Contacts of the strand formed by residues 135 - 145 (chain A) 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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A VAL 3.7 1.8 + - - -
134A PRO* 1.3 75.6 - - - +
136A TYR* 1.3 64.5 + - - -
137A TYR* 3.4 10.6 - - - -
186A GLN* 3.5 3.4 - - - -
187A LEU 2.9 33.0 + - - -
218A LEU* 4.2 3.1 - - - -
220A PHE 3.5 10.5 - - - -
221A PRO* 3.9 0.9 - - - -
222A SER* 3.4 17.7 + - - -
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLY* 1.3 75.0 - - - -
137A TYR* 1.3 53.8 + - - +
184A VAL* 4.1 15.3 - - + -
185A LEU 3.7 2.9 - - - -
186A GLN* 3.6 44.9 + - + -
218A LEU* 3.4 3.5 - - - +
219A ILE* 2.7 34.3 + - + +
220A PHE* 2.9 60.5 + + + +
222A SER* 4.5 10.3 - - - -
88C GLN* 4.6 7.8 + - + +
93C VAL* 3.9 11.9 - - + -
117C THR* 3.5 22.7 - - - -
119C PRO* 3.7 27.9 - - + +
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PRO* 4.0 12.0 - - + +
129A PHE* 3.7 28.2 - + - -
131A CYS* 3.8 15.2 - - - -
132A THR 4.6 1.4 + - - -
133A VAL* 2.3 48.0 + - - +
135A GLY 3.4 18.4 - - - -
136A TYR* 1.3 75.0 - - - +
138A TYR* 1.3 60.0 + - - +
139A PHE* 3.4 22.5 + + + -
183A MET 3.7 0.3 - - - +
184A VAL* 3.1 5.4 - - - -
185A LEU 2.8 33.1 + - - +
187A LEU* 3.9 14.1 - - + -
217A PHE* 3.3 8.1 - - - +
218A LEU* 3.5 43.3 - - + +
219A ILE* 3.9 4.5 - - - -
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Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A TYR* 1.3 73.3 - - - +
139A PHE* 1.3 67.7 - - - +
140A THR* 3.8 21.3 - - + -
182A GLY* 3.7 15.6 + - - -
183A MET* 3.1 32.5 - - - -
184A VAL* 3.8 6.1 - - + -
216A GLY* 3.1 4.5 - - - -
217A PHE* 2.8 74.6 + + + -
219A ILE* 3.7 10.3 - - + +
142B TYR* 5.1 3.6 - + - -
139C TYR* 4.7 8.1 - + - -
141C VAL* 3.2 28.6 - - + +
143C HIS* 4.1 9.4 + - - -
210C SER* 4.1 14.9 + - - -
212C PHE* 3.8 15.7 - + + -
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 4.1 10.8 - + - -
129A PHE* 3.6 48.0 - + + -
137A TYR* 3.4 28.9 - + + -
138A TYR* 1.3 76.4 - - - +
140A THR* 1.3 61.8 + - - +
153A ILE* 3.9 18.5 - - + +
182A GLY* 2.9 3.6 - - - -
183A MET* 2.9 36.4 + - + +
185A LEU* 3.9 26.7 - - + -
187A LEU* 3.8 12.3 - - + -
193A VAL* 3.8 19.3 - - + -
214A PHE* 4.3 8.7 - + + -
215A SER 3.5 6.3 - - - +
216A GLY* 3.8 16.6 - - - -
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Residues in contact with THR 140 (chain A).
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* 3.8 18.5 - - + -
139A PHE* 1.3 76.7 - - - +
141A PHE* 1.3 61.4 + - - +
142A GLN* 3.0 21.1 + - - +
153A ILE* 4.6 1.3 - - - -
181A GLY 3.1 15.2 + - - -
182A GLY* 3.9 1.5 - - - -
213A VAL 4.9 0.2 - - - -
214A PHE* 3.4 6.1 - - - -
215A SER* 3.0 45.0 + - - +
217A PHE* 5.6 1.3 - - + -
142B TYR* 3.4 31.7 + - + +
143C HIS* 4.3 8.3 + - - -
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Residues in contact with PHE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A THR* 1.3 76.4 + - - +
142A GLN* 1.3 68.3 + - - +
143A VAL* 3.9 10.1 - - + -
151A LEU* 3.7 44.0 - - + -
153A ILE* 3.7 41.5 - - + -
167A PHE* 3.8 23.1 - + + -
179A VAL* 4.0 7.6 - - + -
180A SER* 3.2 26.9 - - - -
181A GLY* 2.9 31.8 + - - +
195A VAL* 4.6 12.6 - - + -
213A VAL 3.3 12.6 - - - +
214A PHE* 4.3 9.6 - - + -
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Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A THR* 3.0 36.9 + - - +
141A PHE* 1.3 79.0 + - - +
143A VAL* 1.3 61.7 + - - +
144A LEU 4.2 0.2 + - - -
178A VAL* 3.9 15.3 - - + -
179A VAL 3.4 5.4 - - - -
180A SER* 4.1 1.7 - - - -
211A ASP 4.4 2.1 - - - +
212A SER* 3.3 5.0 - - - -
213A VAL* 2.9 40.9 + - - +
215A SER* 5.4 1.2 + - - -
142B TYR* 4.2 4.9 + - - -
170B PHE* 4.6 8.3 - - + -
182B THR* 3.9 33.8 + - + +
183B GLY* 3.9 5.8 - - - -
184B GLY* 3.1 33.8 + - - +
143C HIS* 5.5 1.6 - - - -
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 5.5 0.7 - - + -
111A PHE* 4.0 30.5 - - + -
141A PHE* 3.9 12.1 - - + -
142A GLN* 1.3 76.9 - - - +
144A LEU* 1.3 68.7 - - - +
145A SER 3.7 0.7 + - - -
149A ILE* 3.5 23.8 - - + -
151A LEU* 3.5 26.9 - - + -
178A VAL* 3.6 3.7 - - - +
179A VAL* 2.8 39.6 + - + +
195A VAL* 5.4 0.2 - - + -
204A ILE* 4.0 16.8 - - + -
212A SER* 3.7 10.5 - - - +
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Residues in contact with LEU 144 (chain A).
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 4.2 0.6 + - - -
143A VAL* 1.3 74.3 - - - +
145A SER* 1.3 61.6 + - - +
176A PHE* 3.6 35.0 - - + -
177A GLN 3.4 18.2 - - - +
178A VAL* 4.1 5.6 - - + +
204A ILE* 3.5 7.3 - - - -
205A TYR* 2.9 44.8 + - + -
210A ALA* 3.4 37.5 - - + -
211A ASP 4.2 8.0 + - - +
212A SER* 2.8 20.2 + - - +
171B CYS 3.5 22.7 - - - +
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Residues in contact with SER 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A VAL 3.7 0.4 + - - -
144A LEU* 1.3 75.5 - - - +
146A GLN* 1.3 69.6 + - - +
147A TRP 3.4 12.2 + - - -
148A GLU 4.0 2.4 - - - -
149A ILE* 3.5 29.4 - - - +
169A ASP* 5.6 1.3 - - - -
175A LEU 3.6 0.2 - - - +
176A PHE* 3.5 4.5 - - - -
177A GLN* 2.8 39.3 + - - -
203A HIS* 2.6 32.3 + - - +
205A TYR* 4.2 1.8 - - - +
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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