Contacts of the helix formed by residues 104 - 112 (chain A) in PDB entry 1I4W
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 ASP 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ASP* 3.8 18.6 - - + +
102A PRO 3.5 2.2 + - - -
103A TYR* 1.3 79.1 - - - +
105A TRP* 1.3 76.1 + - - +
106A SER* 3.1 28.8 + - - -
107A THR* 3.1 29.3 + - - +
108A TYR* 3.5 9.8 - - - -
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Residues in contact with TRP 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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104A ASP* 1.3 76.4 + - - +
106A SER* 1.3 63.5 + - - +
107A THR 3.2 0.7 + - - -
108A TYR* 3.3 10.9 + - - +
109A SER* 3.2 30.3 + - - -
153A CYS* 4.6 7.4 - - - -
158A ASN* 3.6 17.9 - - + -
159A TRP* 3.4 50.0 - + + -
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Residues in contact with SER 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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104A ASP* 3.1 22.5 + - - -
105A TRP* 1.3 80.7 - - - +
107A THR* 1.3 61.6 + - - +
109A SER* 3.4 7.8 + - - -
110A ASN* 3.0 26.5 + - - +
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Residues in contact with THR 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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76A LEU* 4.1 19.3 - - + -
100A ARG* 3.7 33.7 - - + +
101A ASP* 2.7 34.8 + - - +
104A ASP* 3.1 16.7 + - - +
106A SER* 1.3 78.2 - - - +
108A TYR* 1.3 61.3 + - + +
110A ASN* 3.8 3.1 - - - +
111A LEU* 2.8 37.1 + - + +
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Residues in contact with TYR 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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51A LEU* 3.9 14.1 - - + -
53A LEU* 3.5 18.0 - - - +
76A LEU* 3.9 15.0 - - + -
102A PRO* 2.3 41.7 + - - +
103A TYR* 5.1 0.2 - - - -
104A ASP 3.5 20.4 - - - -
105A TRP* 3.3 4.7 + - + +
107A THR* 1.3 73.1 - - - +
109A SER* 1.3 67.7 + - - +
110A ASN 3.0 1.8 - - - -
111A LEU 4.3 0.4 - - - +
112A ILE* 2.9 42.4 + - + +
113A ASP* 3.7 1.6 + - - +
159A TRP* 2.9 42.6 - + + -
160A LEU* 4.1 14.8 - - + -
344A XE 3.5 20.9 - - - -
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Residues in contact with SER 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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105A TRP* 3.2 24.6 + - - +
106A SER* 3.6 12.6 - - - -
108A TYR* 1.3 79.1 - - - +
110A ASN* 1.3 57.2 + - - +
113A ASP* 3.1 23.5 + - - +
114A GLU* 2.9 40.6 + - - +
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Residues in contact with ASN 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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100A ARG* 4.1 10.6 + - - -
106A SER 3.0 17.8 + - - +
107A THR* 3.9 2.5 - - - +
109A SER* 1.3 77.2 - - - +
111A LEU* 1.3 79.9 + - - +
112A ILE 3.3 0.4 - - - -
114A GLU* 3.3 24.5 + - - +
115A GLU* 2.8 55.5 + - - +
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Residues in contact with LEU 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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76A LEU* 3.6 20.9 - - + -
98A LEU* 3.3 30.1 - - + -
100A ARG* 3.1 43.5 - - - +
107A THR* 2.8 21.9 + - + +
110A ASN* 1.3 88.7 + - - +
112A ILE* 1.3 60.9 + - - +
117A ILE* 2.8 49.4 + - + +
118A PHE* 3.2 10.4 + - + +
344A XE 3.7 18.8 - - - -
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Residues in contact with ILE 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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108A TYR* 2.9 26.1 + - + +
111A LEU* 1.3 77.0 - - - +
113A ASP* 1.3 75.6 + - - +
116A ARG* 3.2 25.2 + - - -
118A PHE* 3.0 24.9 - - + +
119A VAL* 4.3 13.4 - - + +
120A PRO* 4.6 4.5 - - + -
160A LEU* 3.9 27.6 - - + -
162A ARG* 4.2 3.1 - - - +
163A PHE* 3.9 31.2 - - + -
344A XE 3.8 19.3 - - - -
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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