Contacts of the helix formed by residues 53 - 71 (chain A) in PDB entry 2B7T
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 THR 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.5 14.8 - - - -
51A GLY 3.0 3.1 + - - +
52A PRO* 1.3 77.6 - - + +
54A LYS* 1.3 62.8 + - - +
55A LYS* 3.7 24.5 + - + +
56A LYS* 3.0 32.9 + - + +
57A ALA* 2.9 23.9 + - - +
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Residues in contact with LYS 54 (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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24A LEU* 3.5 33.4 - - + +
36A PHE* 3.5 33.2 - - + -
38A MET* 3.8 13.5 - - + +
53A THR* 1.3 73.6 + - - +
55A LYS* 1.3 67.7 + - + +
57A ALA* 3.3 4.4 + - - +
58A LYS* 3.0 32.9 + - - +
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Residues in contact with LYS 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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6A PRO* 3.8 25.6 - - + +
53A THR* 3.2 21.2 + - + +
54A LYS* 1.3 85.2 - - + +
56A LYS* 1.3 55.9 + - - +
58A LYS* 3.5 13.5 - - + +
59A LEU* 3.4 23.0 + - - +
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Residues in contact with LYS 56 (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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6A PRO* 5.9 0.2 - - - -
50A SER 5.1 1.6 - - - +
51A GLY* 4.0 11.2 - - - -
52A PRO* 4.0 25.0 - - + +
53A THR* 3.0 25.0 + - + +
55A LYS* 1.3 75.9 - - - +
57A ALA* 1.3 60.4 + - - +
59A LEU* 3.5 19.4 - - + +
60A HIS* 2.9 29.2 + - + +
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Residues in contact with ALA 57 (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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36A PHE* 3.3 29.2 - - + +
37A VAL 4.1 0.9 - - - -
38A MET* 3.7 12.1 - - + +
49A GLY 3.2 17.9 - - - +
50A SER 3.9 0.9 - - - -
51A GLY* 3.5 12.6 - - - +
53A THR 2.9 10.4 + - - +
54A LYS* 3.3 13.0 + - - +
56A LYS* 1.3 74.7 - - - +
58A LYS* 1.3 58.0 + - - +
60A HIS* 3.2 3.3 + - - +
61A ALA* 3.0 25.1 + - - +
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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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5A LEU* 4.4 18.8 - - - +
6A PRO* 5.2 4.7 - - + +
10A LEU* 3.6 30.5 - - + +
22A TYR* 3.7 36.1 + - + -
38A MET* 3.6 36.5 - - + +
54A LYS 3.0 19.6 + - - +
55A LYS* 3.5 19.5 - - + +
57A ALA* 1.3 70.8 - - - +
59A LEU* 1.3 60.7 + - - +
61A ALA* 3.5 2.8 - - - +
62A ALA* 2.9 34.6 + - - +
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Residues in contact with LEU 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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6A PRO* 3.6 26.7 - - + +
8A ASN* 4.7 7.9 - - - +
9A ALA* 3.7 23.8 - - + +
10A LEU* 3.6 16.6 - - + -
55A LYS 3.4 19.8 + - - +
56A LYS* 3.5 27.1 - - + +
57A ALA 3.4 0.6 - - - -
58A LYS* 1.3 75.0 - - - +
60A HIS* 1.3 70.2 + - + +
63A GLU* 2.8 36.9 + - + +
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Residues in contact with HIS 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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49A GLY* 3.8 7.0 - - - -
50A SER* 2.9 40.0 + - - +
56A LYS* 2.9 16.9 + - + +
57A ALA 3.2 9.2 + - - +
59A LEU* 1.3 79.0 - - + +
61A ALA* 1.3 62.4 + - - +
63A GLU* 3.8 13.3 - - - +
64A LYS* 3.1 36.8 + - + -
67A ARG* 5.2 5.3 + - - -
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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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38A MET 3.3 26.5 - - - +
40A VAL* 3.5 15.2 - - + +
47A PHE* 3.4 13.4 - - - +
49A GLY* 3.6 9.8 - - - +
57A ALA 3.0 13.2 + - - +
58A LYS* 3.5 8.3 - - - +
60A HIS* 1.3 77.8 - - - +
62A ALA* 1.3 50.3 + - - +
64A LYS* 3.7 8.9 - - - +
65A ALA* 2.8 33.4 + - - +
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Residues in contact with ALA 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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10A LEU* 4.7 2.7 - - + -
13A LEU* 3.4 42.7 - - + +
20A LEU* 4.4 1.1 - - + -
22A TYR* 4.1 11.9 - - + -
