Contacts of the helix formed by residues 103 - 112 (chain A) in PDB entry 1XXE
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 GLY 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A HIS* 5.6 2.2 - - - -
78A VAL* 3.6 22.9 - - - +
102A SER* 1.3 75.3 + - - +
104A TRP* 1.3 68.0 + - - +
105A GLU 2.9 4.0 + - - -
106A PHE* 3.0 12.5 + - - -
107A TYR* 2.7 25.2 + - - +
175A VAL 3.1 7.9 + - - -
229A PHE* 4.3 12.5 - - - -
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Residues in contact with TRP 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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102A SER* 3.0 13.6 + - - +
103A GLY* 1.3 77.8 - - - +
105A GLU* 1.3 60.0 + - + +
107A TYR* 3.6 34.1 - + - -
108A GLU* 2.6 80.9 + - + +
111A ARG* 5.5 3.4 - - - -
172A GLU* 4.0 16.4 - - - -
175A VAL* 3.1 14.3 + - + +
176A LEU* 3.4 49.0 - - + +
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Residues in contact with GLU 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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13A PHE* 4.1 15.9 - - + -
99A LEU* 4.2 35.3 - - + +
100A ASP* 5.4 9.4 - - + -
102A SER* 4.5 5.0 + - - +
103A GLY 3.0 1.0 - - - -
104A TRP* 1.3 85.0 - - + +
106A PHE* 1.3 64.8 + - + +
108A GLU* 3.6 5.5 - - - +
109A ALA* 3.1 25.6 + - - +
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Residues in contact with PHE 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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13A PHE* 3.5 49.4 - + + -
26A LEU* 4.4 13.0 - - + -
74A HIS* 5.7 5.4 - - + -
75A ILE* 3.4 41.1 - - + -
78A VAL* 4.2 8.5 - - + -
96A ILE* 4.8 4.0 - - + -
97A PRO* 4.4 11.7 - - + -
98A ILE 5.8 0.9 - - - -
99A LEU* 3.2 28.9 - - + -
102A SER 4.6 7.4 - - - -
103A GLY* 3.0 18.5 + - - +
105A GLU* 1.3 76.3 - - + +
107A TYR* 1.3 63.2 + - - +
110A ILE* 2.9 45.5 + - + +
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Residues in contact with TYR 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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78A VAL* 3.9 18.1 - - + +
81A LEU* 5.2 8.5 - - + -
82A LEU* 4.0 35.8 - - + +
103A GLY 2.7 21.9 + - - +
104A TRP* 3.6 29.8 - + - +
106A PHE* 1.3 74.1 - - - +
108A GLU* 1.3 59.0 + - - +
111A ARG* 2.8 64.4 + - - +
171A GLU* 5.5 7.9 - - + +
172A GLU* 3.0 34.4 + - + +
175A VAL* 4.3 22.7 - - + -
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Residues in contact with GLU 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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104A TRP* 2.6 79.8 + - + +
105A GLU* 3.6 8.1 - - - +
107A TYR* 1.3 79.1 - - - +
109A ALA* 1.3 63.8 + - - +
111A ARG* 4.0 7.9 + - - +
112A LYS* 3.6 15.4 + - - +
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Residues in contact with ALA 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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11A LEU* 4.1 10.3 - - + -
13A PHE* 3.8 28.9 - - + -
105A GLU 3.1 5.8 + - - +
108A GLU* 1.3 78.0 - - - +
110A ILE* 1.3 65.5 + - - +
112A LYS* 3.0 6.9 + - - +
113A ASN* 2.6 28.3 - - - +
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Residues in contact with ILE 110 (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 VAL* 4.5 17.7 - - + -
11A LEU* 4.2 18.4 - - + -
13A PHE* 4.8 6.5 - - + -
28A ILE* 4.5 21.3 - - + -
75A ILE* 5.1 2.7 - - + -
78A VAL* 4.5 9.4 - - + -
79A LEU* 4.9 12.1 - - + -
82A LEU* 4.0 12.1 - - + -
84A ILE* 5.0 9.0 - - + -
106A PHE* 2.9 40.4 + - + +
109A ALA* 1.3 76.5 - - - +
111A ARG* 1.3 55.4 + - - +
113A ASN* 2.6 22.7 + - - -
114A ILE* 3.0 28.8 + - + +
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Residues in contact with ARG 111 (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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82A LEU* 4.3 13.7 - - + +
104A TRP* 5.5 4.2 - - - -
107A TYR* 2.8 50.6 + - + +
108A GLU* 4.0 8.7 + - - +
110A ILE* 1.3 77.1 - - - +
112A LYS* 1.3 59.3 + - - +
113A ASN 3.5 0.3 + - - -
114A ILE* 4.0 20.3 + - + +
172A GLU* 3.7 23.0 + - - -
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Residues in contact with LYS 112 (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 LYS* 3.7 10.4 + - - -
108A GLU 3.6 9.0 + - - +
109A ALA* 3.0 6.1 + - - +
110A ILE 3.0 1.2 - - - -
111A ARG* 1.3 78.9 - - - +
113A ASN* 1.3 71.4 + - - +
114A ILE 3.6 1.1 - - - -
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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