Contacts of the helix formed by residues 56 - 65 (chain E) in PDB entry 6X34
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 ILE 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55E VAL* 1.3 84.5 - - + +
57E LYS* 1.3 66.5 + - - +
58E GLY 3.2 1.9 + - - +
59E PHE* 3.3 7.9 + - + +
60E GLU* 3.3 17.8 + - - +
80E VAL 4.1 10.8 - - - +
81E ALA* 4.2 14.1 - - + -
99E PHE* 6.3 1.8 - - + -
1784F VAL 4.1 9.2 + - - +
1785F ALA* 3.9 22.0 - - + +
1786F ALA* 4.3 9.1 - - - +
1787F LEU 5.5 1.1 - - - +
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Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E VAL 3.6 2.3 + - - -
56E ILE* 1.3 74.5 - - - +
58E GLY* 1.3 57.0 + - - +
60E GLU* 3.4 6.0 + - - +
61E GLU* 2.9 32.4 + - - +
80E VAL* 3.5 22.4 + - + +
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Residues in contact with GLY 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E VAL* 5.5 4.5 - - - +
56E ILE* 3.2 2.0 - - - +
57E LYS* 1.3 79.0 - - - +
59E PHE* 1.3 55.9 + - - +
61E GLU* 3.3 7.7 + - - +
62E GLY* 2.9 26.2 + - - -
74E LEU* 5.5 0.3 - - - +
76E CYS* 4.1 19.3 - - - -
80E VAL* 3.5 30.9 + - - +
81E ALA* 5.2 2.0 - - - -
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Residues in contact with PHE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 5.3 4.0 - - + -
26E TYR* 3.9 42.2 - + + -
46E PHE* 4.6 5.4 - + - -
48E PHE* 3.5 40.4 - + - -
55E VAL* 3.6 31.6 - - + -
56E ILE* 3.3 8.0 + - + +
58E GLY* 1.3 74.9 - - - +
60E GLU* 1.3 58.8 + - - +
62E GLY* 3.3 1.5 + - - -
63E ALA* 2.9 29.9 + - + +
74E LEU* 6.1 2.7 - - + -
76E CYS* 4.4 6.0 - - - -
99E PHE* 4.3 29.3 - + + -
101E VAL* 4.2 26.9 - - + -
1784F VAL* 5.8 3.6 - - + +
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Residues in contact with GLU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E PHE* 5.0 10.3 - - + -
50E ILE* 5.3 21.0 - - + +
55E VAL* 5.2 6.5 - - + +
56E ILE 3.3 11.6 + - - +
57E LYS* 3.8 9.6 - - - +
59E PHE* 1.3 83.1 - - - +
61E GLU* 1.3 56.0 + - - +
63E ALA* 3.3 5.8 + - - +
64E ALA* 2.9 30.5 + - - +
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Residues in contact with GLU 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E VAL* 3.4 36.7 - - + +
4E ILE* 5.2 0.9 - - - +
57E LYS* 2.9 19.4 + - - +
58E GLY* 3.3 8.1 + - - +
60E GLU* 1.3 76.3 - - - +
62E GLY* 1.3 61.0 + - - +
64E ALA* 3.6 11.9 + - + +
65E GLN* 3.7 21.2 + - + +
80E VAL* 5.0 11.4 - - - +
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Residues in contact with GLY 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E VAL* 5.5 4.4 - - - +
4E ILE* 4.8 15.9 - - - +
58E GLY 2.9 15.5 + - - -
59E PHE 3.8 2.5 - - - -
60E GLU 3.2 0.2 - - - -
61E GLU* 1.3 78.1 - - - +
63E ALA* 1.3 60.2 + - - +
65E GLN* 3.5 5.4 + - - +
66E MET* 3.4 18.7 + - - +
74E LEU* 4.4 18.8 - - - +
101E VAL* 4.8 8.7 - - - +
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Residues in contact with ALA 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E PRO* 3.3 17.6 - - + +
48E PHE* 4.0 26.9 - - + -
50E ILE* 6.0 3.6 - - + -
59E PHE* 2.9 21.0 + - + +
60E GLU* 3.9 4.5 - - - +
62E GLY* 1.3 74.8 - - - +
64E ALA* 1.3 64.1 + - - +
66E MET* 3.3 20.1 + - - +
101E VAL* 4.9 13.1 - - + +
103E LEU* 4.0 8.1 - - + +
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E PHE* 4.0 9.5 - - - +
16E PRO* 3.4 27.0 - - - +
50E ILE* 5.4 11.2 - - + +
60E GLU 2.9 17.5 + - - +
61E GLU* 3.8 9.6 - - - +
62E GLY 3.3 0.2 - - - -
63E ALA* 1.3 78.8 - - - +
65E GLN* 1.3 64.8 + - + +
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Residues in contact with GLN 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 4.4 28.2 - - + +
15E PHE* 4.5 19.9 - - - -
61E GLU* 3.7 16.8 + - + +
62E GLY 3.5 8.1 + - - +
63E ALA 3.2 0.6 - - - -
64E ALA* 1.3 81.0 + - + +
66E MET* 1.3 65.2 + - - +
67E SER* 5.4 0.3 - - - -
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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