Contacts of the helix formed by residues 62 - 75 (chain D) in PDB entry 6BZE
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 ARG 62 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ARG* 5.8 7.4 - - - +
50C GLU* 3.5 46.0 + - + +
53C GLU* 4.5 4.3 - - - +
28D LEU* 3.4 33.0 + - - +
29D CYS* 5.2 11.5 - - - +
60D SER* 3.1 1.5 - - - +
61D SER* 1.3 81.3 - - - +
63D LYS* 1.3 60.0 + - - +
64D ARG 3.4 0.2 - - - -
65D ALA* 3.1 4.0 - - - +
66D GLY* 2.8 27.9 + - - -
36G ARG 4.7 0.6 + - - -
37G HIS 2.5 30.7 + - - -
38G PHE* 4.5 7.9 - - - +
41G LEU* 4.7 20.5 - - - +
88G ARG* 5.3 7.1 - - - +
90G LYS* 5.2 3.0 - - - +
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Residues in contact with LYS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLU* 2.8 25.1 + - - -
54C GLU* 4.0 4.5 - - - +
58D ARG 4.6 3.4 - - - +
59D THR* 3.5 15.7 - - + -
60D SER* 3.6 17.9 - - - +
62D ARG* 1.3 74.1 - - - +
64D ARG* 1.3 54.7 + - - +
66D GLY* 2.9 4.3 + - - -
67D LYS* 2.4 46.3 + - + +
36G ARG* 2.4 54.9 + - - +
40G HIS* 6.2 1.4 - - - +
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Residues in contact with ARG 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 6.2 0.8 - - - +
35D GLU* 3.1 64.4 + - + +
36D ARG* 3.8 15.2 - - - +
40D HIS* 4.7 10.9 + - + -
55D ILE* 3.4 13.0 - - + -
56D SER* 3.4 39.6 + - - +
59D THR* 3.2 22.6 + - - +
61D SER* 4.2 14.7 - - - +
63D LYS* 1.3 80.3 - - - +
65D ALA* 1.3 54.5 + - - +
67D LYS* 3.0 16.3 - - - +
68D LEU* 2.6 36.6 + - + +
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU* 3.4 18.8 - - + +
32D ILE* 3.5 20.9 - - + -
35D GLU* 2.9 15.1 + - - +
61D SER 3.0 22.7 - - - +
62D ARG* 3.1 10.9 + - - +
64D ARG* 1.3 80.9 - - - +
66D GLY* 1.3 61.6 + - - +
68D LEU* 3.9 0.3 - - - +
69D LEU* 3.1 28.6 + - - +
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Residues in contact with GLY 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ARG* 3.4 21.2 + - - -
28D LEU* 3.4 17.0 - - - +
62D ARG 2.8 16.0 + - - -
63D LYS* 3.2 3.4 - - - -
65D ALA* 1.3 70.1 - - - +
67D LYS* 1.3 68.1 + - - +
69D LEU* 3.5 1.4 + - - +
70D ASP* 3.0 22.1 + - - +
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D GLU* 4.9 1.8 - - - -
55D ILE* 2.3 71.1 + - + +
58D ARG 4.8 2.5 - - - -
59D THR* 2.8 24.5 - - - +
63D LYS* 2.4 37.4 + - + +
64D ARG* 3.0 14.0 + - - +
66D GLY* 1.3 67.5 - - - +
68D LEU* 1.3 65.4 + - - +
70D ASP* 2.8 17.6 + - - +
71D TYR* 3.0 28.1 + - + +
36H ARG* 6.2 0.4 - - - +
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ILE* 5.4 1.6 - - + -
35D GLU* 3.7 31.2 - - + +
39D ASP* 4.0 28.0 - - + +
40D HIS* 5.2 14.8 - - + +
47D LEU* 5.5 13.7 - - + +
55D ILE* 4.8 6.9 - - + +
64D ARG* 2.6 23.9 + - + +
65D ALA 3.9 2.9 - - - +
67D LYS* 1.3 72.0 - - - +
69D LEU* 1.3 80.5 + - + +
71D TYR* 3.6 12.3 + - - +
72D LEU* 3.5 30.1 - - + +
81D THR* 5.3 7.6 - - + +
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 3.7 38.3 - - + +
24D LEU* 4.9 9.9 - - + +
25D ARG* 5.0 12.3 - - - +
27D TYR 4.8 5.4 - - - +
28D LEU* 3.7 17.5 - - + -
