.9 - - - +
55A GLN* 1.3 63.0 + - - +
56A VAL 3.2 2.9 - - - -
57A THR* 2.7 41.7 + - - +
58A LYS* 3.4 19.6 + - - +
92A TRP* 3.9 24.9 - - + +
93A LYS* 4.3 18.1 + - - +
95A PRO* 5.3 0.2 - - - +
98A THR* 4.1 14.9 + - - +
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A THR* 3.1 16.1 + - - +
53A ASN 3.1 5.3 + - - +
54A ASP* 1.3 77.9 - - - +
56A VAL* 1.3 58.4 + - - +
58A LYS* 3.1 29.0 + - - +
59A ASP* 2.8 48.6 + - - +
38B ASP* 3.3 26.4 - - - +
39B LEU 3.5 19.5 - - - +
40B HIS* 3.3 33.7 - - + +
67B HIS* 5.6 0.2 - - - -
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 4.1 14.1 - - + -
43A ASP 3.5 39.3 - - - +
44A LEU* 3.7 11.8 - - + +
48A ASN* 3.9 12.3 - - - +
49A ARG* 3.9 16.6 - - + -
52A THR* 3.4 22.8 + - + +
54A ASP 4.8 0.2 - - - -
55A GLN* 1.3 78.2 - - - +
57A THR* 1.3 60.3 + - - +
59A ASP* 3.8 6.2 - - - +
60A ALA* 2.9 29.1 + - - +
39B LEU 4.5 2.8 + - - +
41B SER 5.7 5.8 - - - +
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.7 11.9 - - + +
49A ARG* 3.3 20.1 - - - +
54A ASP* 2.7 33.2 + - - +
55A GLN 3.1 0.4 - - - -
56A VAL* 1.3 81.5 - - - +
58A LYS* 1.3 61.4 + - - +
60A ALA* 3.4 3.5 + - - +
61A ALA* 3.3 19.8 + - - +
95A PRO* 3.7 34.3 - - + +
98A THR* 3.9 19.5 - - + +
99A ILE* 4.4 7.1 - - + +
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASN 5.1 3.3 + - - -
54A ASP* 3.4 25.8 + - - +
55A GLN* 3.1 30.9 + - - +
57A THR* 1.3 75.5 - - - +
59A ASP* 1.3 64.3 + - - +
61A ALA* 3.2 4.2 + - - +
62A GLU* 3.1 28.2 + - + +
98A THR* 4.2 17.3 - - + -
102A ILE* 4.2 17.1 - - + +
38B ASP* 5.7 3.6 + - - -
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Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 4.1 18.0 + - + -
55A GLN* 2.8 41.4 + - - +
56A VAL* 3.8 7.9 - - - +
58A LYS* 1.3 73.9 - - - +
60A ALA* 1.3 65.5 + - - +
62A GLU* 3.5 8.3 + - - +
63A ALA* 3.0 22.7 + - - +
40B HIS* 2.8 38.0 + - - +
42B TYR* 4.1 11.3 + - - +
67B HIS* 4.9 2.7 + - - -
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.0 0.9 - - + +
13A MET* 3.7 32.5 - - + -
42A TYR* 3.9 24.1 - - + -
44A LEU* 4.5 5.4 - - + -
56A VAL 2.9 17.4 + - - +
57A THR 3.7 5.2 - - - +
59A ASP* 1.3 76.5 - - - +
61A ALA* 1.3 57.9 + - - +
63A ALA* 3.2 3.2 + - - +
64A ILE* 3.0 34.0 + - - +
99A ILE* 5.3 0.9 - - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A THR 3.3 9.8 + - - +
58A LYS 3.2 9.7 + - - +
60A ALA* 1.3 79.6 - - - +
62A GLU* 1.3 62.0 + - - +
64A ILE* 3.2 10.9 + - - +
65A LYS* 3.0 19.4 + - - +
99A ILE* 4.1 21.9 - - + +
102A ILE* 3.6 33.7 - - + -
103A LEU* 3.4 12.8 - - + +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LYS* 3.1 17.9 + - + +
59A ASP* 4.0 7.6 - - - +
61A ALA* 1.3 75.5 - - - +
63A ALA* 1.3 58.7 + - - +
65A LYS* 3.4 23.6 + - - +
66A LYS* 2.9 27.9 + - - +
102A ILE* 3.6 26.4 - - + +
66B LYS* 6.0 7.6 - - - -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.5 17.5 - - + +
40A HIS* 5.0 0.4 - - + -
42A TYR* 3.4 37.0 - - + +
59A ASP 3.0 10.5 + - - +
60A ALA 3.4 9.0 - - - +
61A ALA 3.1 0.2 - - - -
62A GLU* 1.3 75.2 - - - +
64A ILE* 1.3 60.0 + - - +
66A LYS* 3.1 5.6 + - - +
67A HIS* 2.8 35.3 + - + +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.6 20.9 - - + -
13A MET* 3.5 30.3 - - + -
60A ALA 3.0 18.0 + - - +
61A ALA* 3.6 6.3 - - - +
63A ALA* 1.3 74.6 - - - +
65A LYS* 1.3 57.5 + - - +
68A ASN* 2.6 32.2 + - - +
69A VAL 4.5 1.3 - - - +
70A GLY* 4.0 9.6 - - - +
99A ILE* 4.3 7.9 - - + -
103A LEU* 3.6 26.9 - - + -
302A THR* 3.8 13.4 - - + +
303A VAL 3.9 15.0 - - - +
304A GLU* 3.7 18.6 - - + -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 3.0 12.7 + - - +
62A GLU* 3.4 28.7 - - - +
64A ILE* 1.3 77.9 - - - +
66A LYS* 1.3 62.8 + - - +
68A ASN* 3.9 12.1 + - - -
102A ILE* 4.3 23.6 + - + +
103A LEU* 3.8 15.4 - - + +
302A THR* 4.3 7.7 + - - +
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Residues in contact with LYS 66 (chain A).
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 2.9 17.0 + - - +
63A ALA* 3.1 6.7 + - - +
65A LYS* 1.3 79.7 - - - +
67A HIS* 1.3 88.7 + - + +
68A ASN* 4.0 7.6 + - - +
62B GLU* 3.1 29.6 - - - +
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Residues in contact with HIS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A SER* 2.8 31.5 + - - +
11A VAL* 4.0 13.0 - - + -
40A HIS* 3.1 37.0 + + + -
63A ALA* 2.8 27.4 + - + +
66A LYS* 1.3 108.7 + - + +
68A ASN* 1.3 63.5 + - - +
69A VAL 2.9 7.1 + - - +
343A ARG* 2.9 27.0 + - - -
59B ASP* 5.1 1.4 + - - -
62B GLU* 5.3 3.2 + - - -
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE 2.6 21.3 + - - -
65A LYS 3.9 9.5 + - - -
66A LYS 4.0 7.1 + - - +
67A HIS* 1.3 73.7 - - - +
69A VAL* 1.3 61.8 + - - +
299A ASP* 5.1 0.4 + - - -
301A LYS* 3.4 33.7 - - - +
302A THR* 3.0 25.4 + - - +
303A VAL 3.1 24.9 + - - -
342A HIS* 3.7 2.3 - - - -
343A ARG* 5.0 2.9 + - - -
346A LEU* 3.7 17.7 - - + +
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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