Contacts of the helix formed by residues 132 - 145 (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 ASP 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ILE* 4.1 4.2 - - + +
80B VAL* 3.9 18.4 - - + +
83B MET* 3.6 24.9 - - - +
128B LEU 2.8 19.8 + - - +
129B ALA 3.6 0.4 + - - -
131B VAL* 1.3 75.0 - - - +
133B ALA* 1.3 63.5 + - - +
134B SER* 3.0 24.4 + - - -
135B VAL* 3.0 25.4 + - + +
136B ALA* 3.1 9.4 + - - +
257B ALA* 4.9 2.8 - - - +
402B LYS* 2.7 33.2 + - - +
403B TYR* 5.7 0.7 - - - -
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Residues in contact with ALA 133 (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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129B ALA* 3.8 9.2 + - - +
132B ASP* 1.3 72.7 + - - +
134B SER* 1.3 61.3 + - - +
136B ALA* 3.3 8.3 + - - +
137B VAL* 3.0 12.3 + - - +
255B LEU* 3.7 11.2 - - + -
300B GLN* 2.9 35.9 + - + +
304B LEU* 3.7 32.5 - - + -
403B TYR* 5.8 1.8 - - + -
406B ASP* 4.0 12.5 + - + +
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B MET* 4.0 5.5 - - - +
132B ASP* 3.0 14.5 + - - -
133B ALA* 1.3 79.7 - - - +
135B VAL* 1.3 62.3 + - - +
137B VAL* 3.2 20.9 - - - +
138B PHE* 3.4 9.5 + - - +
255B LEU* 3.2 37.8 - - - +
256B ARG 3.7 1.9 + - - -
257B ALA* 3.7 25.0 + - - +
258B SER* 4.0 9.0 - - - -
402B LYS* 4.6 4.9 + - - -
406B ASP* 4.8 0.2 + - - -
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Residues in contact with VAL 135 (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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76B ILE* 3.7 33.9 - - + -
83B MET* 4.2 4.9 - - + -
89B MET* 4.2 16.4 - - + -
93B VAL* 3.9 20.6 - - + -
97B LEU* 4.0 27.9 - - + +
128B LEU* 4.3 7.9 - - + +
132B ASP* 3.0 29.2 + - + +
134B SER* 1.3 75.3 - - - +
136B ALA* 1.3 63.5 + - - +
138B PHE* 3.4 3.7 - - - +
139B CYS* 3.2 20.4 + - - +
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Residues in contact with ALA 136 (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 ILE* 3.5 35.6 - - + +
128B LEU* 4.0 11.8 - - - +
129B ALA* 3.6 25.4 - - + +
132B ASP 3.1 5.5 + - - -
133B ALA 3.5 9.0 - - - +
134B SER 3.2 0.4 - - - -
135B VAL* 1.3 76.5 - - - +
137B VAL* 1.3 57.1 + - - +
139B CYS* 3.1 5.9 + - - +
140B GLU* 2.8 28.2 + - - +
300B GLN* 4.1 3.6 - - + -
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Residues in contact with VAL 137 (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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133B ALA 3.0 10.8 + - - +
134B SER 3.2 13.5 - - - +
136B ALA* 1.3 73.6 - - - +
138B PHE* 1.3 63.7 + - - +
140B GLU* 4.0 18.8 - - - +
141B ILE* 2.8 44.5 + - + +
209B SER* 5.4 1.8 - - - +
255B LEU* 3.8 15.3 - - + -
258B SER* 3.7 21.1 - - - +
297B ILE* 4.3 5.6 - - + -
300B GLN* 3.6 15.4 - - - +
413B TYR* 3.7 25.4 - - + +
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Residues in contact with PHE 138 (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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89B MET* 4.5 11.9 - - + -
94B ILE* 3.8 34.3 - - + -
97B LEU* 3.5 24.5 - - + -
103B MET* 3.5 23.5 - - + +
134B SER 3.4 9.1 + - - +
135B VAL* 3.4 12.1 - - - +
137B VAL* 1.3 83.1 - - + +
139B CYS* 1.3 61.2 + - - +
141B ILE* 3.7 3.1 + - - +
142B GLN* 3.3 20.8 + - - +
171B VAL* 3.4 38.4 - - + -
210B SER* 3.6 20.9 + - - -
213B HIS* 4.9 2.2 - - + -
258B SER* 5.7 3.6 - - - +
1437B CL 3.9 24.0 - - + -
