Contacts of the helix formed by residues 67 - 80 (chain A) in PDB entry 3EZB
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 GLU 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A GLY* 1.3 70.9 - - - -
68A GLU* 1.3 65.7 + - - +
69A LYS 3.2 0.2 - - - -
70A GLU* 3.9 19.5 - - + +
71A ALA* 3.2 24.2 + - + +
317B ARG* 4.3 14.2 + - - +
321B GLN* 5.1 4.9 + - - -
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Residues in contact with GLU 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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65A PHE 5.9 1.3 - - - +
66A GLY* 3.1 2.6 - - - -
67A GLU* 1.3 79.4 - - - +
69A LYS* 1.3 69.4 + - + +
72A ILE* 3.8 10.3 - - + +
315B HIS* 4.5 7.4 + - - -
317B ARG* 2.4 67.3 + - - +
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Residues in contact with LYS 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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61A ALA* 4.1 13.0 - - + -
65A PHE* 3.5 41.3 - - + -
66A GLY 3.4 3.0 + - - +
67A GLU 3.2 0.2 - - - -
68A GLU* 1.3 85.5 - - + +
70A GLU* 1.3 66.1 + - - +
71A ALA 3.3 0.9 - - - -
72A ILE* 3.4 28.1 + - + +
73A PHE* 3.2 20.2 - - + -
165A PRO 5.7 1.6 - - - +
168A THR* 4.1 7.6 + - - +
169A ALA* 4.9 7.2 - - + -
189A HIS* 3.8 24.0 - - - +
193A MET* 3.2 37.2 - - - +
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Residues in contact with GLU 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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58A LYS* 3.7 38.3 + - + +
59A THR* 5.6 2.4 - - - -
61A ALA* 4.3 8.2 - - - +
62A GLY* 4.0 16.1 - - - -
66A GLY 3.2 15.2 + - - +
67A GLU* 3.3 21.3 + - + +
69A LYS* 1.3 79.5 - - - +
71A ALA* 1.3 62.9 + - - +
73A PHE* 3.2 15.3 + - - +
74A GLU* 3.4 10.3 + - - +
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Residues in contact with ALA 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 GLU* 3.2 11.1 + - + +
70A GLU* 1.3 77.6 - - - +
72A ILE* 1.3 67.0 + - - +
74A GLU* 3.0 16.2 + - - +
75A GLY 3.0 18.7 + - - -
317B ARG* 3.1 36.6 - - - +
320B ALA* 3.4 8.0 - - + +
321B GLN* 4.6 11.9 - - + -
324B LYS* 5.7 2.2 - - - +
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Residues in contact with ILE 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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68A GLU* 3.8 15.9 - - + +
69A LYS* 3.4 28.4 + - + +
70A GLU 3.2 1.0 - - - -
71A ALA* 1.3 77.7 - - - +
73A PHE* 1.3 67.2 + - + +
75A GLY* 3.2 2.6 + - - -
76A HIS* 3.2 44.8 + - + +
129A ASP* 6.1 0.2 - - - +
165A PRO* 5.5 10.1 - - + -
189A HIS* 5.1 10.5 - - + -
315B HIS* 5.0 7.4 - - + -
316B THR* 4.2 12.3 - - + +
317B ARG* 3.8 34.5 - - + +
320B ALA* 4.9 2.0 - - - -
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Residues in contact with PHE 73 (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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54A LEU* 4.7 11.0 - - + -
57A ILE* 3.2 38.8 - - + -
58A LYS* 3.9 26.2 - - + -
61A ALA* 3.5 16.6 - - + -
69A LYS* 3.2 22.7 - - + -
70A GLU 3.2 7.9 + - - +
71A ALA 3.2 0.2 - - - -
72A ILE* 1.3 82.3 - - + +
74A GLU* 1.3 58.9 + - - +
76A HIS* 3.1 12.8 + - + +
77A ILE* 2.7 37.4 + - + +
165A PRO 5.3 0.4 - - - -
166A SER* 3.8 29.8 - - - -
169A ALA* 3.4 30.3 - - + -
