Contacts of the helix formed by residues 101 - 109 (chain A) in PDB entry 5X6E
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 5.2 1.8 - - + -
38A CYS* 4.7 0.7 - - - +
97A ILE* 3.0 35.3 - - + +
98A LYS* 2.4 32.2 - - + +
99A ILE 3.1 4.3 - - - +
100A ASN* 1.3 77.5 - - + +
102A LEU* 1.3 107.0 + - - +
103A LYS* 3.5 1.8 + - - +
104A GLU* 3.4 19.7 - - - +
105A LEU* 3.1 32.6 - - + +
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Residues in contact with LEU 102 (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 PHE* 6.4 0.9 - - + -
38A CYS* 3.8 35.9 - - + -
70A MET* 4.0 18.6 - - + -
74A ILE* 4.6 13.7 - - + -
97A ILE* 5.9 2.0 - - + -
98A LYS 4.9 0.2 - - - +
99A ILE* 3.3 15.0 + - + +
100A ASN 3.5 0.2 - - - -
101A GLU* 1.3 98.7 + - - +
103A LYS* 1.3 75.2 + - - +
105A LEU* 2.8 33.2 + - + +
106A LEU* 3.7 31.9 + - + -
116A VAL* 6.1 1.6 - - + -
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Residues in contact with LYS 103 (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 ILE* 2.4 48.6 + - + +
75A ASP* 3.4 22.7 - - + +
77A GLU* 4.5 8.5 - - - +
99A ILE* 4.3 12.1 + - - +
100A ASN 5.0 6.5 - - - +
101A GLU 4.8 0.7 - - - +
102A LEU* 1.3 79.4 - - - +
104A GLU* 1.3 53.6 - - + +
106A LEU* 3.5 10.1 - - - +
107A SER* 2.7 38.1 + - - -
114B PHE* 3.8 35.7 - - + -
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Residues in contact with GLU 104 (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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101A GLU* 3.4 19.5 - - - +
102A LEU 2.9 1.2 + - - -
103A LYS* 1.3 77.7 - - + +
105A LEU* 1.3 66.7 + - + +
107A SER* 3.5 10.3 - - - -
108A LYS* 2.6 36.8 + - + +
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Residues in contact with LEU 105 (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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11A TYR* 2.3 49.1 + - + -
12A LEU* 6.3 2.2 - - + -
15A ASN* 5.7 3.1 - - + +
17A ILE* 4.2 20.9 - - + -
97A ILE* 4.8 3.6 - - + -
101A GLU* 3.1 58.1 - - + +
102A LEU* 2.8 22.5 + - + +
104A GLU* 1.3 87.3 - - + +
106A LEU* 1.3 58.4 + - + +
108A LYS* 3.2 7.5 + - - +
109A ASN 3.5 0.9 + - - -
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Residues in contact with LEU 106 (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 PHE* 5.3 8.3 - - + -
11A TYR* 4.1 7.2 - - + -
74A ILE* 5.2 6.7 - - + -
102A LEU* 3.7 35.2 - - + +
103A LYS* 3.5 17.7 - - - +
105A LEU* 1.3 72.0 - - + +
107A SER* 1.3 63.6 + - - +
108A LYS 3.0 1.1 - - - -
109A ASN 2.6 26.6 - - - +
110A LEU* 3.3 1.6 - - - +
112A HIS* 5.1 1.3 - - + -
113A PHE* 2.9 63.4 - - + +
116A VAL* 3.8 35.0 - - + -
114B PHE* 5.0 2.5 - - + -
117B PHE* 6.3 1.3 - - + -
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LYS 2.7 27.1 + - - -
104A GLU* 3.2 12.5 + - - -
106A LEU* 1.3 73.0 - - - +
108A LYS* 1.3 59.2 + - - +
110A LEU* 4.0 4.9 - - - +
113A PHE* 4.2 2.9 - - - -
110B LEU* 3.2 35.6 - - - +
114B PHE* 4.5 9.4 - - - -
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Residues in contact with LYS 108 (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 LYS* 6.4 0.2 - - - +
11A TYR* 3.1 28.8 + - + +
14A THR* 6.0 3.4 - - - +
104A GLU 2.6 20.2 + - - +
105A LEU* 3.3 3.6 - - - +
106A LEU 3.0 0.2 - - - -
107A SER* 1.3 76.4 - - - +
109A ASN* 1.3 57.3 + - + +
110A LEU* 4.3 1.3 - - - +
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Residues in contact with ASN 109 (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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7A GLU* 5.4 0.4 + - - -
11A TYR* 3.7 27.3 - - + -
105A LEU 3.5 2.6 + - - -
106A LEU* 2.6 22.5 + - - +
108A LYS* 1.3 82.7 - - + +
110A LEU* 1.3 57.0 + - - +
111A THR* 2.6 43.9 + - - -
112A HIS* 2.9 35.0 + - + +
113A PHE* 3.3 13.9 + - - +
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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