32D ILE* 3.8 31.2 - - + -
65D ALA 3.1 23.7 + - - +
66D GLY* 3.9 4.3 - - - +
67D LYS 3.1 0.8 - - - -
68D LEU* 1.3 96.1 - - + +
70D ASP* 1.3 66.1 + - - +
72D LEU* 3.1 25.5 + - + +
73D GLN* 5.6 0.2 - - - -
81D THR* 6.5 0.4 - - + -
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Residues in contact with ASP 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ARG* 4.6 8.8 + - - +
66D GLY 3.0 14.1 + - - +
67D LYS* 2.8 12.9 + - - +
69D LEU* 1.3 78.2 - - - +
71D TYR* 1.3 68.5 + - + +
72D LEU 3.2 1.0 + - - -
73D GLN* 3.5 27.8 + - - +
74D GLU* 4.2 8.3 + - - +
44G LYS* 3.8 11.3 + - - -
49G ARG* 3.1 39.5 + - - -
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Residues in contact with TYR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D LEU* 6.3 1.8 - - + -
48D SER* 4.8 12.3 - - - -
51D ASP* 3.2 19.4 + - + -
55D ILE* 3.5 27.9 - - + +
67D LYS* 3.0 35.9 + - + +
68D LEU* 3.9 9.0 - - - +
69D LEU 3.2 0.6 - - - -
70D ASP* 1.3 83.4 - - + +
72D LEU* 1.3 63.8 + - + +
73D GLN 3.4 0.2 - - - -
74D GLU* 3.0 42.5 - - - +
75D ASN* 3.9 2.1 + - - +
31H LYS* 5.1 2.1 + - - -
33H ILE* 3.3 25.7 - - + +
36H ARG* 2.7 30.0 + - - -
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 4.7 8.7 - - + -
43D ALA* 6.4 0.4 - - + -
47D LEU* 4.8 17.3 - - + -
68D LEU* 3.5 28.0 - - + +
69D LEU* 3.1 14.4 + - + +
71D TYR* 1.3 80.5 - - + +
73D GLN* 1.3 67.0 + - - +
74D GLU 2.9 2.2 - - - -
75D ASN* 2.9 50.0 + - - +
78D GLY* 5.0 5.6 - - - -
81D THR* 3.4 25.8 - - - +
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Residues in contact with GLN 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D THR* 4.7 3.5 + - - +
15D GLU* 5.5 0.7 - - - +
17D LYS* 6.5 0.2 - - - -
18D LYS* 3.6 53.0 + - + +
21D LEU* 3.5 26.9 - - + +
22D GLU* 2.1 41.4 + - - +
25D ARG* 5.1 2.4 - - - +
69D LEU 4.1 1.8 - - - +
70D ASP* 3.7 27.5 - - - +
71D TYR 3.4 0.2 - - - -
72D LEU* 1.3 73.2 - - - +
74D GLU* 1.3 70.9 + - + +
75D ASN 3.7 3.9 - - - +
44G LYS* 4.8 4.5 + - - +
49G ARG* 5.4 2.4 + - - -
30H GLU* 5.0 2.0 - - - +
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Residues in contact with GLU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D THR* 4.8 0.9 + - - -
70D ASP* 4.4 7.2 - - - +
71D TYR* 3.0 31.0 - - - +
73D GLN* 1.3 82.9 - - + +
75D ASN* 1.3 65.1 + - - +
29H CYS 3.4 16.5 - - - +
30H GLU* 3.3 21.5 - - - +
31H LYS* 3.9 29.4 + - - +
33H ILE* 4.3 23.3 + - - +
94H PHE* 2.9 30.6 - - + -
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Residues in contact with ASN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D THR* 4.0 3.6 + - - +
17D LYS* 6.0 0.2 - - - +
46D ILE* 6.3 2.5 - - + -
71D TYR 3.9 1.0 + - - +
72D LEU* 2.9 58.8 + - - +
73D GLN 3.7 4.0 - - - +
74D GLU* 1.3 81.6 - - - +
76D PRO* 1.3 71.6 - - + +
77D LYS* 4.6 8.1 - - + +
78D GLY* 2.8 30.4 + - - +
80D ASP* 5.5 3.0 + - - -
31H LYS* 4.7 9.4 - - - +
93H ASN* 5.7 0.7 - - - +
94H PHE* 3.9 5.4 - - + -
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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