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Residues in contact with GLU 74 (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* 4.9 10.9 - - + +
70A GLU 3.4 5.7 + - - +
71A ALA* 3.0 18.1 + - - +
73A PHE* 1.3 79.7 - - - +
75A GLY* 1.3 54.5 + - - +
77A ILE* 4.2 9.4 - - + +
78A MET* 2.6 48.6 + - + +
320B ALA* 5.1 2.2 - - + -
324B LYS* 2.9 48.9 + - + +
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Residues in contact with GLY 75 (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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71A ALA 3.0 11.1 + - - -
72A ILE 3.2 2.7 + - - -
73A PHE 3.2 0.2 - - - -
74A GLU* 1.3 76.9 - - - +
76A HIS* 1.3 60.0 + - - +
78A MET* 4.0 7.1 - - - +
79A LEU* 3.0 30.5 + - - +
316B THR* 5.6 2.7 - - - -
320B ALA* 3.3 27.7 - - - +
347B LEU* 4.2 9.7 - - - +
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Residues in contact with HIS 76 (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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54A LEU* 6.0 4.9 - - + -
72A ILE* 3.2 32.5 + - + +
73A PHE* 3.1 15.2 + - + +
75A GLY* 1.3 77.3 - - - +
77A ILE* 1.3 60.8 + - + +
79A LEU* 3.8 3.1 - - + +
80A LEU* 2.9 30.2 + - - +
129A ASP* 3.6 36.7 - - + +
130A VAL* 5.2 4.9 - - + +
133A ILE* 3.6 35.2 - - + +
165A PRO* 5.8 4.7 - - + -
166A SER* 4.9 12.1 + - - -
316B THR* 3.8 14.9 - - + +
347B LEU* 5.3 7.4 - - + -
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Residues in contact with ILE 77 (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 SER 6.1 0.2 - - - +
54A LEU* 3.9 43.1 - - + +
55A GLU* 3.5 35.9 - - + +
58A LYS* 4.5 9.9 - - + -
73A PHE* 2.7 32.5 + - + +
74A GLU* 3.7 5.8 - - + +
76A HIS* 1.3 74.8 - - + +
78A MET* 1.3 64.7 + - - +
80A LEU* 3.1 7.5 + - + +
81A GLU* 2.9 47.2 + - + +
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Residues in contact with MET 78 (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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74A GLU* 2.6 29.0 + - + +
75A GLY* 4.0 4.0 - - - +
77A ILE* 1.3 75.2 - - - +
79A LEU* 1.3 62.8 + - - +
81A GLU* 3.3 9.9 + - - +
82A ASP* 3.2 18.0 + - - +
320B ALA* 3.5 17.9 - - - +
323B VAL* 3.9 12.8 - - + -
324B LYS* 3.4 47.6 - - + +
327B LYS* 3.7 32.0 - - + -
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Residues in contact with LEU 79 (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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75A GLY 3.0 20.1 + - - +
76A HIS* 3.8 4.0 - - + +
78A MET* 1.3 77.1 - - - +
80A LEU* 1.3 63.8 + - - +
82A ASP* 3.0 19.1 + - + +
85A LEU* 2.9 18.0 - - - +
130A VAL* 4.3 15.7 - - + -
133A ILE* 5.0 9.9 - - + -
327B LYS* 6.1 2.2 - - - +
347B LEU* 3.6 44.6 - - + +
348B PHE* 3.0 59.5 - - + +
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Residues in contact with LEU 80 (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 PHE* 6.5 1.3 - - + -
47A ARG* 3.4 25.7 + - + +
50A ALA* 5.3 8.1 - - + -
51A SER* 5.8 1.8 - - - +
54A LEU* 3.4 32.3 - - + -
76A HIS 2.9 19.2 + - - +
77A ILE* 3.1 6.9 + - + +
79A LEU* 1.3 80.2 - - - +
81A GLU* 1.3 56.9 + - + +
82A ASP 3.2 4.0 + - - +
85A LEU* 3.3 25.1 - - + +
108A ILE* 5.0 7.2 - - + -
133A ILE* 4.1 26.2 - - + +
137A LEU* 5.0 21.1 - - + -
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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