Contacts of the helix formed by residues 145 - 154 (chain B) in PDB entry 2JIF
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 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B GLU* 4.3 0.7 - - - +
141B ILE* 3.2 30.7 + - + +
144B THR* 1.3 90.6 - - - +
146B ILE* 1.3 63.8 + - - +
148B THR 4.4 0.7 - - - -
149B LEU* 3.2 35.6 + - - +
174B PHE* 3.9 40.6 - - + -
289B SER* 3.5 36.6 - - - +
290B LEU* 4.2 9.4 - - + +
293B GLY* 4.1 1.1 - - - -
414B GLU* 3.8 24.2 - - - +
1433B FAD 6.0 1.3 - - - +
1434B COS 5.3 3.6 - - - -
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Residues in contact with ILE 146 (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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141B ILE* 3.0 17.1 + - + +
142B GLN* 3.5 9.4 - - - +
145B LEU* 1.3 74.9 - - - +
147B ASN* 1.3 68.0 + - - +
148B THR 3.4 0.3 + - - -
149B LEU* 3.4 3.6 + - - +
150B ILE* 3.2 30.8 + - + +
166B LEU* 3.8 33.0 - - + -
172B GLY* 3.9 23.3 - - - +
173B SER 3.6 32.8 - - - +
174B PHE* 3.7 14.8 - - + +
216B LEU* 4.4 6.5 - - + -
218B LEU* 4.3 17.6 - - + +
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Residues in contact with ASN 147 (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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103B MET 2.8 29.1 + - - +
104B GLY* 3.7 12.9 - - - -
107B VAL* 3.7 20.3 - - + +
142B GLN* 2.8 25.9 + - - +
143B ASN* 3.6 15.0 + - - +
146B ILE* 1.3 72.2 - - - +
148B THR* 1.3 56.8 + - - +
150B ILE* 3.4 3.0 + - - +
151B ARG* 2.8 37.5 + - - +
163B LEU* 4.3 6.1 - - - +
166B LEU* 3.5 30.3 + - - +
167B THR* 5.1 0.4 - - - +
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Residues in contact with THR 148 (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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106B GLU* 5.1 5.2 + - - -
143B ASN 3.0 15.1 + - - -
144B THR 3.5 18.8 + - - +
145B LEU 4.4 0.2 - - - -
146B ILE 3.3 0.6 - - - -
147B ASN* 1.3 78.8 - - - +
149B LEU* 1.3 59.0 + - + +
151B ARG* 3.4 9.6 + - - +
152B LYS* 2.9 66.3 + - + +
289B SER* 5.2 9.6 - - - -
292B GLU* 3.3 22.6 + - - +
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Residues in contact with LEU 149 (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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145B LEU 3.2 23.0 + - - +
146B ILE 3.4 4.7 + - - +
148B THR* 1.3 79.7 - - + +
150B ILE* 1.3 57.5 + - - +
152B LYS* 6.4 0.4 - - + -
153B HIS* 2.9 48.8 + - + +
174B PHE* 3.8 17.9 - - + -
218B LEU* 3.8 22.0 - - + -
220B MET* 4.9 2.5 - - + -
276B LEU* 3.9 16.8 - - + +
285B TYR* 3.5 42.0 - - + +
289B SER* 3.7 23.3 - - - +
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Residues in contact with ILE 150 (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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146B ILE* 3.2 17.5 + - + +
147B ASN 3.9 2.9 - - - +
149B LEU* 1.3 76.1 - - - +
151B ARG* 1.3 61.8 + - - +
154B GLY* 2.9 30.2 + - - +
158B GLN* 4.6 7.2 - - + +
159B LYS* 3.8 19.3 - - + +
162B TYR* 4.3 8.1 - - + -
163B LEU* 3.8 25.1 - - + -
166B LEU* 3.3 32.3 - - + -
216B LEU* 4.0 17.3 - - + -
218B LEU* 4.7 2.0 - - + -
236B LEU* 4.3 19.3 - - + -
276B LEU* 4.3 11.2 - - + -
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Residues in contact with ARG 151 (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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106B GLU* 3.3 35.4 + - - +
107B VAL* 4.1 14.4 - - - -
108B ASP* 4.8 2.8 + - - +
147B ASN* 2.8 26.1 + - - +
148B THR* 3.7 7.7 - - - +
150B ILE* 1.3 76.3 - - - +
152B LYS* 1.3 67.9 + - + +
159B LYS* 3.2 28.0 + - - +
163B LEU* 4.2 13.2 - - + -
1436B CL 3.0 32.3 - - + +
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Residues in contact with LYS 152 (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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148B THR* 2.9 49.3 + - + +
149B LEU* 6.4 0.7 - - + -
151B ARG* 1.3 82.8 - - + +
153B HIS* 1.3 85.6 + - + +
154B GLY 5.0 1.0 - - - +
159B LYS* 5.7 0.2 - - - -
292B GLU* 3.2 17.4 + - - -
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Residues in contact with HIS 153 (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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149B LEU* 2.9 39.2 + - + +
152B LYS* 1.3 97.0 + - + +
154B GLY* 1.3 65.1 + - - +
155B THR* 3.8 2.3 + - - +
158B GLN* 4.3 0.5 - - - +
276B LEU* 3.8 15.6 - - + +
277B GLY* 3.6 28.5 + - - -
284B LYS* 5.7 1.1 - - + -
285B TYR* 3.3 45.8 + + + +
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Residues in contact with GLY 154 (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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150B ILE* 2.9 21.8 + - - -
151B ARG 5.0 0.2 - - - +
152B LYS 3.7 2.0 - - - +
153B HIS* 1.3 79.1 - - - +
155B THR* 1.3 68.3 + - - +
156B GLU* 4.5 1.0 - - - +
158B GLN* 3.5 14.4 - - - -
159B LYS* 3.7 16.2 + - - -
276B LEU* 3.8 8.5 - - - +
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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