Contacts of the helix formed by residues 101 - 108 (chain A) in PDB entry 1EBF
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 PHE 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.5 39.7 - - + -
74A ASP* 3.3 49.8 - - - -
77A ILE* 3.7 15.5 - - + -
97A TYR* 3.5 29.8 + + - -
98A ILE 2.5 18.5 + - - +
100A GLY* 1.3 75.9 - - - +
102A TYR* 1.3 63.7 + - - +
103A THR 3.3 2.7 - - - -
104A LYS* 2.9 28.6 + - + +
105A PHE* 3.0 20.5 + - + -
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Residues in contact with TYR 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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89A LEU* 4.9 2.5 - - + -
91A ASP* 2.6 33.0 + - + +
98A ILE* 3.5 17.9 - - + -
99A ALA* 3.1 26.1 + - - +
100A GLY 3.5 0.2 - - - -
101A PHE* 1.3 75.6 - - - +
103A THR* 1.3 55.6 - - - +
105A PHE* 2.7 31.8 + + - +
106A VAL* 2.9 16.6 + - - +
112A ILE* 3.6 27.1 - - + -
114A THR* 3.3 24.1 + - + +
116A ASN* 3.6 7.1 - - + +
119A ALA* 3.3 24.9 - - + -
120A PHE* 3.7 22.4 - + - -
126A THR* 5.8 1.3 - - + -
130A LEU* 3.6 22.7 - - + -
140A VAL* 4.9 0.7 - - + -
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Residues in contact with THR 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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99A ALA 4.9 0.4 + - - -
100A GLY 5.1 3.5 + - - -
101A PHE 3.3 0.8 - - - -
102A TYR* 1.3 76.0 - - - +
104A LYS* 1.3 58.8 + - - +
106A VAL* 3.4 7.7 + - - +
107A GLU* 2.8 39.7 + - + +
126A THR* 4.4 13.0 - - - +
129A ALA* 4.0 27.1 - - + +
130A LEU* 4.1 10.3 - - - +
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Residues in contact with LYS 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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74A ASP* 2.7 38.6 + - - +
77A ILE* 4.0 17.1 - - + +
100A GLY 5.7 0.2 + - - -
101A PHE* 2.9 25.7 + - + +
103A THR* 1.3 76.9 - - - +
105A PHE* 1.3 67.4 + - - +
107A GLU* 4.3 8.3 - - + -
108A ASN* 2.9 44.6 + - - +
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Residues in contact with PHE 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 ILE* 4.8 1.3 - - + -
73A LEU* 4.2 14.1 - - + -
76A LEU* 4.3 16.6 - - + -
77A ILE* 3.7 29.4 - - + -
80A LEU* 4.5 7.4 - - + -
89A LEU* 3.4 47.3 - - + -
98A ILE* 4.7 4.9 - - + -
101A PHE* 3.0 45.8 + - + -
102A TYR* 2.7 17.8 + + - +
104A LYS* 1.3 71.8 - - - +
106A VAL* 1.3 63.5 + - - +
108A ASN* 2.9 14.7 + - - +
109A GLY 3.4 0.2 + - - -
110A ILE* 3.1 44.1 + - + +
112A ILE* 4.0 12.1 - - + -
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Residues in contact with VAL 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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102A TYR 2.9 15.7 + - - +
103A THR* 3.7 9.6 - - - +
105A PHE* 1.3 75.6 - - - +
107A GLU* 1.3 58.0 + - - +
109A GLY 2.9 17.3 + - - -
110A ILE 3.6 9.6 - - - +
112A ILE* 4.1 9.9 - - + -
129A ALA 4.6 14.6 - - - +
130A LEU* 4.3 10.5 - - + +
133A ASN 6.2 1.1 - - - +
137A ASN* 3.4 21.7 - - + +
138A GLY 3.2 30.0 + - - +
140A VAL* 3.5 29.8 - - + -
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Residues in contact with GLU 107 (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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103A THR* 2.8 29.2 + - + +
104A LYS* 3.9 9.9 - - - +
105A PHE 3.3 0.2 - - - -
106A VAL* 1.3 76.3 - - - +
108A ASN* 1.3 63.5 + - - +
109A GLY 3.2 2.5 + - - -
137A ASN* 3.8 19.8 + - - +
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Residues in contact with ASN 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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77A ILE* 3.5 24.7 - - + +
81A LYS* 3.3 45.3 - - + +
104A LYS* 2.9 40.1 + - - +
105A PHE 2.9 6.4 + - - +
107A GLU* 1.3 84.6 + - - +
109A GLY* 1.3 62.8 + - - +
110A ILE* 3.3 10.3 + - + +
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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