Contacts of the helix formed by residues 55 - 72 (chain A) in PDB entry 6EXT
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 LYS 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.5 0.5 - - - +
52A VAL* 2.8 45.8 + - + +
53A ASP 4.2 2.2 - - - +
54A ARG* 1.3 83.5 - - + +
56A THR* 1.3 64.8 + - - +
57A SER* 3.2 4.2 + - - -
58A GLU* 3.5 29.3 + - + +
59A PHE* 3.7 9.4 + - - +
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Residues in contact with THR 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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51A LEU* 4.1 18.8 - - + -
53A ASP* 6.0 0.4 - - - -
54A ARG* 3.6 9.9 + - - +
55A LYS* 1.3 81.9 - - - +
57A SER* 1.3 67.1 + - - +
59A PHE* 3.0 2.4 + - - +
60A TYR* 3.0 46.7 + - + -
78A GLU* 5.2 0.3 + - - -
82A ARG* 3.6 31.7 + - - +
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Residues in contact with SER 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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55A LYS* 3.2 1.7 - - - -
56A THR* 1.3 80.7 + - - +
58A GLU* 1.3 63.9 + - - +
60A TYR 3.4 0.2 + - - -
61A ALA* 2.9 27.9 + - - +
78A GLU* 2.6 39.7 + - - +
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Residues in contact with GLU 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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55A LYS* 3.5 27.9 + - + +
56A THR 3.2 0.4 - - - -
57A SER* 1.3 81.4 + - - +
59A PHE* 1.3 63.9 + - - +
61A ALA* 3.8 5.3 - - - +
62A LYS* 3.1 33.9 + - - +
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Residues in contact with PHE 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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44A VAL* 4.0 13.0 - - + -
47A HIS* 3.3 31.6 - - + -
50A GLU* 4.0 9.2 - - + +
51A LEU* 3.7 44.2 - - + -
55A LYS 3.7 4.0 + - - +
56A THR 3.0 7.7 + - - +
58A GLU* 1.3 79.8 - - - +
60A TYR* 1.3 85.6 + + - +
62A LYS* 3.1 11.6 + - + +
63A ILE* 2.9 54.1 + - + +
119A TRP* 3.5 35.7 - + - -
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Residues in contact with TYR 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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51A LEU* 5.0 3.5 - - + +
56A THR* 3.0 48.9 + - + +
57A SER* 5.2 0.4 - - - -
59A PHE* 1.3 95.1 - + - +
61A ALA* 1.3 65.1 + - - +
63A ILE* 4.3 2.7 - - + -
64A ALA* 2.9 25.6 + - - +
78A GLU* 4.0 27.8 - - + +
81A CYS* 3.8 5.2 - - - +
82A ARG* 3.9 41.7 + - + +
85A ILE* 3.7 36.1 - - + +
119A TRP* 3.5 22.5 + + - -
123A LEU* 4.8 6.8 - - - +
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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 SER* 2.9 20.5 + - - +
58A GLU* 3.8 7.0 - - - +
60A TYR* 1.3 77.0 - - - +
62A LYS* 1.3 56.9 + - - +
64A ALA* 3.4 6.0 + - - +
65A ARG* 3.0 29.5 + - - +
78A GLU* 4.1 17.5 - - + +
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Residues in contact with LYS 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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47A HIS* 4.3 11.4 - - + +
50A GLU* 2.9 41.7 + - + +
58A GLU* 3.1 27.6 + - - +
59A PHE* 3.1 9.1 + - + +
61A ALA* 1.3 76.2 - - - +
63A ILE* 1.3 61.9 + - + +
65A ARG* 3.2 6.6 + - - +
66A ILE* 2.9 47.4 + - + +
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Residues in contact with ILE 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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40A LEU* 3.5 29.3 - - + +
43A LEU* 3.8 32.9 - - + +
44A VAL* 4.0 15.7 - - + -
47A HIS* 4.0 17.0 - - + -
59A PHE* 2.9 53.0 + - + +
60A TYR* 3.9 5.4 - - + +
62A LYS* 1.3 79.6 - - + +
