Contacts of the helix formed by residues 158 - 174 (chain B) in PDB entry 1J38
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 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TYR* 4.2 5.4 + - - -
156B SER* 3.3 11.9 + - - +
157B ARG* 1.3 76.8 - - - +
159B HIS* 1.3 63.6 + - - +
160B GLU* 3.1 20.0 + - - +
161B GLU* 2.6 41.8 + - + +
162B LEU* 2.9 29.5 + - - +
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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
----------------------------------------------------------
157B ARG 3.8 3.2 - - - -
158B ASP* 1.3 74.7 - - - +
160B GLU* 1.3 95.5 + - + +
162B LEU* 4.1 10.8 - - - -
163B ALA* 2.9 30.5 + - - +
243B TYR* 3.8 13.0 - + + -
247B VAL* 4.0 35.7 - - + +
257B HIS* 3.4 9.3 + - - +
258B LEU* 3.8 22.4 - - + -
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TYR* 3.7 19.8 + - + +
158B ASP* 3.1 13.5 + - - +
159B HIS* 1.3 104.5 + - + +
161B GLU* 1.3 60.0 + - - +
163B ALA* 3.4 7.5 + - - +
164B TYR* 2.9 26.2 + - - +
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TYR* 3.4 30.8 + - + +
136B LYS* 2.9 35.1 + - - +
152B VAL* 4.3 9.8 - - + +
156B SER* 2.6 30.1 + - - +
158B ASP* 2.6 27.3 + - - +
160B GLU* 1.3 69.6 - - - +
162B LEU* 1.3 67.1 + - - +
164B TYR* 3.1 13.1 + - - +
165B TYR* 3.1 35.4 + - + -
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Residues in contact with LEU 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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152B VAL* 3.8 5.6 - - + +
153B ILE* 3.6 45.5 - - + +
156B SER* 3.6 25.1 - - - +
158B ASP 2.9 27.7 + - - +
159B HIS* 3.7 4.7 - - - +
161B GLU* 1.3 76.4 - - - +
163B ALA* 1.3 64.0 + - - +
165B TYR* 3.2 6.1 + - - +
166B TRP* 3.0 20.6 + - - +
243B TYR* 3.5 24.0 - - - +
257B HIS* 3.0 37.3 - - + +
258B LEU* 4.2 5.8 - - + -
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B HIS 2.9 18.7 + - - +
160B GLU* 3.5 7.6 - - - +
162B LEU* 1.3 75.3 - - - +
164B TYR* 1.3 66.5 + - - +
166B TRP* 2.8 7.9 + - - +
167B ARG* 2.8 27.5 + - + +
257B HIS* 3.4 15.8 - - + +
482B PRO* 4.4 13.5 - - + +
483B VAL* 5.9 3.4 - - + -
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Residues in contact with TYR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 5.1 0.4 - - + -
133B CYS* 2.7 41.7 + - - +
134B ASP 4.2 1.6 + - - -
135B TYR* 3.3 47.3 - + + -
160B GLU 2.9 14.1 + - - +
161B GLU 3.1 9.1 + - - +
163B ALA* 1.3 76.1 - - - +
165B TYR* 1.3 77.2 + + - +
167B ARG* 3.1 32.2 + - - +
168B GLU* 3.0 63.7 + - + +
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Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 3.8 28.3 - - + +
133B CYS 4.2 0.4 - - - -
134B ASP* 3.2 18.0 + - - -
135B TYR* 3.0 25.5 + - + +
143B LEU* 3.8 11.2 - - + +
149B ILE* 4.3 17.1 - - + +
152B VAL* 3.2 40.9 - - + +
153B ILE* 3.5 22.7 - - + -
161B GLU* 3.1 34.8 + - + -
162B LEU 3.2 1.5 + - - +
164B TYR* 1.3 94.9 - + - +
166B TRP* 1.3 64.4 + - - +
168B GLU* 4.2 1.9 - - - +
169B PHE* 3.2 26.0 + - - +
262B MET* 4.0 3.1 - - - +
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Residues in contact with TRP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 4.6 1.7 - - + +
162B LEU 3.0 11.2 + - - +
163B ALA* 2.8 9.4 + - - +
165B TYR* 1.3 75.6 - - - +
167B ARG* 1.3 74.0 + - - +
168B GLU 3.3 0.3 + - - -
169B PHE* 3.3 1.0 + - - -
170B TYR* 2.9 74.6 + + + -
256B MET* 3.6 18.6 - - + +
257B HIS* 4.2 15.9 - - + -
262B MET* 3.9 22.7 + - - -
470B TRP* 4.0 8.7 - + - -
481B PRO* 3.7 16.6 - - + -
482B PRO* 3.3 33.9 - - + -
483B VAL* 4.0 13.2 - - + -
485B ARG* 3.3 40.2 - - - -
491B ASP* 4.2 1.6 - - - -
