Contacts of the strand formed by residues 177 - 187 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D VAL 3.6 1.0 - - - +
144D LEU* 3.6 2.2 - - - -
145D SER* 2.8 39.0 + - - +
146D GLN* 5.4 2.5 - - - -
147D TRP 5.8 0.9 - - - +
169D ASP* 3.6 33.2 - - + +
171D THR* 3.5 31.4 - - - +
172D ASN 5.7 0.7 - - - +
173D LYS* 5.1 1.0 - - - +
175D LEU* 3.3 30.2 + - - +
176D PHE* 1.3 80.8 + - - +
178D VAL* 1.3 63.3 + - - +
179D VAL 3.9 0.9 + - - -
172E ASP* 3.4 4.3 - - - -
173E TYR 3.4 8.5 + - - +
1224E CA 2.4 28.6 - - - -
173F GLN* 3.4 10.4 + - - +
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Residues in contact with VAL 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D GLN* 3.8 30.7 - - + -
143D VAL 3.3 8.1 - - - +
144D LEU* 3.8 11.0 - - + -
169D ASP* 4.9 4.2 - - - +
177D GLN* 1.3 73.9 - - - +
179D VAL* 1.3 66.9 + - - +
180D SER* 3.8 2.9 + - - -
211D ASP 5.6 1.3 - - - +
170E PHE* 5.2 9.2 - - + -
171E CYS 3.5 26.7 - - - +
172E ASP* 3.2 22.1 + - - +
180E VAL 5.7 1.0 - - - +
181E THR* 3.9 10.3 - - - +
182E THR* 3.8 18.0 - - + +
174F VAL* 5.2 7.3 + - - +
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Residues in contact with VAL 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D PHE* 3.8 3.9 - - + -
142D GLN* 3.4 2.1 - - - -
143D VAL* 2.9 42.1 + - + +
149D ILE* 3.9 23.8 - - + -
151D LEU* 3.8 28.5 - - + -
167D PHE* 3.6 22.4 - - + +
168D CYS* 3.5 34.1 - - - +
169D ASP* 3.7 7.1 - - + +
177D GLN 3.9 2.4 + - - -
178D VAL* 1.3 72.8 - - - +
180D SER* 1.3 61.5 + - - +
174F VAL* 4.2 6.1 - - + +
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Residues in contact with SER 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D PHE* 3.2 19.5 - - - -
142D GLN* 4.3 2.7 - - - -
167D PHE* 3.3 22.5 - - - +
178D VAL* 3.8 3.0 + - - -
179D VAL* 1.3 76.2 - - - +
181D GLY* 1.3 59.2 + - - +
182E THR* 3.5 31.2 - - - +
143F HIS* 3.0 20.6 + - - -
174F VAL* 3.6 19.3 + - - +
176F SER* 3.8 6.9 - - - -
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Residues in contact with GLY 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D THR* 2.8 17.8 + - - -
141D PHE* 3.0 25.9 + - - -
167D PHE* 3.8 18.4 - - - -
180D SER* 1.3 78.3 - - - +
182D GLY* 1.3 57.9 + - - -
143F HIS* 3.4 19.5 + - - -
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Residues in contact with GLY 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D TYR* 3.8 16.6 + - - -
139D PHE 2.9 16.2 - - - -
140D THR* 3.9 0.2 - - - -
153D ILE* 3.9 6.5 - - - -
167D PHE* 4.1 10.7 - - - -
181D GLY* 1.3 74.3 - - - -
183D MET* 1.3 66.0 + - - +
143F HIS* 3.7 3.7 - - - -
208F VAL* 3.4 23.6 - - - +
210F SER* 4.5 1.0 + - - -
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Residues in contact with MET 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D TYR* 3.2 12.7 - - - -
139D PHE* 2.9 31.8 + - - +
153D ILE* 4.5 25.1 - - + -
164D SER* 3.7 24.5 - - - +
165D LEU* 4.9 7.9 - - + +
167D PHE* 6.1 3.6 - - + -
182D GLY* 1.3 76.2 - - - +
184D VAL* 1.3 69.5 + - - +
185D LEU* 3.3 39.6 + - + -
95F THR* 4.0 16.4 - - + -
116F LEU* 3.3 29.6 - - + -
208F VAL* 4.9 1.3 - - + -
210F SER* 4.1 1.3 - - - -
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Residues in contact with VAL 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D TYR* 4.1 16.4 - - + -
137D TYR 3.1 9.9 - - - +
138D TYR* 3.7 17.9 - - + -
183D MET* 1.3 86.9 - - - +
185D LEU* 1.3 62.6 + - - +
186D GLN 4.3 0.2 - - - -
219D ILE* 3.7 17.9 - - + -
93F VAL* 3.6 28.5 - - + -
94F PHE 4.0 4.3 - - - +
95F THR* 3.0 21.9 + - - +
116F LEU* 5.1 1.9 - - - +
117F THR* 3.9 26.4 - - + +
210F SER* 4.5 0.9 - - - -
212F PHE* 4.0 8.7 - - + -
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Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ARG* 5.7 7.0 - - - +
135D GLY 3.6 0.2 - - - +
137D TYR* 2.8 35.9 + - - +
139D PHE* 3.8 25.8 - - + -
153D ILE* 4.2 13.0 - - + +
155D SER* 4.4 15.9 - - - +
162D ARG* 5.9 0.9 - - - +
164D SER* 5.6 1.8 - - - +
183D MET* 3.3 34.0 + - + -
184D VAL* 1.3 75.7 - - - +
186D GLN* 1.3 62.9 + - - +
187D LEU* 3.5 17.3 + - + +
193D VAL* 4.0 25.1 - - + -
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Residues in contact with GLN 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C SER* 4.2 21.6 + - - +
135D GLY* 3.4 12.1 - - - +
136D TYR* 3.2 51.1 + - + -
162D ARG* 4.6 5.0 + - - -
184D VAL* 4.3 0.6 + - - +
185D LEU* 1.3 72.2 - - - +
187D LEU* 1.3 70.7 + - - +
188D GLN* 4.4 1.7 + - + +
191D ASP* 4.6 0.3 - - - +
222D SER* 4.3 11.3 + - - +
89F LYS* 5.5 0.2 + - - -
117F THR* 5.1 7.3 + - - +
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Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D PHE* 3.8 18.2 - - + -
131D CYS* 3.9 20.9 - - + -
134D PRO* 3.4 5.0 - - - +
135D GLY 2.9 29.0 + - - -
137D TYR* 4.0 11.4 - - + -
139D PHE* 3.7 17.9 - - + -
155D SER* 4.6 1.1 - - - +
162D ARG* 3.8 19.7 - - - +
185D LEU* 3.9 22.0 - - + +
186D GLN* 1.3 85.4 - - - +
188D GLN* 1.3 63.1 + - - +
191D ASP* 3.6 8.3 - - + +
193D VAL* 3.6 33.9 - - + -
222D SER* 5.1 0.5 + - - -
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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