Contacts of the helix formed by residues 114 - 129 (chain A) in PDB entry 3K4H
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ASN* 1.3 71.2 - - - +
115A ASN* 1.3 54.7 + - - +
116A TYR* 3.6 9.7 + - - +
117A THR* 2.7 35.1 + - - +
118A ALA* 2.9 27.5 + - - +
273A ILE* 3.7 23.4 - - + +
274A ILE 4.5 1.4 + - - -
276A HIS* 4.1 12.4 + - + +
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Residues in contact with ASN 115 (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 ASP* 3.3 19.0 + - - -
113A ASN* 2.7 16.9 + - - +
114A ASP* 1.3 68.4 - - - +
116A TYR* 1.3 67.4 + - - +
118A ALA* 3.9 5.6 - - - +
119A ALA* 3.1 26.0 + - - +
145A VAL* 3.5 10.0 - - + +
148A ASP* 4.0 21.6 + - + +
149A ARG* 2.7 41.7 + - + +
227A PHE* 4.5 3.1 - - - -
245A VAL* 4.7 0.9 - - - +
2C GLC 3.1 31.1 + - - -
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Residues in contact with TYR 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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100A LYS* 6.1 0.7 - - - +
114A ASP* 3.2 8.6 + - - +
115A ASN* 1.3 77.7 - - - +
117A THR* 1.3 68.7 + - - +
120A ARG* 3.0 49.3 + - + +
148A ASP* 3.9 21.5 - - + +
151A ALA* 3.7 13.2 - - + -
152A GLY* 3.5 30.9 - - - -
155A ASP* 2.5 37.8 + - - +
116B TYR* 4.6 15.9 - + - -
120B ARG* 2.5 17.3 + - - -
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Residues in contact with THR 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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114A ASP* 2.7 34.2 + - - +
116A TYR* 1.3 84.6 - - - +
118A ALA* 1.3 65.4 + - - +
120A ARG* 3.5 8.4 - - + +
121A GLU* 2.9 45.0 + - + +
276A HIS* 4.9 4.0 - - + -
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Residues in contact with ALA 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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113A ASN* 6.1 0.7 - - + -
114A ASP 2.9 14.8 + - - +
115A ASN* 3.3 9.1 + - - +
117A THR* 1.3 75.2 - - - +
119A ALA* 1.3 57.5 + - - +
121A GLU* 3.0 7.0 + - - +
122A VAL* 2.9 31.7 + - - +
227A PHE* 4.0 21.5 - - + -
243A VAL* 4.7 2.6 - - + +
245A VAL* 6.0 0.4 - - + -
276A HIS* 3.5 38.3 + - + +
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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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115A ASN 3.1 16.7 + - - +
116A TYR 3.9 2.9 - - - +
118A ALA* 1.3 73.4 - - - +
120A ARG* 1.3 65.7 + - - +
122A VAL* 3.4 3.7 + - - +
123A ALA* 2.9 24.8 + - - +
149A ARG* 3.2 37.9 - - + +
152A GLY* 4.1 2.5 - - - -
153A MSE 3.9 4.8 - - - +
197A MSE 3.9 21.2 - - + +
227A PHE* 4.3 3.0 - - - -
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Residues in contact with ARG 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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116A TYR* 3.0 45.8 + - + +
117A THR* 3.3 14.8 + - + +
119A ALA* 1.3 74.4 - - - +
121A GLU* 1.3 58.9 + - + +
123A ALA* 3.2 3.1 + - - +
124A GLU* 2.8 57.2 + - - +
152A GLY* 3.2 24.3 - - - +
155A ASP* 4.4 0.4 - - - +
156A ALA* 4.0 14.5 - - - +
159A LEU* 3.6 21.1 - - - +
116B TYR* 2.6 35.4 + - - -
120B ARG* 4.8 0.6 - - - +
155B ASP* 2.6 19.2 + - - -
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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 THR* 2.9 32.8 + - + +
118A ALA* 3.0 5.9 + - - +
120A ARG* 1.3 73.3 - - + +
122A VAL* 1.3 60.1 + - + +
124A GLU* 3.2 17.2 + - - +
125A TYR* 2.8 31.1 + - - +
276A HIS* 2.7 34.1 + - - -
278A LEU* 4.8 11.5 - - + +
