Contacts of the helix formed by residues 155 - 165 (chain D) in PDB entry 1N33
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 LEU 155 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436A C 4.1 3.4 - - - +
437A U 2.9 52.5 - - - +
438A G 5.7 0.4 - - - +
120D LEU* 6.1 0.9 - - + -
125D HIS* 4.1 12.8 - - + +
152D SER* 3.0 39.9 - - - +
153D ARG 2.6 10.1 + - - -
154D ASN* 1.3 76.3 - - - +
156D GLU* 1.3 71.2 + - - +
157D LEU* 4.4 3.1 - - + +
158D ILE* 3.4 19.1 - - + +
159D ARG* 2.8 27.6 + - - +
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Residues in contact with GLU 156 (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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435A C 4.0 9.9 + - - -
436A C 3.9 34.1 - - - +
154D ASN 4.1 1.0 + - - -
155D LEU* 1.3 78.0 - - - +
157D LEU* 1.3 71.3 + - - +
159D ARG* 4.7 3.4 - - - -
160D GLN* 2.7 40.9 + - + +
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Residues in contact with LEU 157 (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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407A G 5.2 5.2 - - - +
436A C 4.0 36.1 + - - +
437A U 5.0 5.6 - - - +
110D PHE 4.4 8.1 - - - +
116D GLN* 3.8 34.5 - - + +
119D GLN* 5.7 3.4 - - - +
120D LEU* 4.2 26.5 - - + -
155D LEU* 5.1 3.6 - - + -
156D GLU* 1.3 81.1 + - - +
158D ILE* 1.3 62.0 + - + +
160D GLN* 4.2 4.0 - - - -
161D ASN* 2.8 52.0 + - - +
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Residues in contact with ILE 158 (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 PHE* 4.7 7.9 - - + +
120D LEU* 5.4 12.8 - - + -
125D HIS* 5.0 4.3 - - + -
148D VAL* 3.5 32.5 - - + -
152D SER* 2.7 38.1 - - - +
153D ARG 3.6 11.4 - - - +
155D LEU* 3.3 15.7 + - + +
156D GLU 2.9 1.4 + - - -
157D LEU* 1.3 78.9 - - + +
159D ARG* 1.3 68.5 + - - +
161D ASN* 3.0 3.8 + - - -
162D LEU* 2.6 36.0 + - + +
181D MET* 4.1 19.7 - - - -
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Residues in contact with ARG 159 (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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153D ARG 4.5 7.0 - - - +
154D ASN* 4.6 18.2 + - - +
155D LEU 2.8 24.3 + - - +
156D GLU* 3.7 3.6 - - - +
158D ILE* 1.3 72.8 - - - +
160D GLN* 1.3 67.9 + - - +
162D LEU* 4.9 2.0 - - - -
163D GLU* 2.6 44.7 + - - +
181D MET* 3.7 23.3 - - - +
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Residues in contact with GLN 160 (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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156D GLU* 2.7 35.1 + - + +
157D LEU* 3.5 6.3 - - - +
159D ARG* 1.3 77.0 - - - +
161D ASN* 1.3 71.8 + - - +
163D GLU* 3.4 8.7 + - - +
164D ALA* 3.0 24.9 + - - +
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Residues in contact with ASN 161 (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 GLY 4.1 7.2 + - - +
110D PHE 3.5 14.4 - - - +
111D ALA* 3.3 4.2 - - - +
112D VAL* 2.9 49.6 - - - +
116D GLN* 3.7 0.6 + - - -
157D LEU* 2.8 39.6 + - - +
158D ILE 3.0 0.8 + - - +
160D GLN* 1.3 88.6 + - - +
162D LEU* 1.3 63.3 + - - +
164D ALA* 3.0 17.8 + - - +
165D MET* 3.2 14.2 + - - +
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Residues in contact with LEU 162 (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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108D LEU 4.5 3.1 - - - +
109D GLY 4.5 0.4 - - - +
110D PHE* 3.5 54.3 - - + +
158D ILE* 2.6 27.7 + - + +
159D ARG* 4.2 1.8 - - - +
161D ASN* 1.3 74.2 - - - +
163D GLU* 1.3 59.8 + - - +
165D MET* 3.2 21.4 - - + +
176D LEU* 5.7 4.5 - - + -
178D VAL* 3.2 36.2 - - + +
181D MET* 3.1 54.3 - - + -
182D LYS 5.7 0.2 - - - +
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Residues in contact with GLU 163 (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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159D ARG* 2.6 42.8 + - - +
160D GLN* 3.4 6.0 + - - +
162D LEU* 1.3 69.6 - - - +
164D ALA* 1.3 52.2 + - - +
165D MET 2.7 15.2 + - - -
166D LYS* 2.7 52.7 + - + +
178D VAL* 5.0 0.9 - - - -
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Residues in contact with ALA 164 (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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160D GLN* 3.0 22.3 + - - +
161D ASN* 3.0 11.4 + - - +
163D GLU* 1.3 75.6 - - - +
165D MET* 1.3 58.9 + - - +
166D LYS 3.3 3.8 + - - +
168D ARG* 4.3 14.2 + - - +
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Residues in contact with MET 165 (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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107D ARG 4.9 3.6 - - - +
108D LEU* 3.8 27.1 - - - +
109D GLY* 3.7 23.3 - - - +
161D ASN 3.2 13.1 + - - +
162D LEU* 3.2 19.7 - - + +
163D GLU 2.7 1.0 + - - -
164D ALA* 1.3 77.2 - - - +
166D LYS* 1.3 66.8 + - - +
167D GLY 3.3 0.3 + - - -
168D ARG* 3.0 73.3 + - + +
169D LYS 5.4 1.8 - - - +
170D VAL* 5.0 9.2 - - + -
176D LEU* 4.9 11.4 - - + -
178D VAL* 4.0 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