Contacts of the strand formed by residues 139 - 149 (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 GLY 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B VAL 3.6 2.0 + - - -
138B PRO* 1.3 75.8 - - - +
140B LEU* 1.3 62.6 + - - -
141B TYR* 3.4 12.6 - - - -
188B LYS* 3.4 16.7 - - - -
189B LEU 2.8 33.7 + - - -
219B LEU* 4.4 0.9 - - - -
221B PHE 3.4 11.0 - - - -
223B ASP* 3.9 5.9 + - - -
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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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92A ARG* 3.7 8.7 - - + +
94A ALA* 3.9 4.9 - - + -
116A THR* 3.6 31.0 - - + -
118A GLN* 3.5 36.1 - - + -
139B GLY* 1.3 71.9 - - - -
141B TYR* 1.3 55.5 + - - +
186B VAL* 4.1 11.2 - - + -
187B LEU 3.5 0.9 - - - -
188B LYS* 3.8 21.7 - - + +
219B LEU* 3.3 8.3 - - - +
220B LEU* 2.7 44.4 + - + -
221B PHE* 3.0 36.3 + - + +
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Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.7 24.1 - - + +
125B ASN* 5.3 0.2 + - - -
133B PHE* 3.5 30.7 - + - -
135B CYS* 4.0 12.5 - - - -
136B LYS 4.8 0.5 + - - -
137B VAL* 2.6 31.7 + - - +
139B GLY 3.4 18.2 - - - -
140B LEU* 1.3 73.7 - - - +
142B TYR* 1.3 60.9 + - - +
143B PHE* 3.5 26.7 - + + -
186B VAL* 3.3 7.3 - - - +
187B LEU 2.8 31.5 + - - +
189B LEU* 4.0 11.9 - - + -
218B PHE* 3.2 23.3 - - - +
219B LEU* 3.6 29.7 - - + +
220B LEU* 4.0 4.3 - - - +
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Residues in contact with TYR 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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138A TYR* 5.1 3.0 - + - -
140A THR* 3.4 31.4 + - + +
142A GLN* 4.2 4.2 + - - -
215A SER* 4.6 3.8 - - - -
217A PHE* 3.9 15.0 - + + -
141B TYR* 1.3 73.9 - - - +
143B PHE* 1.3 65.4 + - - +
144B THR* 3.8 28.7 + - + -
184B GLY* 4.0 7.7 - - - -
185B MET* 3.5 29.6 - - - -
186B VAL* 3.7 16.2 - - + -
217B GLY* 3.0 4.7 - - - -
218B PHE* 3.0 70.5 + + + -
220B LEU* 4.1 12.5 - - + +
139C TYR* 4.2 14.0 + + - -
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Residues in contact with PHE 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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97B PHE* 4.0 18.2 - + - -
133B PHE* 3.7 25.8 - + + -
141B TYR* 3.5 26.0 - + + -
142B TYR* 1.3 77.3 - - - +
144B THR* 1.3 62.2 + - - +
157B LEU* 5.0 8.7 - - + -
184B GLY* 3.0 4.7 - - - -
185B MET* 2.9 38.9 + - + +
187B LEU* 3.8 29.8 - - + -
189B LEU* 3.7 27.1 - - + -
195B VAL* 3.9 23.6 - - + -
215B PHE* 4.4 9.4 - + + -
216B SER 3.4 5.2 - - - +
217B GLY* 4.0 13.0 - - - -
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Residues in contact with THR 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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142B TYR* 3.8 24.7 + - + -
143B PHE* 1.3 77.2 - - - +
145B TYR* 1.3 71.1 + - - +
146B HIS* 4.0 14.2 + - + +
182B THR* 4.1 2.3 + - - -
183B GLY 3.3 13.4 + - - -
184B GLY* 4.1 0.2 - - - -
215B PHE* 3.6 4.6 - - - -
216B SER* 2.8 56.5 + - - +
218B PHE* 5.3 2.2 - - + -
139C TYR* 3.5 26.2 + - + +
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Residues in contact with TYR 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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115B PHE* 5.3 2.0 - + + -
144B THR* 1.3 78.3 + - - +
146B HIS* 1.3 65.5 + - - +
147B ALA* 4.0 27.4 - - + -
153B LEU* 5.6 2.4 - - + +
155B VAL* 3.0 31.6 - - + +
170B PHE* 3.3 30.5 + + - +
181B THR* 4.4 10.8 - - + +
182B THR* 2.6 39.3 + - - -
183B GLY* 3.0 36.8 + - - -
197B LEU* 3.8 36.3 - - + -
205B LEU* 6.2 0.2 - - + -
214B ILE* 3.1 16.2 - - - +
215B PHE* 4.2 2.7 - + + -
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Residues in contact with HIS 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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115B PHE* 5.5 0.3 - - - -
144B THR* 4.0 13.6 + - + +
145B TYR* 1.3 77.2 - - - +
147B ALA* 1.3 61.5 + - - +
180B VAL* 4.4 0.9 - - + -
181B THR 3.2 7.4 - - - +
182B THR* 3.2 22.3 + - + -
213B SER* 3.2 3.3 - - - -
214B ILE* 2.8 44.1 + - + +
216B SER* 6.2 0.2 - - - -
139C TYR* 4.5 2.2 + - - -
141C VAL* 4.3 12.7 - - + +
143C HIS* 5.3 1.6 - + - -
164C PHE* 3.7 22.1 - - + -
176C SER* 3.2 22.9 + - - +
177C GLY* 3.4 25.2 + - - -
178C GLY* 3.3 28.4 + - - -
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Residues in contact with ALA 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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115B PHE* 6.2 1.6 - - + -
145B TYR* 4.0 19.4 - - + -
146B HIS* 1.3 74.4 - - - +
148B SER* 1.3 62.5 + - - +
149B SER* 4.9 0.7 - - - -
153B LEU* 3.8 14.2 - - + +
179B GLN 3.9 0.2 - - - +
180B VAL* 3.3 4.8 - - - +
181B THR* 2.9 36.9 + - + +
205B LEU* 3.7 28.7 - - + -
212B ASN 4.4 0.2 - - - -
213B SER* 3.5 6.1 - - - +
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Residues in contact with SER 148 (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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147B ALA* 1.3 75.3 - - - +
149B SER* 1.3 62.4 + - - +
178B PHE* 6.5 0.2 - - - -
179B GLN 3.3 10.6 + - - -
180B VAL* 4.4 3.7 - - - +
205B LEU* 3.5 5.5 - - - +
206B LEU* 2.9 27.4 + - - -
211B ALA* 3.5 34.1 - - - +
212B ASN 2.6 24.3 + - - -
213B SER* 3.0 9.3 + - - -
164C PHE* 4.1 11.4 - - - -
165C CYS 4.7 2.5 + - - -
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Residues in contact with SER 149 (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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147B ALA 4.9 0.9 - - - -
148B SER* 1.3 75.7 - - - +
150B ARG* 1.3 59.9 + - - +
151B GLY 2.7 26.0 + - - -
153B LEU* 4.1 8.5 - - - -
178B PHE* 3.4 5.5 - - - +
179B GLN* 2.9 49.0 + - - +
204B SER 3.0 23.1 + - - -
206B LEU* 4.0 11.6 - - - +
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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