Contacts of the helix formed by residues 145 - 159 (chain B) in PDB entry 2J16
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 SER 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B CYS* 4.5 0.8 - - - -
144B LEU* 1.3 79.8 - - - +
146B ARG* 1.3 61.3 + - - +
147B SER 3.6 1.3 - - - +
148B ALA* 3.8 1.8 + - - +
149B THR* 2.7 33.4 + - - -
178B ASN 3.7 9.4 - - - -
179B PRO* 3.7 7.7 - - - +
180B SER* 3.1 24.9 + - - -
183B LEU* 3.3 15.0 - - - +
1198B SO4 3.1 19.3 + - - -
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 3.6 23.5 + - + +
89B ALA* 3.8 14.2 - - - +
91B GLU* 2.8 39.2 + - - -
109B TRP* 2.6 64.4 + - + -
110B GLU* 4.0 15.8 - - - +
111B HIS* 4.3 7.0 - - - +
140B CYS* 4.2 2.4 - - + +
141B GLN* 3.9 2.0 - - - +
145B SER* 1.3 72.7 - - - +
147B SER* 1.3 65.0 + - - +
149B THR* 3.3 8.4 + - - -
150B LEU* 3.1 18.0 + - - +
183B LEU* 4.0 18.4 - - + -
1198B SO4 2.8 49.4 + - - +
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.5 25.8 - - - +
88B VAL* 3.7 7.5 - - - +
138B ILE* 3.6 19.7 - - - +
139B HIS 3.9 12.6 - - - -
140B CYS* 2.8 31.2 + - - -
143B GLY* 4.7 0.5 - - - -
146B ARG* 1.3 74.7 - - - +
148B ALA* 1.3 64.6 + - - +
150B LEU* 3.4 2.7 + - - +
151B ILE* 3.1 28.2 + - - +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.3 6.4 - - + +
143B GLY 5.8 0.6 - - - +
144B LEU 3.9 22.0 - - - +
145B SER 3.8 4.3 + - - +
146B ARG 3.3 0.2 - - - -
147B SER* 1.3 78.7 + - - +
149B THR* 1.3 56.5 + - - +
151B ILE* 3.4 2.0 + - - +
152B ILE* 2.8 38.1 + - + +
170B LEU* 3.8 23.5 - - + +
177B ILE* 3.9 20.4 - - + -
179B PRO* 4.6 6.5 - - + -
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TRP* 4.7 2.2 - - + -
115B ILE* 3.7 31.2 - - + -
145B SER 2.7 19.1 + - - -
146B ARG* 3.4 11.7 - - - -
147B SER 3.3 0.2 - - - -
148B ALA* 1.3 77.2 - - - +
150B LEU* 1.3 57.2 + - - +
152B ILE* 3.4 2.5 + - - +
153B ALA* 2.9 27.5 + - - +
179B PRO* 3.5 15.3 - - - +
183B LEU* 3.8 20.3 - - + +
187B LEU* 3.7 28.2 - - + +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 4.0 12.8 - - + -
88B VAL* 3.8 18.8 - - + -
109B TRP* 4.1 13.0 - - + -
119B LEU* 4.4 12.3 - - + -
122B LEU* 3.6 34.8 - - + -
123B THR* 4.4 6.5 - - + -
126B ILE* 3.8 24.7 - - + -
138B ILE* 3.7 23.6 - - + -
146B ARG 3.1 9.8 + - - +
147B SER* 3.4 7.8 + - - +
149B THR* 1.3 78.1 - - - +
151B ILE* 1.3 58.3 + - - +
153B ALA* 3.1 7.0 + - - +
154B TYR* 2.9 25.5 + - - +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 4.2 9.0 - - + -
64B LEU* 4.2 16.2 - - + -
68B ILE* 4.3 9.6 - - + -
69B TYR 4.2 3.1 - - - +
70B LEU* 4.1 29.4 - - + -
126B ILE* 5.5 2.0 - - + -
138B ILE* 3.8 35.7 - - + -
147B SER 3.1 18.6 + - - +
148B ALA* 3.8 3.8 - - - +
150B LEU* 1.3 71.9 - - - +
152B ILE* 1.3 61.5 + - - +
154B TYR* 3.2 9.2 + - + +
155B ILE* 2.9 39.1 + - + +
170B LEU* 3.9 22.2 - - + -
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ALA* 2.8 27.9 + - + +
149B THR 3.7 4.5 - - - +
151B ILE* 1.3 76.0 - - - +
153B ALA* 1.3 58.1 + - - +
155B ILE* 3.4 7.7 + - - +
156B MET* 3.0 34.6 + - - +
163B LEU* 3.8 26.5 - - + -
166B SER* 3.9 14.0 - - - +
