Contacts of the strand formed by residues 179 - 188 (chain B) in PDB entry 4JZJ
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 TYR 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A HIS* 5.8 0.2 - - - -
111B GLU* 2.9 40.3 + - - +
144B ASN 3.3 0.7 + - - -
145B PHE* 3.0 50.7 + - + +
146B TYR* 3.4 31.1 + + - -
148B ARG* 3.4 45.9 + - + -
169B VAL* 4.1 12.8 - - + -
170B THR* 3.5 23.3 - - - +
171B GLU* 4.3 1.1 - - - -
172B GLN* 3.7 34.6 + - + -
178B THR* 1.3 75.5 - - - +
180B SER* 1.3 66.7 + - - +
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A HIS* 3.3 24.9 + - - -
173A PHE* 3.1 16.7 - - - -
142B LEU 3.4 8.3 - - - -
143B ASN* 2.9 26.6 + - - -
144B ASN* 3.1 12.8 + - - -
145B PHE* 3.7 2.2 - - - -
169B VAL* 3.4 2.2 - - - +
170B THR* 2.8 38.4 + - - -
178B THR* 4.6 0.2 + - - -
179B TYR* 1.3 73.9 + - - +
181B LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 181 (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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173A PHE* 3.7 4.2 - - - -
141B LEU* 3.4 5.2 - - - +
142B LEU* 2.8 45.8 + - + +
145B PHE* 3.7 23.3 - - + -
148B ARG 5.3 3.8 - - - +
150B ALA* 5.2 9.0 - - + +
152B VAL* 3.9 27.1 - - + -
167B GLU* 3.6 28.3 - - + +
168B SER 3.3 9.9 - - - +
169B VAL* 3.9 20.6 - - + -
180B SER* 1.3 75.6 - - - +
182B SER* 1.3 75.3 + - - +
183B SER* 4.1 3.6 - - - +
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 3.6 33.8 - - - +
186A SER* 4.0 10.9 + - - -
188A VAL* 5.9 0.7 - - - -
139B VAL* 5.1 6.1 - - - -
140B CYS 3.5 7.6 - - - -
141B LEU* 4.6 2.5 - - - +
166B GLN 3.8 0.2 - - - +
167B GLU* 3.1 5.7 - - - +
168B SER* 2.9 37.7 + - - -
181B LEU* 1.3 76.1 - - - +
183B SER* 1.3 60.8 + - - +
184B THR* 4.3 8.3 + - - -
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Residues in contact with SER 183 (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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139B VAL* 3.3 4.0 - - - -
140B CYS* 3.0 35.7 + - - -
152B VAL* 3.7 26.2 + - - +
154B TRP* 2.8 26.3 + - - -
165B SER* 4.4 5.2 + - - -
166B GLN 3.2 7.7 + - - -
167B GLU* 3.9 14.3 + - - +
181B LEU* 4.1 4.4 - - - +
182B SER* 1.3 74.1 - - - +
184B THR* 1.3 63.3 + - - +
185B LEU 4.0 0.2 - - - -
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Residues in contact with THR 184 (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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148A LEU* 5.0 9.5 - - + +
150A LYS* 5.1 2.7 - - - +
186A SER* 5.3 2.3 + - - -
137B SER* 4.2 14.6 - - - +
138B VAL 3.7 2.2 - - - +
139B VAL* 3.8 20.3 - - + +
164B ASN 3.9 0.2 - - - +
165B SER* 3.3 7.1 - - - -
166B GLN* 2.8 37.9 + - - +
182B SER* 4.5 8.7 + - - -
183B SER* 1.3 73.9 + - - +
185B LEU* 1.3 61.2 + - - +
186B THR* 3.5 29.1 + - + +
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Residues in contact with LEU 185 (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 SER* 3.7 0.9 - - - -
138B VAL* 2.9 40.2 + - + +
154B TRP* 3.6 47.7 - - + +
155B LYS 6.0 0.2 - - - +
156B VAL* 5.2 1.1 - - + -
161B GLN* 4.4 16.6 - - + -
164B ASN* 3.2 49.4 - - - +
165B SER* 4.1 6.1 - - - -
183B SER 4.0 0.8 + - - -
184B THR* 1.3 70.4 - - - +
186B THR* 1.3 59.6 + - - +
187B LEU* 3.6 23.6 + - + -
198B TYR* 4.7 12.3 - - + -
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Residues in contact with THR 186 (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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150A LYS* 3.3 18.4 - - - +
178A GLN* 5.8 0.4 - - - +
135B THR* 6.4 1.8 - - - -
136B ALA 3.3 3.1 - - - +
137B SER* 3.1 27.4 - - - +
164B ASN* 3.3 21.8 + - - +
165B SER* 5.4 0.2 - - - -
166B GLN* 5.8 4.2 + - - -
184B THR* 3.7 23.1 + - + -
185B LEU* 1.3 70.5 - - - +
187B LEU* 1.3 66.4 + - - +
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Residues in contact with LEU 187 (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 THR* 3.4 3.1 - - - -
136B ALA* 2.4 49.8 + - + +
138B VAL* 5.3 3.1 - - + -
156B VAL* 5.9 2.2 - - + -
161B GLN* 5.3 3.8 - - - +
164B ASN* 3.4 29.8 - - - +
185B LEU* 3.6 23.8 - - + +
186B THR* 1.3 79.0 - - - +
188B SER* 1.3 61.7 + - - +
191B ASP* 4.8 14.1 - - + +
192B TYR* 4.5 12.6 - - + +
195B HIS* 6.3 1.8 - - + -
198B TYR* 3.7 34.8 - - + +
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Residues in contact with SER 188 (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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134B GLY 4.3 5.6 - - - -
135B THR* 4.2 8.3 - - - +
136B ALA 4.0 0.4 - - - -
187B LEU* 1.3 76.7 - - - +
189B LYS* 1.3 64.0 + - - +
190B ALA* 3.6 7.6 + - - +
191B ASP* 3.0 27.4 + - - +
192B TYR* 3.1 20.1 + - - +
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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
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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