Contacts of the helix formed by residues 109 - 124 (chain D) in PDB entry 4H7Y
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 ASN 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D ARG* 3.4 15.6 - - - +
104D GLU* 2.9 41.0 + - + +
105D LEU* 4.3 0.6 + - - -
107D GLN* 3.8 17.4 + - - +
108D GLY* 1.3 80.0 - - - +
110D VAL* 1.3 58.0 + - - +
111D LYS 3.3 2.7 - - - -
112D LYS* 3.3 12.4 + - + -
113D SER* 2.9 28.3 + - - -
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LEU* 3.9 20.0 - - + -
108D GLY* 3.4 14.0 + - - +
109D ASN* 1.3 74.4 - - - +
111D LYS* 1.3 60.2 + - + +
113D SER* 3.4 7.7 + - - -
114D LYS* 3.0 28.4 + - + +
138D LEU* 4.3 18.0 - - + +
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Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ASN 3.3 0.6 - - - -
110D VAL* 1.3 80.5 - - + +
112D LYS* 1.3 58.1 + - - +
114D LYS* 3.3 6.8 + - - +
115D GLN* 2.9 41.1 + - - +
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Residues in contact with LYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ASP* 3.3 33.2 + - - -
84A GLN* 4.9 3.9 + - - -
87D ARG* 5.4 0.2 - - - +
100D PHE* 5.6 4.0 - - - -
104D GLU* 4.1 24.2 - - + +
109D ASN* 3.3 18.8 + - + +
111D LYS* 1.3 75.3 - - - +
113D SER* 1.3 60.4 + - - +
115D GLN* 3.2 23.6 + - + +
116D LEU* 2.8 56.1 + - + +
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ALA* 2.8 36.5 + - - +
104D GLU* 4.1 5.3 - - - +
105D LEU* 3.7 17.1 - - - +
109D ASN 2.9 17.7 + - - -
110D VAL* 3.5 9.2 - - - -
112D LYS* 1.3 76.9 - - - +
114D LYS* 1.3 62.6 + - - +
116D LEU* 3.3 3.0 + - - +
117D LEU* 3.2 24.9 + - - +
138D LEU* 4.2 10.2 - - - +
145D LEU* 4.2 5.7 - - - +
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D VAL* 3.0 16.2 + - + +
111D LYS* 3.3 7.4 + - - +
113D SER* 1.3 75.7 - - - +
115D GLN* 1.3 57.8 + - + +
117D LEU* 3.3 3.7 + - - +
118D GLN* 2.9 67.4 + - + +
135D LEU* 4.4 6.5 - - + -
138D LEU* 3.5 22.4 - - + +
139D ASN* 3.6 28.8 + - - +
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Residues in contact with GLN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LYS* 2.9 24.7 + - + +
112D LYS* 3.2 34.5 + - + +
114D LYS* 1.3 75.9 - - + +
116D LEU* 1.3 57.5 + - - +
118D GLN* 3.9 12.7 - - - +
119D LYS* 2.9 33.5 + - - +
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ARG* 3.4 34.4 + - - +
97D HIS* 4.5 10.8 + - + +
100D PHE* 3.6 42.0 - - + -
101D ALA* 3.8 18.2 - - + +
104D GLU* 3.6 20.6 - - + -
112D LYS* 2.8 42.0 + - + +
113D SER 3.5 4.5 - - - +
114D LYS 3.2 0.2 - - - -
115D GLN* 1.3 78.7 - - - +
117D LEU* 1.3 57.0 + - - +
119D LYS* 3.4 4.8 + - - +
120D ALA* 3.0 27.4 + - - +
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D HIS 4.6 1.8 - - - +
98D ILE* 3.8 28.7 - - + +
101D ALA* 3.6 22.9 - - + -
113D SER 3.2 9.7 + - - +
114D LYS 3.3 2.4 + - - +
116D LEU* 1.3 76.6 - - - +
118D GLN* 1.3 61.5 + - - +
120D ALA* 3.2 7.2 + - - +
121D VAL* 3.1 26.2 + - - +
131D LEU* 4.3 9.8 - - + +
134D ALA* 3.9 28.0 - - + +
135D LEU* 3.7 24.0 - - + +
138D LEU* 3.8 28.0 - - + -
145D LEU* 4.3 6.7 - - + -
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Residues in contact with GLN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS* 2.9 56.6 + - + +
115D GLN* 3.9 12.4 - - - +
117D LEU* 1.3 73.4 - - - +
119D LYS* 1.3 60.6 + - - +
121D VAL* 3.3 9.9 + - - +
122D GLU* 2.9 27.4 + - - +
135D LEU* 4.2 13.7 - - + +
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Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP 4.6 4.6 + - - -
78A ASP* 4.7 3.8 + - - +
87D ARG* 4.5 17.5 - - - +
97D HIS* 6.0 2.5 - - + +
115D GLN 2.9 19.1 + - - +
116D LEU* 3.7 6.3 - - - +
118D GLN* 1.3 76.5 - - - +
120D ALA* 1.3 58.6 + - - +
122D GLU* 3.1 26.2 + - - +
123D ARG* 2.9 68.0 + - + +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D HIS* 3.6 43.9 + - + -
116D LEU 3.0 14.0 + - - +
117D LEU 3.4 9.6 - - - +
118D GLN 3.2 0.2 - - - -
119D LYS* 1.3 78.2 - - - +
121D VAL* 1.3 62.2 + - - +
123D ARG* 3.3 3.0 + - - +
124D GLY 3.1 17.7 + - - -
125D ALA* 3.1 13.0 + - + +
131D LEU* 3.9 17.9 - - + -
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU 3.1 15.4 + - - +
118D GLN* 3.6 7.9 - - - +
119D LYS 3.3 0.2 - - - -
120D ALA* 1.3 74.8 - - - +
122D GLU* 1.3 64.8 + - - +
124D GLY* 3.1 13.4 + - - +
125D ALA 5.1 0.4 - - - +
128D LEU* 4.1 21.5 - - + +
131D LEU* 3.9 28.7 - - + -
132D GLU* 5.4 1.3 - - + +
135D LEU* 4.1 17.5 - - + -
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Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D GLN 2.9 13.5 + - - +
119D LYS* 3.4 31.7 + - - +
121D VAL* 1.3 78.7 - - - +
123D ARG* 1.3 86.2 + - - +
124D GLY* 3.5 0.7 + - - -
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Residues in contact with ARG 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 3.0 30.0 + - - +
78A ASP* 2.7 38.1 + - - +
91D LYS* 6.4 1.3 - - + -
97D HIS* 5.7 6.5 - - + -
119D LYS* 2.9 44.8 + - + +
120D ALA* 4.0 5.4 - - - +
121D VAL 3.2 0.2 - - - -
122D GLU* 1.3 111.7 + - - +
124D GLY* 1.3 61.2 + - - +
125D ALA* 3.8 2.0 + - + +
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Residues in contact with GLY 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LYS* 4.6 1.0 - - - +
120D ALA 3.1 3.2 + - - -
121D VAL* 3.1 12.2 + - - -
122D GLU 3.3 0.8 - - - -
123D ARG* 1.3 80.0 - - - +
125D ALA* 1.3 67.7 + - - +
126D VAL* 3.5 15.2 + - - +
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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