Contacts of the strand formed by residues 179 - 189 (chain B) in PDB entry 2JG8
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 GLN 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B SER* 3.3 5.2 - - - -
149B SER* 2.9 61.0 + - - +
151B GLY 3.2 6.9 + - - -
153B LEU* 4.3 3.8 - - - +
172B ASP* 2.8 43.0 + - - +
174B ALA* 3.8 15.7 - - + +
177B THR* 5.7 0.7 - - + -
178B PHE* 1.3 76.1 - - - +
180B VAL* 1.3 62.5 + - - +
181B THR* 4.9 5.0 - - - +
1224B CA 2.2 36.3 - - - -
165C CYS 3.6 8.8 - - - +
166C GLY* 4.7 2.7 - - - -
173C GLN* 5.6 5.4 - - - +
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Residues in contact with VAL 180 (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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178A VAL 5.8 0.3 - - - +
146B HIS* 4.4 1.1 - - + -
147B ALA 3.3 13.0 - - - +
148B SER* 4.6 2.7 - - - +
172B ASP* 4.5 2.8 - - - +
179B GLN* 1.3 79.0 - - - +
181B THR* 1.3 69.8 + - - +
164C PHE* 3.8 26.2 - - + -
165C CYS 3.6 16.7 + - - +
166C GLY* 4.6 3.0 - - - +
174C VAL 4.3 9.6 - - - +
175C ASN* 3.7 32.8 - - + +
176C SER* 3.4 28.7 + - - +
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Residues in contact with THR 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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178A VAL* 3.9 11.2 - - - +
145B TYR* 4.4 12.5 + - + +
146B HIS* 3.2 6.1 - - - +
147B ALA* 2.9 43.3 + - + +
153B LEU* 4.2 22.0 - - + -
170B PHE* 5.9 0.9 - - - +
172B ASP* 2.7 44.3 + - + +
179B GLN* 4.2 4.9 - - - +
180B VAL* 1.3 75.0 - - - +
182B THR* 1.3 72.7 + - - +
176C SER* 4.5 1.3 - - - -
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Residues in contact with THR 182 (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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142A GLN* 3.9 14.9 + - + +
178A VAL* 3.9 13.3 - - + +
180A SER* 3.6 28.5 - - - +
144B THR* 4.1 2.3 + - - -
145B TYR* 2.6 33.0 + - - -
146B HIS* 3.2 14.7 + - + -
170B PHE* 4.4 5.5 - - - +
181B THR* 1.3 88.1 + - - +
183B GLY* 1.3 64.4 + - - +
143C HIS* 4.9 2.9 - - + -
176C SER* 3.3 24.5 - - - +
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Residues in contact with GLY 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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142A GLN* 3.8 11.4 - - - -
142B TYR* 5.3 0.2 - - - -
144B THR* 3.3 6.1 + - - -
145B TYR* 3.0 46.4 + - - -
170B PHE* 3.8 16.6 - - - -
182B THR* 1.3 79.0 + - - +
184B GLY* 1.3 57.5 + - - -
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Residues in contact with GLY 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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142A GLN* 3.1 18.8 + - - +
213A VAL* 3.9 5.9 - - - +
215A SER* 4.7 2.0 - - - -
142B TYR* 4.0 16.8 - - - -
143B PHE 3.0 13.5 - - - -
144B THR* 4.1 0.2 - - - -
157B LEU* 5.4 0.4 - - - -
170B PHE* 3.7 15.6 - - - -
183B GLY* 1.3 73.7 - - - -
185B MET* 1.3 69.5 + - - +
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Residues in contact with MET 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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96A SER* 3.4 28.3 - - - -
98A ILE* 4.1 2.9 - - + -
115A ILE* 3.9 16.6 - - + -
213A VAL* 3.7 22.2 - - + -
215A SER* 4.3 1.6 - - - -
142B TYR* 3.5 8.8 - - - -
143B PHE* 2.9 35.7 + - + +
157B LEU* 3.5 22.4 - - + -
167B VAL* 4.7 1.8 - - + -
168B VAL* 3.6 42.4 - - + -
184B GLY* 1.3 76.8 - - - +
186B VAL* 1.3 61.3 + - - +
187B LEU* 3.6 27.8 + - + -
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Residues in contact with VAL 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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94A ALA* 4.0 16.4 - - + -
95A PHE 3.7 15.3 - - - +
96A SER* 2.6 24.1 + - - +
115A ILE* 4.3 0.2 - - - +
116A THR* 2.7 35.7 + - + -
215A SER* 4.2 4.7 - - - -
216A GLY 4.4 2.0 - - - +
217A PHE* 4.2 18.4 - - + -
140B LEU* 4.1 5.6 - - + -
141B TYR 3.3 10.8 - - - +
142B TYR* 3.7 19.5 - - + -
185B MET* 1.3 76.5 - - - +
187B LEU* 1.3 65.1 + - - +
220B LEU* 4.0 15.9 - - + -
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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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115A ILE* 3.8 11.9 - - + -
116A THR* 3.6 3.1 - - - +
139B GLY 3.6 0.9 - - - +
140B LEU* 3.5 5.2 - - - -
141B TYR* 2.8 33.6 + - - +
143B PHE* 3.8 29.6 - - + -
157B LEU* 4.3 13.0 - - + -
159B ARG* 3.3 31.4 - - + +
167B VAL* 4.1 9.6 - - + -
185B MET* 3.6 20.2 - - + -
186B VAL* 1.3 83.2 - - - +
188B LYS* 1.3 61.2 + - - +
189B LEU* 3.7 17.7 + - + +
195B VAL* 4.2 17.3 - - + -
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Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ARG* 3.1 23.0 - - - +
116A THR* 4.0 12.0 + - + -
118A GLN* 3.4 29.9 + - - +
139B GLY* 3.4 15.3 - - - +
140B LEU* 3.8 18.3 - - + +
159B ARG* 4.1 10.9 + - - +
187B LEU* 1.3 71.0 - - - +
189B LEU* 1.3 67.8 + - - +
190B GLU* 5.5 1.4 - - - +
193B GLU* 4.1 4.0 - - - +
223B ASP* 2.8 38.2 + - - +
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Residues in contact with LEU 189 (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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133B PHE* 3.9 17.9 - - + -
135B CYS* 4.0 15.5 - - + -
138B PRO* 3.2 5.9 - - - +
139B GLY 2.8 37.7 + - - +
141B TYR* 4.0 8.7 - - + -
143B PHE* 3.7 30.1 - - + -
159B ARG* 3.8 29.6 - - + -
187B LEU* 3.8 19.1 - - + -
188B LYS* 1.3 76.5 - - - +
190B GLU* 1.3 59.4 + - - +
193B GLU* 3.4 17.5 - - + +
195B VAL* 3.9 14.6 - - + -
223B ASP* 4.7 1.7 - - - +
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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