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA* 2.8 17.7 + - + +
164B TYR* 3.1 35.0 + - - +
166B TRP* 1.3 85.7 - - + +
168B GLU* 1.3 91.6 + - - +
170B TYR* 3.5 0.7 + - - +
171B ASP* 3.0 51.6 + - - +
482B PRO* 6.2 0.2 - - + -
483B VAL* 4.6 26.9 - - + -
485B ARG* 4.7 4.5 - - - +
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Residues in contact with GLU 168 (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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132B VAL* 3.9 21.8 - - + +
133B CYS* 5.3 2.8 + - - -
164B TYR* 3.0 54.2 + - + +
165B TYR* 4.2 3.8 - - - +
167B ARG* 1.3 110.3 + - - +
169B PHE* 1.3 61.0 + - - +
171B ASP* 3.7 4.4 + - - +
172B LYS* 3.5 43.5 + - - +
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PHE* 3.9 9.6 - + - -
130B VAL* 3.7 28.3 - - + -
132B VAL* 4.4 6.7 - - + +
145B LEU* 3.7 43.1 - - + -
149B ILE* 4.8 7.9 - - + -
165B TYR 3.2 18.0 + - - +
166B TRP 4.0 1.3 - - - +
168B GLU* 1.3 76.9 - - - +
170B TYR* 1.3 62.9 + + - +
172B LYS* 3.4 1.2 + - - -
173B ALA* 2.9 52.7 + - + +
262B MET* 4.0 28.3 - - + -
263B TRP* 4.4 5.4 - - - -
494B ALA* 3.2 33.2 - - + -
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Residues in contact with TYR 170 (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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166B TRP* 2.9 65.6 + + + +
167B ARG 4.1 0.7 - - - +
169B PHE* 1.3 81.2 - + - +
171B ASP* 1.3 57.3 + - - +
174B GLY* 2.9 29.3 + - - -
175B THR* 3.4 4.0 + - - -
256B MET* 4.0 9.7 - - - +
262B MET* 3.4 29.0 + - + -
263B TRP* 3.7 15.3 - + - -
469B PHE* 5.5 1.9 - + - -
470B TRP* 3.9 8.3 - + - -
485B ARG* 3.4 16.6 - - - +
491B ASP* 3.1 39.2 - - + +
494B ALA* 3.6 28.7 - - + -
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Residues in contact with ASP 171 (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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167B ARG* 3.0 40.1 + - - +
168B GLU* 4.1 5.5 - - - +
170B TYR* 1.3 75.1 - - - +
172B LYS* 1.3 60.3 + - + +
175B THR* 3.2 29.2 - - + +
176B ALA* 3.2 10.4 + - - +
485B ARG* 2.4 34.7 + - - -
489B ASP* 4.1 2.8 - - - +
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Residues in contact with LYS 172 (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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126B ASN* 2.9 19.2 + - - +
130B VAL* 4.0 19.7 - - + +
131B LYS 3.2 29.3 + - - +
132B VAL* 4.0 16.6 - - + +
168B GLU* 3.5 31.8 + - - +
169B PHE 3.4 2.8 + - - +
170B TYR 3.2 0.2 - - - -
171B ASP* 1.3 81.6 - - + +
173B ALA* 1.3 60.3 + - - +
174B GLY 3.4 0.2 - - - -
176B ALA* 3.1 20.2 - - - +
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Residues in contact with ALA 173 (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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126B ASN* 3.9 12.1 - - - +
127B PHE* 4.3 9.4 - - + +
130B VAL* 4.0 7.9 - - + -
169B PHE* 2.9 52.5 + - + +
172B LYS* 1.3 75.2 - - - +
174B GLY* 1.3 60.2 + - - +
177B VAL* 4.1 2.9 - - - +
493B PRO* 3.3 22.2 - - - +
494B ALA* 3.8 7.6 - - - -
499B SER* 4.1 3.8 + - - -
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Residues in contact with GLY 174 (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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170B TYR 2.9 13.3 + - - -
173B ALA* 1.3 78.2 - - - +
175B THR* 1.3 66.0 + - - +
176B ALA 3.2 1.1 - - - -
177B VAL* 2.9 25.1 + - - +
178B ARG 4.1 0.5 + - - -
490B PHE* 2.9 18.1 - - - +
491B ASP* 4.3 2.0 - - - -
493B PRO* 3.6 13.2 - - - +
494B ALA* 3.9 9.1 - - - +
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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