Contacts of the helix formed by residues 113 - 130 (chain A) in PDB entry 1QF6
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 THR 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ARG* 5.4 2.5 - - - +
111A THR* 3.6 15.5 - - + +
112A LEU* 1.3 76.4 - - - +
114A GLN* 1.3 58.8 + - - +
115A GLU* 3.2 30.7 + - - +
116A ASP* 2.9 38.2 + - - +
117A VAL* 3.0 12.2 + - - +
5B A 6.0 1.8 - - - +
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Residues in contact with GLN 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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112A LEU 4.0 0.2 + - - -
113A THR* 1.3 71.7 - - - +
115A GLU* 1.3 77.0 + - - +
117A VAL* 4.0 11.8 - - + +
118A GLU* 3.3 41.1 + - - +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A THR* 3.2 27.7 + - - +
114A GLN* 1.3 102.4 + - - +
116A ASP* 1.3 63.9 + - - +
118A GLU* 3.0 16.1 + - - +
119A ALA* 2.9 25.1 + - - +
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 3.5 23.1 - - + -
110A ARG* 2.5 45.0 + - - +
112A LEU* 3.7 6.5 - - + -
113A THR* 2.9 35.2 + - - +
115A GLU* 1.3 77.3 - - - +
117A VAL* 1.3 56.7 + - - +
119A ALA* 2.8 10.5 + - - +
120A LEU* 2.7 35.7 + - - +
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.3 21.5 - - + +
113A THR 3.0 17.2 + - - +
114A GLN* 4.1 9.9 - - + +
116A ASP* 1.3 75.3 - - - +
118A GLU* 1.3 60.8 + - - +
120A LEU* 3.6 8.6 - - - +
121A GLU* 3.2 22.7 + - - +
198A LEU* 3.9 28.3 - - + +
199A MET 4.6 8.1 - - - +
201A THR* 3.8 31.6 - - + +
218A ILE* 4.7 3.6 - - + -
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Residues in contact with GLU 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 GLN* 3.3 38.3 + - + +
115A GLU* 3.0 19.1 + - - +
116A ASP 3.0 0.4 - - - -
117A VAL* 1.3 79.4 - - - +
119A ALA* 1.3 62.5 + - - +
121A GLU* 3.5 6.6 + - - +
122A LYS* 3.1 22.3 + - - +
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Residues in contact with ALA 119 (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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86A LEU* 3.9 12.9 - - + +
87A TRP* 5.1 2.9 - - + -
115A GLU 2.9 11.7 + - - +
116A ASP* 2.8 14.5 + - - +
118A GLU* 1.3 73.1 - - - +
120A LEU* 1.3 61.3 + - - +
122A LYS* 3.2 8.4 + - - +
123A ARG* 2.9 28.4 + - - +
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Residues in contact with LEU 120 (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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79A LEU* 3.9 13.9 - - + -
83A ILE* 3.3 42.4 - - + +
86A LEU* 3.5 10.9 - - + +
87A TRP* 3.5 17.7 - - + -
112A LEU* 5.7 2.0 - - + -
116A ASP 2.7 17.6 + - - +
117A VAL* 3.6 7.4 - - - +
119A ALA* 1.3 70.5 - - - +
121A GLU* 1.3 59.9 + - - +
122A LYS 2.9 0.7 + - - -
123A ARG* 3.0 4.3 + - - +
124A MET* 2.7 47.8 + - + +
198A LEU* 3.4 26.0 - - + -
218A ILE* 4.2 15.9 - - + -
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Residues in contact with GLU 121 (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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117A VAL 3.2 15.2 + - - +
118A GLU* 3.9 7.1 - - - +
120A LEU* 1.3 78.5 - - - +
122A LYS* 1.3 57.8 + - - +
124A MET* 3.4 6.8 - - - +
125A HIS* 3.0 63.5 + - + +
196A PHE* 3.5 10.6 - - + +
197A LYS* 3.4 23.4 + - - +
198A LEU* 2.8 44.2 + - + +
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Residues in contact with LYS 122 (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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118A GLU 3.1 13.5 + - - +
119A ALA* 3.4 11.9 - - - +
120A LEU 2.9 1.2 + - - -
121A GLU* 1.3 75.1 - - - +
