Contacts of the helix formed by residues 119 - 132 (chain B) in PDB entry 3HKS
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 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B PRO* 3.1 3.7 - - + +
118B THR* 1.3 76.0 - - - +
120B ASP* 1.3 60.1 + - - +
121B GLY* 3.3 8.7 + - - -
122B LEU* 3.1 48.8 + - + +
123B THR* 3.0 30.1 + - - -
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Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B THR 3.8 8.8 - - - +
119B ASP* 1.3 72.6 + - - +
121B GLY* 1.3 58.2 + - - +
123B THR* 3.8 7.6 - - - +
124B ALA* 2.9 33.3 + - - +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ASP* 3.3 9.3 + - - -
120B ASP* 1.3 79.2 - - - +
122B LEU* 1.3 59.6 + - - +
124B ALA* 4.1 4.3 - - - +
125B GLN* 3.1 35.4 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B PRO* 3.7 17.0 - - + -
119B ASP* 3.1 30.4 + - + +
121B GLY* 1.3 74.2 - - - +
123B THR* 1.3 63.1 + - - +
125B GLN* 3.4 19.7 + - - +
126B MET* 3.1 28.2 + - - +
149B ILE* 3.7 23.8 - - + +
150B CYS* 3.8 18.2 - - - +
151B ALA* 4.2 11.2 - - - +
152B VAL* 3.7 21.1 - - + +
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.7 21.3 - - + +
117B PRO* 2.8 42.4 + - - +
119B ASP 3.0 12.4 + - - -
120B ASP* 3.8 8.7 - - - +
122B LEU* 1.3 77.3 - - - +
124B ALA* 1.3 56.3 + - - +
126B MET* 3.4 5.1 + - - +
127B ARG* 3.0 41.6 + - - +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ASP 2.9 20.8 + - - +
121B GLY* 4.1 4.7 - - - +
123B THR* 1.3 70.8 - - - +
125B GLN* 1.3 58.0 + - + +
127B ARG* 4.0 5.6 - - - +
128B LEU* 2.8 40.6 + - + +
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLY 3.1 28.6 + - - +
122B LEU* 3.6 24.3 - - - +
123B THR 3.4 0.2 - - - -
124B ALA* 1.3 76.3 - - - +
126B MET* 1.3 56.5 + - - +
128B LEU* 4.8 4.7 - - - -
129B GLY* 2.9 27.7 + - - -
136B ILE* 4.5 4.7 - - - +
152B VAL* 3.7 33.7 + - + +
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 4.0 19.8 - - + +
95B ILE* 3.7 9.4 - - + +
101B VAL* 3.7 31.9 - - + -
116B LEU* 3.8 5.4 - - + -
117B PRO* 3.7 27.6 - - - -
122B LEU 3.1 16.7 + - - +
123B THR 3.7 3.4 - - - +
125B GLN* 1.3 77.0 - - - +
127B ARG* 1.3 56.5 + - - +
129B GLY 3.9 0.2 - - - -
130B PHE* 2.9 32.1 + - - +
136B ILE* 4.8 3.3 - - + +
138B VAL* 3.8 22.4 - - + -
149B ILE* 4.3 10.3 - - + -
152B VAL* 3.5 29.6 - - + -
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 3.8 21.6 - - + +
116B LEU* 4.4 15.0 - - + -
123B THR* 3.0 36.5 + - + +
124B ALA* 4.0 5.4 - - - +
126B MET* 1.3 74.1 - - - +
128B LEU* 1.3 57.5 + - - +
130B PHE* 3.4 1.7 + - - +
131B ASP* 2.9 48.4 + - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ALA* 2.8 25.9 + - + +
125B GLN* 4.3 3.6 - - - +
127B ARG* 1.3 70.3 - - - +
129B GLY* 1.3 64.9 + - - +
131B ASP* 3.4 7.2 + - + +
132B GLU* 3.0 56.1 + - + +
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLN 2.9 23.2 + - - -
128B LEU* 1.3 73.8 - - - +
130B PHE* 1.3 59.4 + - - +
132B GLU* 3.5 3.9 + - - -
133B GLY 3.3 2.9 + - - -
134B LYS* 2.9 36.5 + - - +
136B ILE* 3.8 23.3 - - - -
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Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 4.3 13.0 - - + -
93B ILE 3.4 25.1 - - - -
94B ASP* 3.7 26.0 - - - -
95B ILE* 3.9 26.7 - - + -
126B MET 2.9 18.9 + - - +
127B ARG 3.6 3.4 - - - +
129B GLY* 1.3 74.5 - - - +
131B ASP* 1.3 73.9 + - - +
133B GLY* 3.0 15.4 + - - -
134B LYS 4.8 1.3 - - - -
136B ILE* 4.2 2.9 - - - +
161B EDO 3.8 33.1 + - - -
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ARG* 2.9 39.2 + - - +
128B LEU* 3.8 8.7 - - + +
130B PHE* 1.3 83.3 - - - +
132B GLU* 1.3 61.5 + - + +
133B GLY 3.3 0.7 + - - -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 3.0 49.1 + - + +
129B GLY* 4.0 2.3 - - - +
130B PHE 3.1 0.4 - - - -
131B ASP* 1.3 77.2 - - + +
133B GLY* 1.3 62.2 + - - +
134B LYS* 3.5 36.5 + - + +
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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