167B TYR* 3.9 39.9 - - + +
170B LEU* 4.0 17.7 - - + -
177B ILE* 4.4 4.0 - - + -
179B PRO* 4.6 6.3 - - + -
184B ILE* 6.3 0.2 - - + -
187B LEU* 3.8 16.2 - - + -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.7 26.2 - - + -
123B THR* 3.9 5.7 - - + +
149B THR 2.9 14.7 + - - +
150B LEU 3.1 9.2 + - - +
152B ILE* 1.3 73.3 - - - +
154B TYR* 1.3 65.7 + - - +
156B MET* 3.3 1.3 + - - -
157B LYS* 3.2 14.0 + - - +
187B LEU* 3.8 12.8 - - + -
190B TRP* 3.1 35.9 + - + +
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.0 11.2 - - + -
66B GLU* 3.2 27.7 + - - +
68B ILE* 3.6 20.9 - - + -
123B THR* 3.7 15.9 - - + +
126B ILE* 3.6 35.4 - - + -
127B HIS* 4.0 13.2 + - + -
130B THR* 3.9 17.8 + - - +
150B LEU 2.9 13.2 + - - +
151B ILE* 3.2 11.6 + - + +
153B ALA* 1.3 74.6 - - - +
155B ILE* 1.3 69.6 + - - +
156B MET 3.2 0.3 + - - -
157B LYS 3.3 1.2 + - - -
158B TYR* 3.0 59.9 + + + +
159B HIS* 4.0 10.4 + + - -
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Residues in contact with ILE 155 (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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65A PRO* 4.4 5.4 - - + -
64B LEU* 3.8 41.1 - - + -
151B ILE* 2.9 30.8 + - + +
152B ILE* 3.8 7.0 - - - +
154B TYR* 1.3 78.6 - - + +
156B MET* 1.3 62.9 + - - +
159B HIS* 3.1 37.5 + - + +
160B ASN 3.8 0.7 + - - -
161B LEU* 3.8 22.1 + - + -
166B SER* 3.5 35.0 - - - +
169B LEU* 4.6 5.6 - - + -
170B LEU* 4.8 8.7 - - + +
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Residues in contact with MET 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 3.0 33.3 + - - +
153B ALA 3.4 6.1 - - - +
154B TYR 3.1 0.4 - - - -
155B ILE* 1.3 75.3 - - - +
157B LYS* 1.3 60.6 + - - +
160B ASN* 3.2 5.4 + - - -
161B LEU 3.2 34.9 + - - +
162B SER 3.9 2.0 - - - +
163B LEU* 3.9 27.4 - - + +
166B SER* 3.3 16.2 - - - +
187B LEU* 3.4 29.6 - - - +
190B TRP* 3.9 12.6 - - + -
191B GLU* 3.5 30.5 - - + +
194B LEU* 3.8 14.1 - - + +
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Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO* 4.8 12.1 + - - +
123B THR* 4.1 8.4 + - - +
124B SER* 4.6 4.9 + - - -
153B ALA 3.2 11.7 + - - +
156B MET* 1.3 78.6 - - - +
158B TYR* 1.3 105.8 + - + +
160B ASN* 3.4 13.2 + - - +
190B TRP* 3.9 20.6 - - + -
194B LEU* 3.6 29.1 - - + +
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Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 5.1 8.3 + - - -
123B THR* 3.1 25.1 - - - -
124B SER* 3.3 24.4 + - - -
127B HIS* 3.4 40.5 - + + +
154B TYR* 3.0 52.2 + + + +
157B LYS* 1.3 115.0 + - + +
159B HIS* 1.3 68.3 + - - +
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Residues in contact with HIS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO* 3.5 47.8 + - + +
66A GLU* 3.9 14.8 + - + +
67A LYS* 3.6 16.3 + - - +
159A HIS* 6.2 1.6 - + - -
66B GLU* 2.7 31.8 + - - -
154B TYR* 4.0 10.7 + + - -
155B ILE* 3.1 29.5 + - + +
158B TYR* 1.3 82.8 + - - +
160B ASN* 1.3 70.8 + - - +
161B LEU* 3.3 9.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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