Contacts of the helix formed by residues 136 - 147 (chain B) in PDB entry 3JXI
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 ASN 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A PHE* 5.3 0.9 - - - +
260A GLN* 4.0 14.9 + - - +
264A GLU* 6.1 2.4 - - - +
134B VAL* 4.5 12.7 - - + +
135B PHE* 1.3 75.1 - - - +
137B ARG* 1.3 59.2 + - - +
138B PRO* 3.2 15.3 - - + +
139B ILE* 3.1 33.3 + - - +
140B LEU* 2.9 29.8 + - - +
171B PHE* 3.9 14.0 - - - -
345C ASP* 5.3 6.5 + - - +
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Residues in contact with ARG 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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136B ASN* 1.3 75.4 - - - +
138B PRO* 1.3 74.6 - - + +
140B LEU* 4.3 3.8 - - - -
141B PHE* 2.9 53.4 + - + +
169B GLU 3.4 9.5 + - - -
170B GLU* 3.3 34.6 + - - +
171B PHE* 4.2 8.0 - - - -
172B ARG 3.0 37.5 + - - +
173B GLU* 4.1 1.1 - - - +
174B PRO* 3.9 27.3 - - - +
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Residues in contact with PRO 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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259A PHE* 3.4 43.5 - - + +
260A GLN* 4.1 13.2 - - - +
136B ASN* 3.2 14.4 - - + +
137B ARG* 1.3 96.4 - - + +
139B ILE* 1.3 55.8 + - - +
141B PHE* 4.1 3.8 - - + +
142B ASP* 3.0 30.7 + - - +
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Residues in contact with ILE 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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220A VAL* 3.3 35.4 - - + +
221A TYR* 5.9 3.4 - - + -
259A PHE* 3.3 32.8 - - + -
264A GLU* 5.5 1.8 - - - +
134B VAL* 4.4 13.9 - - + +
135B PHE* 4.1 14.8 - - + -
136B ASN* 3.1 35.8 + - - +
138B PRO* 1.3 74.6 - - - +
140B LEU* 1.3 64.5 + - - +
142B ASP* 3.6 1.9 + - - +
143B ILE* 3.1 36.0 + - + +
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Residues in contact with LEU 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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135B PHE* 5.0 7.2 - - + -
136B ASN 2.9 18.8 + - - +
137B ARG* 3.8 3.4 - - - +
139B ILE* 1.3 77.9 - - - +
141B PHE* 1.3 66.5 + - + +
143B ILE* 3.3 6.0 + - - +
144B VAL* 3.2 33.2 + - + +
152B LEU* 4.1 13.0 - - + -
155B LEU* 3.6 33.7 - - + -
166B LEU* 3.9 18.6 - - + -
171B PHE* 3.9 31.4 - - + -
180B CYS* 4.0 24.9 - - + -
199B LEU* 4.5 0.4 - - + -
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Residues in contact with PHE 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 ARG* 2.9 45.1 + - + +
138B PRO* 4.1 3.6 - - + +
140B LEU* 1.3 78.3 - - + +
142B ASP* 1.3 60.2 + - - +
144B VAL* 3.8 4.6 - - - +
145B SER* 2.3 36.1 + - - -
171B PHE 3.5 24.9 - - - -
173B GLU* 3.9 33.4 - - + -
178B LYS* 3.9 8.1 - - + -
179B THR 4.3 4.3 - - - -
180B CYS* 4.0 26.7 - - + -
183B LYS* 4.6 24.7 - - + -
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Residues in contact with ASP 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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218A ARG* 5.5 0.5 + - - -
220A VAL* 3.8 4.9 - - + +
257A ARG* 2.8 38.4 + - - -
259A PHE* 3.7 16.6 - - + -
138B PRO 3.0 20.3 + - - +
139B ILE 3.8 4.3 - - - +
141B PHE* 1.3 76.6 - - - +
143B ILE* 1.3 62.7 + - - +
145B SER* 3.8 4.0 - - - -
146B ARG* 2.9 65.5 + - - +
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Residues in contact with ILE 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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220A VAL* 4.4 11.7 - - + -
133B LYS* 6.1 0.4 - - - -
135B PHE* 3.9 17.3 - - + -
139B ILE* 3.1 24.7 - - + +
140B LEU* 3.3 7.4 + - - +
141B PHE 3.3 0.6 - - - -
142B ASP* 1.3 77.6 - - - +
144B VAL* 1.3 58.7 + - - +
146B ARG* 3.4 21.3 + - - +
147B GLY 2.8 22.3 + - - -
148B SER* 3.0 37.3 + - - +
151B GLY* 3.4 31.4 - - - +
152B LEU* 3.6 22.4 - - + +
195B THR* 4.5 0.9 - - + -
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Residues in contact with VAL 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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140B LEU* 3.2 26.2 + - + +
141B PHE* 3.8 7.9 - - - +
143B ILE* 1.3 73.7 - - - +
145B SER* 1.3 63.0 + - - +
147B GLY 3.3 1.6 + - - +
152B LEU* 4.5 4.5 - - + -
180B CYS* 3.7 26.0 - - + +
183B LYS* 3.5 26.7 - - + -
184B ALA* 4.0 5.9 - - + +
187B ASN* 4.3 0.2 - - - +
193B ASN* 2.6 31.5 + - - -
195B THR* 4.0 21.1 - - + +
199B LEU* 4.1 23.8 - - + -
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Residues in contact with SER 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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141B PHE 2.3 27.8 + - - -
142B ASP* 3.8 5.6 - - - -
144B VAL* 1.3 73.4 - - - +
146B ARG* 1.3 66.3 + - - +
147B GLY 3.2 0.2 - - - -
183B LYS* 2.9 27.8 - - - -
187B ASN* 3.4 34.6 - - - +
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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
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174A PRO* 4.5 2.4 - - - +
175A SER* 2.9 54.4 + - - +
176A THR* 4.0 2.8 - - - +
218A ARG* 3.5 54.1 + - - +
219A ASP* 3.8 9.3 - - - +
220A VAL* 3.8 18.0 - - - +
257A ARG* 3.9 2.4 - - - +
142B ASP* 2.9 47.1 + - - +
143B ILE* 3.8 24.5 - - - +
145B SER* 1.3 78.3 - - - +
147B GLY* 1.3 58.7 + - - +
148B SER* 3.9 15.7 + - - +
151B GLY* 5.8 1.2 - - - -
187B ASN 5.6 0.4 - - - -
189B SER* 5.3 4.3 + - - -
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Residues in contact with GLY 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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175A SER* 3.4 7.7 + - - -
143B ILE 2.8 9.0 + - - -
144B VAL 3.3 5.1 + - - -
145B SER 3.2 3.2 - - - -
146B ARG* 1.3 78.6 - - - +
148B SER* 1.3 56.9 + - - -
149B PRO* 3.2 12.6 - - - +
187B ASN 5.2 0.7 - - - -
193B ASN* 3.2 29.2 - - - +
194B ASP* 4.7 5.0 + - - +
195B THR* 3.7 5.6 - - - -
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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