Contacts of the helix formed by residues 155 - 167 (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 THR 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B HIS 3.8 2.0 + - - +
154B GLY* 1.3 76.4 - - - -
156B GLU* 1.3 59.8 + - - +
157B GLU* 3.6 8.0 + - - +
158B GLN* 3.1 40.1 + - - +
159B LYS* 2.9 27.2 + - - +
275B ILE 5.9 0.4 - - - +
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Residues in contact with GLU 156 (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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111B TYR* 4.0 14.9 + - - -
154B GLY 4.5 0.7 - - - +
155B THR* 1.3 74.0 - - - +
157B GLU* 1.3 57.7 + - - +
159B LYS* 2.6 36.3 + - - +
160B ALA* 3.0 29.0 + - - +
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Residues in contact with GLU 157 (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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155B THR* 3.2 7.0 + - - +
156B GLU* 1.3 77.6 - - - +
158B GLN* 1.3 60.8 + - + +
160B ALA* 3.3 5.5 + - - +
161B THR* 2.8 35.8 + - - +
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Residues in contact with GLN 158 (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* 4.8 4.3 - - + -
153B HIS 4.3 1.0 - - - +
154B GLY* 3.5 12.1 - - - -
155B THR* 3.1 45.0 + - - +
157B GLU* 1.3 76.5 - - + +
159B LYS* 1.3 57.6 + - - +
161B THR* 4.5 4.3 - - - -
162B TYR* 2.9 41.3 + - + +
236B LEU* 3.9 26.2 - - + +
273B ALA 2.7 28.8 + - - +
274B ASN* 4.0 1.1 - - - +
275B ILE 3.1 23.3 + - - +
276B LEU* 3.8 7.4 - - - +
277B GLY 5.1 0.5 + - - -
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Residues in contact with LYS 159 (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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111B TYR* 3.6 29.9 - - + +
150B ILE* 3.8 16.4 - - + +
151B ARG* 3.2 29.6 + - - +
152B LYS 5.8 0.2 + - - -
154B GLY 3.7 15.3 + - - +
155B THR 2.9 15.4 + - - +
156B GLU* 2.6 32.6 + - - +
158B GLN* 1.3 77.3 - - - +
160B ALA* 1.3 58.0 + - - +
163B LEU* 3.0 49.2 + - + +
164B PRO* 3.2 5.5 - - - +
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Residues in contact with ALA 160 (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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111B TYR* 3.9 14.8 - - + -
156B GLU 3.0 20.1 + - - +
157B GLU* 3.3 8.0 + - - +
159B LYS* 1.3 76.0 - - - +
161B THR* 1.3 60.2 + - - +
164B PRO* 3.3 17.8 - - - +
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Residues in contact with THR 161 (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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157B GLU* 2.8 21.5 + - - +
158B GLN* 3.7 5.6 - - - -
160B ALA* 1.3 79.7 - - - +
162B TYR* 1.3 87.5 + - + +
164B PRO* 3.8 4.2 - - - +
165B GLN* 3.5 28.3 + - - +
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Residues in contact with TYR 162 (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* 4.3 10.1 - - + -
158B GLN* 2.9 33.7 + - + +
161B THR* 1.3 91.0 - - + +
163B LEU* 1.3 61.1 + - - +
164B PRO 3.4 0.4 - - - -
165B GLN* 3.1 23.2 + - - +
166B LEU* 2.8 43.4 + - + +
170B LYS* 4.6 7.0 - - + -
216B LEU* 3.7 33.4 - - + +
236B LEU* 3.9 28.9 - - + -
238B ASP* 3.1 24.4 + - - -
274B ASN* 3.4 22.5 + - - -
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Residues in contact with LEU 163 (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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107B VAL* 4.2 22.2 - - + -
111B TYR* 3.5 40.6 - - + -
147B ASN* 4.3 20.6 - - - +
150B ILE* 3.8 25.8 - - + -
151B ARG* 4.2 7.0 - - + -
159B LYS* 3.0 32.6 + - + +
162B TYR* 1.3 76.4 - - - +
164B PRO* 1.3 65.8 - - + +
166B LEU* 3.3 5.9 + - + +
167B THR* 3.0 30.5 + - - +
1436B CL 4.2 11.0 - - + -
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Residues in contact with PRO 164 (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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110B GLU 5.5 0.4 - - - +
111B TYR* 3.3 32.1 - - + +
159B LYS 3.2 13.0 - - - +
160B ALA 3.3 21.1 - - - +
161B THR 3.8 3.4 - - - +
162B TYR 3.6 2.2 - - - -
163B LEU* 1.3 91.4 - - + +
165B GLN* 1.3 51.3 + - + +
167B THR* 3.2 9.9 + - - -
168B THR* 2.4 31.1 + - - +
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Residues in contact with GLN 165 (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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161B THR* 3.5 28.0 + - - +
162B TYR* 3.1 19.6 + - - +
164B PRO* 1.3 76.4 - - + +
166B LEU* 1.3 63.2 + - - +
168B THR* 3.1 5.0 + - - -
169B GLU* 2.9 25.0 + - + +
170B LYS* 2.7 71.1 + - + +
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Residues in contact with LEU 166 (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* 3.3 8.8 - - - -
103B MET 3.4 8.0 - - - +
142B GLN* 2.8 28.7 + - - +
146B ILE* 3.8 16.6 - - + -
147B ASN* 3.5 23.1 - - - +
150B ILE* 3.3 34.5 - - + -
162B TYR* 2.8 22.2 + - + +
163B LEU* 3.3 9.8 + - + +
165B GLN* 1.3 78.6 - - + +
167B THR* 1.3 57.8 + - + +
168B THR 3.4 0.2 - - - -
170B LYS* 3.4 26.2 - - + +
171B VAL 4.4 0.7 - - - -
172B GLY* 4.1 9.2 - - - +
216B LEU* 4.2 15.0 - - + -
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.7 21.3 - - - +
101B GLY* 5.5 2.4 - - - -
103B MET* 4.3 7.9 + - - +
104B GLY* 3.9 21.5 + - - -
107B VAL* 3.8 26.5 - - + -
111B TYR 2.7 25.7 + - - +
112B GLY* 3.5 20.2 + - - +
113B GLY* 4.0 3.6 - - - -
147B ASN* 5.1 0.2 - - - +
163B LEU 3.0 11.8 + - - +
164B PRO 3.2 9.5 + - - -
165B GLN 3.2 0.2 - - - -
166B LEU* 1.3 78.3 - - + +
168B THR* 1.3 61.5 + - - +
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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