Contacts of the helix formed by residues 108 - 118 (chain A) in PDB entry 1Q6D
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 PRO 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A TRP* 3.3 59.2 - - + +
57A GLY* 3.6 8.9 - - - -
60A GLU 3.6 10.8 - - - +
61A LEU* 4.5 6.1 - - + -
107A ILE* 1.3 90.8 - - + +
109A GLN* 1.3 65.8 + - - +
110A TRP* 3.4 29.6 - - + +
111A VAL* 3.0 17.4 + - + +
112A LEU* 3.1 10.0 + - - +
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Residues in contact with GLN 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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61A LEU* 3.9 24.5 + - + +
107A ILE 3.3 4.2 + - - -
108A PRO* 1.3 72.7 - - - +
110A TRP* 1.3 58.0 + - - +
112A LEU* 3.1 25.6 + - - +
113A ASP* 2.9 53.7 + - - +
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Residues in contact with TRP 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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56A TRP* 4.7 3.4 - + - -
60A GLU* 2.8 53.4 + - - -
61A LEU 3.4 15.7 + - - +
62A LYS 5.1 1.8 - - - +
63A GLY* 3.5 19.3 - - - -
64A PRO* 3.8 20.6 - - + -
108A PRO* 3.4 8.4 - - + +
109A GLN* 1.3 78.9 - - - +
111A VAL* 1.3 81.0 + - + +
113A ASP* 3.6 13.9 + - - +
114A ILE* 3.5 25.6 + - + +
145A PHE* 4.4 15.9 - - + -
146A HIS* 3.8 27.7 + + - +
148A ARG* 3.6 19.3 - - - -
153A ILE* 4.0 12.6 - - + -
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Residues in contact with VAL 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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56A TRP* 3.8 21.5 - - + -
107A ILE* 3.9 21.8 - - + -
108A PRO* 3.0 12.6 + - + +
110A TRP* 1.3 111.4 - - + +
112A LEU* 1.3 67.5 + - - +
113A ASP 3.1 0.2 - - - -
114A ILE* 3.0 18.4 + - - +
115A GLY 3.0 9.2 + - - -
121A ILE* 4.0 4.9 - - + +
135A LEU* 4.0 20.9 - - + -
145A PHE* 4.2 17.9 - - + -
153A ILE* 5.0 1.1 - - + -
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Residues in contact with LEU 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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106A PRO* 4.2 15.7 - - + -
107A ILE* 3.2 54.5 - - + +
108A PRO 3.1 5.7 + - - +
109A GLN* 3.1 32.2 + - - +
111A VAL* 1.3 79.0 - - - +
113A ASP* 1.3 61.2 + - - +
115A GLY* 3.1 12.8 + - - +
116A GLU* 3.2 17.7 + - - +
122A PHE* 4.4 16.4 - - + -
132A LYS* 4.7 16.6 - - + +
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Residues in contact with ASP 113 (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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109A GLN* 2.9 40.0 + - - +
110A TRP* 3.6 17.0 - - - +
111A VAL 3.1 0.2 - - - -
112A LEU* 1.3 77.3 - - - +
114A ILE* 1.3 62.3 + - + +
116A GLU* 3.1 27.4 + - - +
117A SER* 3.8 4.5 + - - -
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Residues in contact with ILE 114 (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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110A TRP* 3.5 19.9 + - + +
111A VAL* 3.0 8.2 + - - +
113A ASP* 1.3 77.4 - - + +
115A GLY* 1.3 58.2 + - - +
116A GLU 3.1 0.5 + - - -
117A SER* 3.1 12.5 + - - +
118A ASN* 3.0 30.9 + - + +
121A ILE* 4.4 5.2 - - + -
144A ILE* 4.1 17.3 - - + +
145A PHE* 3.6 48.9 - - + -
146A HIS* 3.9 26.2 - - + +
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Residues in contact with GLY 115 (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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111A VAL 3.0 9.9 + - - -
112A LEU 3.1 7.5 + - - -
114A ILE* 1.3 78.8 - - - +
116A GLU* 1.3 61.0 + - - +
117A SER 3.3 0.2 - - - -
118A ASN 3.4 18.0 - - - +
119A HIS* 3.5 15.6 + - - -
121A ILE* 3.3 24.2 - - - +
122A PHE* 3.8 15.0 - - - -
132A LYS* 5.9 0.8 - - - -
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Residues in contact with GLU 116 (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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112A LEU 3.2 14.1 + - - +
113A ASP* 3.2 18.6 - - - +
114A ILE 3.0 0.8 - - - -
115A GLY* 1.3 81.3 - - - +
117A SER* 1.3 59.9 + - - +
118A ASN 3.4 0.2 - - - -
119A HIS* 3.2 27.8 + - - -
132A LYS* 4.3 16.8 + - - -
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Residues in contact with SER 117 (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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113A ASP 3.8 3.0 + - - -
114A ILE* 3.1 18.0 + - - +
116A GLU* 1.3 80.0 - - - +
118A ASN* 1.3 61.2 + - - +
119A HIS* 4.1 3.3 + - - -
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Residues in contact with ASN 118 (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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114A ILE* 3.0 14.4 + - + +
115A GLY* 3.4 12.4 - - - +
117A SER* 1.3 82.4 - - - +
119A HIS* 1.3 60.4 + - - +
120A ASP* 3.0 33.4 + - - +
121A ILE* 3.4 28.6 - - + +
144A ILE* 4.1 7.6 - - - +
211A LYS* 4.6 8.3 + - - +
212A TYR* 3.0 23.9 + - - -
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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