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Residues in contact with VAL 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 ALA 2.9 17.6 + - - +
119A ALA 3.8 7.0 - - - +
121A GLU* 1.3 75.9 - - + +
123A ALA* 1.3 57.0 + - - +
125A TYR* 3.2 8.5 + - - +
126A LEU* 3.0 33.7 + - + +
197A MSE 3.8 24.0 - - + -
225A VAL* 3.8 30.7 - - + -
227A PHE* 4.6 5.6 - - + -
243A VAL* 3.7 28.7 - - + -
278A LEU* 4.0 17.7 - - + +
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Residues in contact with ALA 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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119A ALA 2.9 17.9 + - - +
122A VAL* 1.3 75.1 - - + +
124A GLU* 1.3 61.5 + - - +
126A LEU* 3.4 8.5 + - - +
127A ILE* 2.9 40.8 + - + +
134A ILE* 4.9 3.5 - - + +
153A MSE 3.9 21.3 - - + +
156A ALA* 3.6 23.6 - - + -
157A LEU* 4.8 4.7 - - + -
197A MSE 5.5 0.9 - - - -
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Residues in contact with GLU 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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120A ARG* 2.8 53.9 + - - +
121A GLU* 3.6 16.3 - - - +
123A ALA* 1.3 76.7 - - - +
125A TYR* 1.3 52.5 + - - +
127A ILE* 3.2 8.0 + - + +
128A SER* 2.8 37.4 + - - -
156A ALA* 4.7 8.7 - - + +
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Residues in contact with TYR 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 2.8 13.8 + - - +
122A VAL* 3.3 11.2 - - - +
123A ALA 3.2 0.2 - - - -
124A GLU* 1.3 75.2 - - - +
126A LEU* 1.3 63.4 + - + +
128A SER* 2.7 25.9 + - - -
129A LEU* 3.2 29.9 + - + +
225A VAL* 4.4 13.9 - - + -
241A SER* 5.5 0.9 - - - -
278A LEU* 4.1 21.5 - - + -
280A LYS* 3.5 53.0 - - + +
284A CYS* 3.5 35.6 + - - +
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Residues in contact with LEU 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 VAL* 3.0 30.8 + - + +
123A ALA* 3.9 5.6 - - - +
125A TYR* 1.3 74.2 - - + +
127A ILE* 1.3 61.7 + - - +
129A LEU* 3.0 32.5 + - + +
131A HIS* 3.3 16.4 + - + +
134A ILE* 4.0 25.1 - - + -
195A ALA* 3.9 31.4 - - + -
196A ILE 4.9 9.9 - - - +
197A MSE 5.1 3.1 - - + -
223A SER* 4.3 7.6 - - - -
225A VAL* 4.0 23.3 - - + -
284A CYS* 4.1 14.8 - - - -
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Residues in contact with ILE 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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123A ALA 2.9 29.5 + - - +
124A GLU* 3.2 9.2 + - + +
126A LEU* 1.3 73.0 - - - +
128A SER* 1.3 61.7 + - - +
130A GLY* 2.9 20.3 + - - -
131A HIS 4.0 6.5 - - - +
132A LYS* 5.8 0.5 + - - -
134A ILE* 3.8 17.9 - - + -
156A ALA* 3.8 21.8 - - + +
157A LEU* 3.6 22.9 - - + -
160A ALA* 4.1 13.0 - - + -
162A ILE* 3.9 25.1 - - + -
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Residues in contact with SER 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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124A GLU 2.8 14.7 + - - -
125A TYR* 2.7 25.7 + - - -
127A ILE* 1.3 77.5 - - - +
129A LEU* 1.3 60.1 + - - +
130A GLY 3.2 1.3 + - - -
288A HIS* 3.8 11.8 + - - -
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Residues in contact with LEU 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 TYR* 3.2 42.4 + - + +
126A LEU* 3.0 25.3 + - + +
128A SER* 1.3 82.8 + - - +
130A GLY* 1.3 55.3 + - - +
131A HIS* 3.5 9.2 - - + -
284A CYS* 4.2 14.8 - - + -
285A GLU 3.6 15.5 - - - +
286A GLY* 4.0 18.6 - - - +
287A HIS* 2.7 33.3 + - - +
288A HIS* 3.6 13.4 + - + -
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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