123A ARG* 1.3 66.4 + - - +
125A HIS* 3.1 9.0 + - + +
126A GLU* 2.9 47.7 + - + +
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Residues in contact with ARG 123 (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 ALA* 3.4 23.3 - - + -
85A GLN* 2.8 46.6 - - - +
86A LEU* 3.4 36.0 - - + +
119A ALA 2.9 12.9 + - - +
120A LEU 3.5 6.3 - - - +
122A LYS* 1.3 74.7 - - - +
124A MET* 1.3 61.7 + - - +
126A GLU* 3.1 25.9 + - - +
127A LEU* 3.0 31.5 + - - +
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Residues in contact with MET 124 (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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75A CYS* 5.0 2.7 - - - +
78A LEU* 3.5 25.3 - - + +
79A LEU* 3.1 50.0 - - + +
82A ALA* 4.0 10.8 - - + -
102A PHE* 5.4 2.2 - - - -
120A LEU* 2.7 40.8 + - + +
121A GLU* 3.4 7.2 - - - +
123A ARG* 1.3 72.6 - - - +
125A HIS* 1.3 65.6 + - - +
126A GLU 3.1 1.0 + - - -
127A LEU* 3.3 0.7 + - - -
128A ALA* 3.2 22.5 + - - +
196A PHE* 3.4 28.5 - - + -
198A LEU* 4.2 18.2 - - - -
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Residues in contact with HIS 125 (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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121A GLU* 3.0 57.6 + - + +
122A LYS* 3.7 6.4 - - - +
124A MET* 1.3 75.4 - - - +
126A GLU* 1.3 56.2 + - + +
128A ALA* 3.6 2.2 + - + +
129A GLU* 2.6 52.3 + - - +
194A HIS* 3.6 23.8 + - - -
196A PHE* 3.2 33.9 + + - -
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Residues in contact with GLU 126 (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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122A LYS* 2.9 45.7 + - + +
123A ARG* 3.2 33.6 + - - +
124A MET 3.1 0.4 - - - -
125A HIS* 1.3 74.7 - - + +
127A LEU* 1.3 68.1 + - + +
129A GLU* 3.1 18.2 + - - +
130A LYS* 3.3 16.6 + - - +
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Residues in contact with LEU 127 (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 LEU* 3.9 15.0 - - + -
81A HIS* 3.9 23.6 - - + +
82A ALA* 3.8 26.2 - - + +
85A GLN* 3.7 23.1 - - - +
123A ARG* 3.0 32.7 + - - +
124A MET 3.3 0.4 + - - +
126A GLU* 1.3 74.9 - - + +
128A ALA* 1.3 63.0 + - - +
130A LYS* 3.1 48.5 + - - +
131A ASN 3.9 0.2 + - - -
132A TYR* 3.5 19.2 - - + -
176A GLU* 4.1 0.7 - - - +
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Residues in contact with ALA 128 (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 LEU* 3.7 15.8 - - + +
124A MET 3.2 15.7 + - - +
125A HIS* 3.9 4.5 - - - +
127A LEU* 1.3 78.2 - - - +
129A GLU* 1.3 53.7 + - - +
130A LYS 3.3 0.2 - - - -
131A ASN* 3.2 11.7 + - - +
190A MET* 3.8 20.2 - - + +
193A CYS 3.5 26.0 - - - +
194A HIS* 2.7 28.5 - - - +
196A PHE* 4.4 3.4 - - + -
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Residues in contact with GLU 129 (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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125A HIS* 2.6 42.4 - - + +
126A GLU* 3.1 9.8 + - - +
128A ALA* 1.3 73.8 - - - +
130A LYS* 1.3 64.0 + - - +
131A ASN* 2.9 17.7 + - - +
194A HIS* 3.8 26.2 + - - +
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Residues in contact with LYS 130 (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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85A GLN* 5.5 0.8 + - - -
126A GLU* 3.3 9.5 + - - +
127A LEU* 3.1 36.6 + - - +
129A GLU* 1.3 77.5 - - - +
131A ASN* 1.3 67.1 + - - +
132A TYR* 3.4 7.8 + - + +
176A GLU* 3.5 35.2 + - - +
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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