Contacts of the strand formed by residues 177 - 187 (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 GLN 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A VAL 3.8 0.3 - - - +
144A LEU* 3.4 2.7 - - - +
145A SER* 2.8 37.8 + - - +
146A GLN 5.5 2.5 - - - +
147A TRP 6.0 0.4 - - - +
169A ASP* 3.5 30.5 - - + +
171A THR* 3.4 33.4 - - - +
172A ASN 5.7 1.1 - - - +
173A LYS* 5.5 2.6 - - - +
175A LEU* 3.3 21.2 + - - +
176A PHE* 1.3 77.0 + - - +
178A VAL* 1.3 63.6 + - - +
179A VAL 3.9 0.7 + - - -
172B ASP* 3.4 2.9 - - - +
173B TYR 3.8 8.9 + - - -
174B ALA* 5.4 1.8 - - - +
175B TYR 6.0 0.4 - - - +
1224B CA 2.3 28.5 - - - -
173C GLN* 3.3 11.6 + - - +
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Residues in contact with VAL 178 (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* 3.9 23.8 - - + -
143A VAL 3.6 7.0 - - - +
144A LEU* 4.1 11.4 - - + -
169A ASP* 4.5 8.1 - - - +
177A GLN* 1.3 73.5 - - - +
179A VAL* 1.3 72.1 + - - +
180A SER* 4.0 5.1 + - - +
211A ASP 5.7 1.8 - - - +
170B PHE* 5.5 9.2 - - + -
171B CYS 3.4 27.8 - - - +
172B ASP* 3.3 22.2 + - + +
180B VAL 5.8 0.2 - - - +
181B THR* 3.9 9.7 - - - +
182B THR* 3.9 15.0 - - + +
174C VAL* 5.2 8.0 + - - +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 3.9 3.1 - - + +
142A GLN* 3.4 2.1 - - - -
143A VAL 2.8 43.6 + - - +
149A ILE* 3.7 36.3 - - + +
151A LEU* 3.9 15.5 - - + -
167A PHE* 3.5 29.4 - - + +
168A CYS* 3.6 23.1 - - - +
169A ASP* 3.8 7.8 - - + +
177A GLN 3.9 1.4 + - - -
178A VAL* 1.3 74.2 - - - +
180A SER* 1.3 62.5 + - - +
174C VAL* 4.1 8.7 - - + +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 3.2 20.6 - - - -
142A GLN* 4.1 3.8 - - - -
167A PHE* 3.4 18.2 - - - +
178A VAL* 4.0 3.3 + - - -
179A VAL* 1.3 79.3 - - - +
181A GLY* 1.3 60.1 + - - +
182B THR* 3.6 25.7 - - - +
143C HIS* 3.2 23.8 + - - -
174C VAL* 3.5 25.0 + - - +
176C SER* 3.9 3.3 - - - -
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A THR* 3.1 5.4 + - - -
141A PHE* 2.9 39.7 + - - -
167A PHE* 3.7 19.7 - - - -
180A SER* 1.3 78.7 - - - +
182A GLY* 1.3 57.6 + - - -
143C HIS* 3.7 17.5 + - - -
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Residues in contact with GLY 182 (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* 3.7 18.8 + - - -
139A PHE 2.9 15.0 - - - -
140A THR* 3.9 2.0 - - - -
153A ILE* 4.0 5.1 - - - +
167A PHE* 4.1 9.4 - - - -
181A GLY* 1.3 74.7 - - - -
183A MET* 1.3 66.3 + - - +
143C HIS* 3.7 4.4 - - - -
208C VAL* 3.5 22.7 - - - +
210C SER* 4.5 1.0 + - - -
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Residues in contact with MET 183 (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 3.7 0.3 - - - +
138A TYR* 3.1 13.6 - - - -
139A PHE* 2.9 31.9 + - + +
153A ILE* 4.6 23.8 - - + -
164A SER* 3.5 25.4 - - - +
165A LEU* 4.6 6.1 - - + -
167A PHE* 6.4 1.8 - - + -
182A GLY* 1.3 75.7 - - - +
184A VAL* 1.3 68.9 + - - +
185A LEU* 3.5 37.3 + - + -
95C THR* 4.0 14.4 - - + -
116C LEU* 3.2 36.6 - - + -
208C VAL* 4.9 0.9 - - + -
210C SER* 4.2 1.6 - - - -
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Residues in contact with VAL 184 (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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136A TYR* 4.1 18.4 - - + -
137A TYR 3.1 9.9 - - - +
138A TYR* 4.0 9.6 - - + -
183A MET* 1.3 89.6 - - - +
185A LEU* 1.3 62.7 + - - +
186A GLN 4.3 0.2 - - - -
219A ILE* 3.9 15.3 - - + -
93C VAL* 3.7 34.1 - - + -
94C PHE 3.9 8.3 - - - +
95C THR* 2.9 24.4 + - - +
116C LEU* 5.0 1.2 - - - +
117C THR* 3.7 24.4 - - + +
210C SER* 4.6 1.8 - - - -
212C PHE* 4.1 6.5 - - + -
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Residues in contact with LEU 185 (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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135A GLY 3.7 0.3 - - - +
137A TYR* 2.8 33.8 + - - +
139A PHE* 3.9 29.4 - - + -
153A ILE* 4.3 12.6 - - + +
154A VAL 5.6 0.2 - - - -
155A SER* 4.2 20.4 - - - +
162A ARG* 5.6 1.8 - - - +
164A SER* 5.6 2.5 - - - +
183A MET* 3.5 32.3 + - + -
184A VAL* 1.3 74.4 - - - +
186A GLN* 1.3 64.0 + - - +
187A LEU* 3.6 15.2 + - + +
193A VAL* 4.1 22.2 - - + -
111F ARG* 6.1 3.1 - - - +
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Residues in contact with GLN 186 (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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135A GLY* 3.5 11.7 - - - +
136A TYR* 3.6 50.3 + - + -
162A ARG* 4.5 4.9 + - - -
184A VAL* 4.3 0.4 - - - +
185A LEU* 1.3 73.9 - - - +
187A LEU* 1.3 69.0 + - - +
188A GLN* 5.8 0.5 - - - +
191A ASP* 4.6 0.5 - - - +
222A SER* 4.7 9.4 + - - +
117C THR* 5.2 8.1 + - - +
126F SER* 4.2 23.2 + - - +
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Residues in contact with LEU 187 (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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129A PHE* 4.0 3.1 - - + -
131A CYS* 3.8 29.2 - - + -
134A PRO* 3.5 4.0 - - - +
135A GLY 2.9 33.3 + - - +
137A TYR* 3.9 11.7 - - + -
139A PHE* 3.8 19.3 - - + -
155A SER* 4.8 0.7 - - - -
162A ARG* 4.0 11.9 - - - +
185A LEU* 3.9 25.6 - - + +
186A GLN* 1.3 83.8 - - - +
188A GLN* 1.3 64.5 + - - +
191A ASP* 3.6 15.5 - - + +
193A VAL* 3.6 31.9 - - + -
222A SER* 4.9 0.9 + - - -
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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