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Residues in contact with CYS 139 (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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97B LEU* 5.0 3.4 - - + -
102B LEU* 3.4 26.9 - - - -
103B MET* 4.3 12.3 - - - -
105B ILE* 4.4 2.9 - - - -
124B VAL* 3.9 15.0 - - - -
125B ILE* 4.5 7.6 - - + -
128B LEU* 3.5 30.5 - - + -
135B VAL 3.2 3.2 + - - +
136B ALA 3.1 9.8 + - - +
138B PHE* 1.3 80.8 - - - +
140B GLU* 1.3 60.7 + - - +
142B GLN* 3.5 1.4 + - - +
143B ASN* 2.9 34.7 + - - +
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Residues in contact with GLU 140 (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 ILE* 3.7 33.0 - - + -
136B ALA 2.8 19.0 + - - +
137B VAL* 3.1 10.3 + - - +
139B CYS* 1.3 71.3 - - - +
141B ILE* 1.3 81.4 + - - +
144B THR* 2.8 55.6 + - - +
145B LEU* 4.3 1.4 - - - +
293B GLY* 3.3 10.7 - - - +
296B GLY* 3.8 16.2 - - - -
297B ILE* 3.7 21.0 - - + +
300B GLN* 6.0 0.2 - - + -
414B GLU* 2.9 23.6 - - - +
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Residues in contact with ILE 141 (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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137B VAL* 2.8 37.9 + - + +
138B PHE 4.1 2.9 - - - +
140B GLU* 1.3 83.4 - - - +
142B GLN* 1.3 62.7 + - - +
145B LEU* 3.2 25.8 + - + +
146B ILE* 3.0 29.0 + - + +
172B GLY 3.8 20.4 - - - +
173B SER* 4.7 0.9 - - - -
174B PHE* 4.4 12.1 - - + +
209B SER* 3.4 34.8 - - - +
210B SER* 3.9 13.7 - - - +
258B SER* 5.3 0.4 - - - +
1433B FAD 4.7 3.8 - - - +
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Residues in contact with GLN 142 (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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98B PHE* 3.9 5.5 - - - -
103B MET* 3.4 49.6 - - + +
138B PHE 3.3 10.3 + - - +
139B CYS 3.8 4.0 - - - +
140B GLU 3.4 0.4 - - - -
141B ILE* 1.3 78.2 - - - +
143B ASN* 1.3 58.4 + - - +
146B ILE* 3.5 5.5 - - - +
147B ASN* 2.8 35.8 + - - +
166B LEU* 2.8 37.4 + - - +
170B LYS 2.9 20.2 + - - -
171B VAL* 3.7 4.2 - - - +
172B GLY* 3.0 27.5 + - - +
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Residues in contact with ASN 143 (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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102B LEU 2.8 26.0 + - - -
103B MET* 3.7 7.7 - - - +
104B GLY 3.6 4.3 + - - -
105B ILE* 2.9 40.0 + - - +
106B GLU* 4.4 8.2 + - - +
121B THR* 4.0 20.0 - - + +
139B CYS* 2.9 32.3 + - - +
142B GLN* 1.3 80.5 - - - +
144B THR* 1.3 61.1 + - + +
145B LEU 3.5 0.2 - - - -
147B ASN* 3.6 10.2 + - - +
148B THR* 3.0 26.9 + - - -
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Residues in contact with THR 144 (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* 5.3 0.4 - - - +
118B PHE* 4.5 11.2 - - + -
121B THR* 3.8 27.1 - - + -
125B ILE* 4.1 4.7 - - + -
140B GLU* 2.8 55.0 + - + +
143B ASN* 1.3 73.9 - - + +
145B LEU* 1.3 65.3 + - - +
148B THR* 3.5 22.0 + - - +
289B SER* 3.9 10.0 - - - +
292B GLU* 4.3 10.9 - - - +
293B GLY* 3.6 14.9 - - - -
296B GLY* 4.8 5.8 - - - -
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Residues in contact with LEU 145 (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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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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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