64A ALA* 1.3 57.9 + - - +
66A ILE* 3.8 3.0 - - + +
67A GLY* 2.8 28.6 + - - -
81A CYS* 3.9 8.7 - - - -
85A ILE* 4.4 1.1 - - + -
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Residues in contact with ALA 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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40A LEU* 5.9 0.9 - - - -
60A TYR 2.9 17.4 + - - +
61A ALA* 3.6 6.3 - - - +
63A ILE* 1.3 75.7 - - - +
65A ARG* 1.3 64.0 + - - +
67A GLY* 3.9 0.6 - - - -
68A TYR* 3.0 25.1 + - - +
73A LEU* 5.7 2.3 - - - +
74A ALA 5.3 1.9 - - - +
76A HIS* 3.8 28.8 + - + +
77A THR 4.4 3.1 - - - +
81A CYS* 3.8 21.5 - - + -
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Residues in contact with ARG 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 17.8 + - - +
62A LYS* 3.6 6.7 - - - +
64A ALA* 1.3 77.6 - - - +
66A ILE* 1.3 61.5 + - + +
68A TYR* 3.3 5.2 + - - +
69A GLU* 2.8 71.4 + - + +
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Residues in contact with ILE 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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43A LEU* 3.6 27.9 - - + +
47A HIS* 3.8 26.2 - - + +
62A LYS* 2.9 39.8 + - + +
63A ILE* 4.2 3.1 - - - +
65A ARG* 1.3 82.0 - - + +
67A GLY* 1.3 57.7 + - - +
69A GLU* 4.3 9.0 - - - +
70A ASP* 2.9 50.4 + - - +
71A GLU 3.8 0.2 + - - -
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Residues in contact with GLY 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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43A LEU* 3.5 19.8 - - - +
63A ILE 2.8 17.0 + - - -
64A ALA 3.9 0.9 - - - -
66A ILE* 1.3 77.6 - - - +
68A TYR* 1.3 56.3 + - - +
71A GLU* 3.0 24.6 + - - +
73A LEU* 3.1 34.2 + - - +
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Residues in contact with TYR 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 ALA 3.0 18.3 + - - +
65A ARG* 3.6 3.6 - - - +
67A GLY* 1.3 78.6 - - - +
69A GLU* 1.3 84.8 + - + +
70A ASP 3.4 0.2 + - - -
72A GLY* 3.5 14.0 + - - -
73A LEU* 3.2 29.9 - - - +
74A ALA* 4.3 6.5 - - - +
75A ILE* 3.6 39.8 - - + +
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Residues in contact with GLU 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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65A ARG* 2.8 63.9 + - + +
66A ILE* 4.2 6.2 - - - +
68A TYR* 1.3 91.3 - - + +
70A ASP* 1.3 69.4 + - - +
72A GLY 5.2 0.2 + - - -
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Residues in contact with ASP 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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43A LEU* 5.6 1.2 - - + +
66A ILE* 2.9 33.4 + - + +
69A GLU* 1.3 90.4 - - - +
71A GLU* 1.3 74.8 + - + +
72A GLY 3.6 1.3 - - - -
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Residues in contact with GLU 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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36A GLU* 5.8 0.2 - - - +
39A LYS* 3.3 65.5 + - + +
42A ARG* 6.4 0.2 - - - -
43A LEU* 4.1 27.7 - - + +
67A GLY* 3.0 14.4 + - - +
70A ASP* 1.3 91.4 - - + +
72A GLY* 1.3 64.0 + - - +
73A LEU* 3.2 8.2 + - + +
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Residues in contact with GLY 72 (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 GLU* 4.5 5.1 - - - +
67A GLY 3.2 2.0 + - - -
68A TYR* 3.5 12.3 + - - -
69A GLU 5.2 0.2 + - - -
70A ASP 3.6 1.4 - - - -
71A GLU* 1.3 78.8 - - - +
73A LEU* 1.3 67.5 + - - +
74A ALA 3.7 0.2 + - - -
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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