Contacts of the helix formed by residues 123 - 136 (chain H) in PDB entry 4U0Z
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 GLU 123 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122H ARG* 1.4 75.4 - - - +
124H LYS* 1.4 63.1 + - - +
126H GLN* 3.9 9.8 - - - +
127H LYS* 3.4 45.2 + - - +
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Residues in contact with LYS 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H MET* 4.6 12.1 - - + -
122H ARG 3.3 5.0 - - - +
123H GLU* 1.4 76.7 - - - +
125H ALA* 1.4 57.5 + - - +
127H LYS* 4.0 4.5 + - - +
128H LEU* 3.3 34.4 + - + +
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Residues in contact with ALA 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H ALA 3.4 23.3 - - - +
116H MET* 3.9 14.0 - - + +
117H LYS* 4.0 8.7 - - - +
122H ARG* 3.3 11.7 + - - +
124H LYS* 1.4 76.3 - - - +
126H GLN* 1.3 54.3 + - - +
127H LYS 3.3 0.4 - - - -
128H LEU* 3.0 8.2 + - - +
129H PHE* 2.7 44.6 + - + -
149H PHE* 4.3 14.4 - - + -
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Residues in contact with GLN 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H ARG 3.0 16.4 + - - +
123H GLU* 4.1 10.2 - - - +
124H LYS 3.6 0.2 - - - -
125H ALA* 1.3 75.9 - - - +
127H LYS* 1.4 58.8 + - + +
129H PHE* 3.6 5.0 + - - +
130H MET* 3.2 37.8 + - + +
146H PHE* 4.1 12.7 - - + -
149H PHE* 3.9 28.3 - - + -
153H ASP* 4.4 8.7 - - - +
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Residues in contact with LYS 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H GLU* 3.4 30.3 + - - +
124H LYS* 4.4 4.7 - - - +
125H ALA 3.3 0.4 - - - -
126H GLN* 1.4 76.7 - - + +
128H LEU* 1.4 58.1 + - - +
130H MET* 3.5 8.5 + - - +
131H HIS* 3.0 27.2 + - - +
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Residues in contact with LEU 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H ALA* 3.4 38.4 - - + +
112H GLN* 3.8 20.6 - - + +
113H ALA* 3.6 25.6 - - + +
116H MET* 4.5 5.8 - - + -
124H LYS* 3.3 24.4 + - + +
125H ALA 3.0 6.6 + - - +
127H LYS* 1.4 75.7 - - - +
129H PHE* 1.3 62.4 + - - +
131H HIS* 3.3 10.1 + - + +
132H ALA* 3.1 22.5 + - - +
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Residues in contact with PHE 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H LEU* 3.6 18.8 - - + -
113H ALA* 3.9 25.5 - - + +
114H LEU* 4.5 13.9 - - + -
117H LYS* 5.0 1.8 - - + -
125H ALA* 2.7 30.8 + - + +
126H GLN 3.7 3.1 - - - +
128H LEU* 1.3 70.7 - - - +
130H MET* 1.4 61.7 + - - +
132H ALA* 3.3 7.3 + - - +
133H LEU* 3.2 31.1 + - - +
142H ALA* 4.3 3.8 - - + -
145H GLU* 3.6 28.9 - - + -
146H PHE* 3.5 53.2 - + + -
149H PHE* 3.7 28.3 - + + -
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Residues in contact with MET 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H GLN* 3.2 24.4 + - + +
127H LYS* 3.6 9.2 - - - +
128H LEU 3.3 0.2 - - - -
129H PHE* 1.4 75.3 - - - +
131H HIS* 1.4 60.6 + - - +
133H LEU* 3.5 8.8 + - - +
134H LYS* 2.9 36.8 + - + +
146H PHE* 3.7 29.6 - - + -
158H GLN* 4.6 8.3 - - - +
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Residues in contact with HIS 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ALA 6.1 1.1 - - - -
109H ALA* 3.8 17.1 - - + +
127H LYS 3.0 14.8 + - - +
128H LEU* 3.4 15.4 - - + +
129H PHE 3.3 0.4 - - - -
130H MET* 1.4 74.7 - - - +
132H ALA* 1.4 51.0 + - - +
134H LYS* 2.9 11.3 + - + +
135H MET* 2.8 69.8 + - + +
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Residues in contact with ALA 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ALA* 3.8 13.6 - - - +
109H ALA* 3.8 18.4 - - + -
110H LEU* 4.2 9.6 - - + +
128H LEU 3.1 14.0 + - - +
129H PHE* 3.3 10.9 + - - +
131H HIS* 1.4 74.1 + - - +
133H LEU* 1.4 57.5 + - - +
135H MET* 3.6 7.7 - - - +
136H ASP* 3.2 23.8 + - - +
139H PHE* 4.0 18.7 - - + -
142H ALA* 4.4 7.2 - - + -
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Residues in contact with LEU 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H PHE* 3.2 26.3 + - + +
130H MET* 4.0 9.2 - - - +
131H HIS 3.2 0.2 - - - -
132H ALA* 1.4 72.6 - - - +
134H LYS* 1.4 61.0 + - - +
135H MET 3.3 2.0 - - - -
136H ASP 3.4 15.7 - - - +
137H PRO* 3.1 38.9 - - + +
139H PHE* 4.2 2.2 - - + -
142H ALA* 3.8 35.2 - - + -
143H LEU* 3.6 32.3 - - + +
146H PHE* 4.1 24.2 - - + -
162H LEU* 6.0 1.1 - - + -
165H ARG* 4.4 6.3 - - - +
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Residues in contact with LYS 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H MET* 2.9 26.4 + - + +
131H HIS* 2.9 12.3 + - + +
133H LEU* 1.4 75.5 - - - +
135H MET* 1.4 62.9 + - + +
137H PRO* 5.0 2.6 - - - +
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Residues in contact with MET 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ALA* 4.1 33.7 - - + +
131H HIS* 2.8 50.6 + - + +
132H ALA* 3.6 9.9 - - - +
134H LYS* 1.4 78.1 - - - +
136H ASP* 1.4 58.5 + - - +
137H PRO* 4.5 1.3 - - - +
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Residues in contact with ASP 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ALA* 4.9 10.8 - - + +
132H ALA 3.2 15.0 + - - +
133H LEU* 3.3 6.7 - - - +
134H LYS 3.5 0.2 - - - -
135H MET* 1.4 82.7 - - + +
137H PRO* 1.4 66.6 - - - +
138H ASP* 3.2 27.6 + - - +
139H PHE* 3.4 32.6 + - + +
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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