40A VAL* 3.4 16.5 - - + +
58A LYS 2.9 20.4 + - - +
59A LEU* 4.1 1.6 - - - +
61A ALA* 1.3 69.2 - - - +
63A GLU* 1.3 65.5 + - - +
65A ALA* 3.5 2.5 - - - +
66A LEU* 3.1 21.5 + - - +
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Residues in contact with GLU 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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8A ASN* 6.3 0.4 - - - +
9A ALA* 3.9 19.0 - - + +
12A GLN* 3.5 21.5 + - - +
13A LEU* 4.3 2.1 - - - +
59A LEU* 2.8 26.0 + - + +
60A HIS* 3.8 13.4 - - - +
62A ALA* 1.3 72.2 - - - +
64A LYS* 1.3 59.1 + - - +
67A ARG* 2.8 78.9 + - - +
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Residues in contact with LYS 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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47A PHE* 3.9 17.5 - - + -
48A GLU 2.9 45.6 + - - +
49A GLY* 3.7 5.9 - - - -
60A HIS* 3.1 31.1 + - + +
61A ALA 4.1 6.3 - - - -
63A GLU* 1.3 79.7 - - - +
65A ALA* 1.3 58.2 + - - +
67A ARG* 3.7 31.9 - - - +
68A SER* 2.7 40.7 + - - -
73A PRO* 5.6 0.7 - - - +
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Residues in contact with ALA 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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20A LEU* 4.4 0.2 - - + -
40A VAL* 3.8 13.2 - - + -
42A VAL* 4.3 9.6 - - + -
47A PHE* 3.7 36.4 - - + -
61A ALA 2.8 21.7 + - - +
62A ALA* 3.2 7.1 + - - +
64A LYS* 1.3 74.7 - - - +
66A LEU* 1.3 67.4 + - + +
68A SER* 3.9 1.7 - - - -
69A PHE* 3.0 26.3 + - - +
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Residues in contact with LEU 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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12A GLN* 4.5 7.0 - - - +
13A LEU* 3.2 41.1 - - + -
16A ILE* 3.4 36.8 - - + -
17A LYS* 3.7 14.6 - - + -
20A LEU* 3.7 17.7 - - + -
42A VAL* 3.6 20.6 - - + -
62A ALA 3.1 5.0 + - - +
63A GLU 4.3 1.3 - - - +
65A ALA* 1.3 76.5 - - - +
67A ARG* 1.3 58.4 + - - +
69A PHE* 3.3 21.2 + - + +
70A VAL* 2.8 36.3 + - + +
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Residues in contact with ARG 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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12A GLN* 4.4 7.4 - - - +
60A HIS* 5.2 6.7 + - - -
63A GLU* 2.8 60.6 + - - +
64A LYS* 3.7 22.7 - - - +
66A LEU* 1.3 69.8 - - - +
68A SER* 1.3 56.2 + - - +
70A VAL* 3.3 5.2 + - - +
71A GLN* 2.9 43.8 + - + +
72A PHE 3.5 4.4 + - - -
73A PRO* 2.8 50.5 + - - +
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Residues in contact with SER 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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47A PHE* 3.8 23.5 - - - -
64A LYS* 2.7 26.4 + - - -
67A ARG* 1.3 73.4 - - - +
69A PHE* 1.3 59.3 + - - +
71A GLN 3.5 0.7 + - - -
72A PHE* 3.0 27.3 + - - +
73A PRO* 2.7 30.6 + - - -
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Residues in contact with PHE 69 (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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16A ILE* 4.7 6.7 - - + -
17A LYS* 3.6 25.6 - - + -
42A VAL* 5.0 12.8 - - + -
43A ASN* 3.5 23.6 - - + -
45A GLN* 5.7 2.2 - - - -
47A PHE* 4.9 8.2 - + + -
65A ALA 3.0 21.3 + - - +
66A LEU* 3.5 29.4 - - + +
68A SER* 1.3 75.7 - - - +
70A VAL* 1.3 65.2 + - + +
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Residues in contact with VAL 70 (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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16A ILE* 4.8 22.2 - - + -
66A LEU 2.8 24.8 + - - +
67A ARG* 3.9 4.3 - - - +
69A PHE* 1.3 87.8 - - + +
71A GLN* 1.3 62.3 + - + +
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Residues in contact with GLN 71 (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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67A ARG* 2.9 21.7 + - + +
68A SER 3.5 0.8 + - - -
70A VAL* 1.3 85.2 - - + +
72A PHE* 1.3 100.4 + - - +
73A PRO* 4.5 5.1 - - - +
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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