Contacts of the strand formed by residues 213 - 221 (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 VAL 213 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D SER* 4.4 1.6 - - - -
97D ALA 3.3 10.1 - - - +
98D ILE* 4.1 8.5 - - + -
111D PHE* 3.6 5.0 - - - -
141D PHE* 3.3 7.3 - - - +
142D GLN* 2.9 42.3 + - - +
211D ASP* 4.8 0.7 - - + -
212D SER* 1.3 81.3 - - - +
214D PHE* 1.3 64.3 + - - +
215D SER* 3.7 21.3 - - - +
168E VAL* 4.7 3.8 - - + -
170E PHE* 3.5 34.8 - - + -
184E GLY 3.9 9.4 - - - +
185E MET* 3.9 22.2 - - + -
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Residues in contact with PHE 214 (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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95D PHE* 3.3 30.2 - + + -
96D SER* 3.3 0.3 - - - -
97D ALA 2.8 30.8 + - - -
109D VAL 5.4 0.2 - - - -
111D PHE* 3.4 41.9 - + + -
122D TYR* 4.0 17.3 - + - -
127D GLY 4.2 9.6 - - - -
129D PHE* 5.1 0.2 - - + -
139D PHE* 4.3 20.4 - + + -
140D THR 3.5 12.1 - - - -
141D PHE* 4.4 0.7 - - + -
153D ILE* 5.0 4.9 - - + -
193D VAL* 4.3 10.8 - - + -
194D TRP* 4.3 14.8 - - - -
195D VAL* 3.7 23.6 - - + -
213D VAL* 1.3 72.8 - - - +
215D SER* 1.3 75.8 + - - +
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Residues in contact with SER 215 (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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95D PHE* 3.4 12.8 - - - -
96D SER* 2.4 30.1 + - - -
139D PHE* 3.5 2.3 - - - -
140D THR* 2.9 49.8 + - - +
142D GLN* 5.4 0.8 + - - -
213D VAL* 3.7 10.5 - - - +
214D PHE* 1.3 78.0 - - - +
216D GLY* 1.3 59.4 + - - +
217D PHE* 5.6 0.7 - - - -
142E TYR* 4.5 6.5 - - - -
184E GLY 4.4 1.8 + - - -
185E MET* 4.2 4.0 - - - -
186E VAL* 4.1 10.2 + - - -
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Residues in contact with GLY 216 (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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94D ALA* 3.5 1.0 - - - +
95D PHE* 2.9 49.6 + - - +
129D PHE* 5.7 1.1 - - - -
137D TYR* 5.6 0.4 - - - -
138D TYR 3.0 13.7 - - - -
139D PHE* 3.8 7.4 - - - -
215D SER* 1.3 77.4 - - - +
217D PHE* 1.3 68.7 + - - +
186E VAL* 4.2 0.7 - - - +
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Residues in contact with PHE 217 (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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93D PRO 3.6 6.7 - - - +
94D ALA* 4.0 8.7 - - + -
129D PHE* 6.2 0.4 - - - -
137D TYR* 3.2 11.4 - - - -
138D TYR* 2.9 68.5 + + + -
140D THR* 5.9 1.8 - - + -
215D SER 5.6 0.2 - - - -
216D GLY* 1.3 79.6 - - - +
218D LEU* 1.3 71.8 + - - +
219D ILE* 4.3 3.8 - - + -
142E TYR* 3.9 27.6 - + + -
186E VAL* 4.2 9.0 - - + -
218E PHE* 3.9 17.9 - + - -
220E LEU* 3.5 42.8 - - + -
221E PHE* 5.0 1.1 - - + -
212F PHE* 4.0 18.8 - + - -
214F LEU* 5.2 1.3 - - + -
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Residues in contact with LEU 218 (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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91D PRO* 4.1 26.5 - - + +
93D PRO* 3.1 40.6 + - + +
133D VAL* 4.2 9.0 - - + +
135D GLY* 4.3 1.1 - - - -
136D TYR 3.5 17.7 - - - +
137D TYR* 3.5 36.2 - - + +
217D PHE* 1.3 79.6 - - - +
219D ILE* 1.3 61.4 + - - +
220D PHE* 3.5 23.8 - - - +
221D PRO* 3.8 13.7 - - + -
220E LEU* 4.8 2.4 - - - +
221E PHE* 3.6 21.7 - - + -
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Residues in contact with ILE 219 (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* 2.5 17.8 + - + +
137D TYR 3.8 12.6 - - - -
138D TYR* 3.9 15.7 - - + +
184D VAL* 3.7 37.2 - - + -
217D PHE* 4.3 6.1 - - + -
218D LEU* 1.3 76.7 - - - +
220D PHE* 1.3 78.7 + - + +
221E PHE* 5.8 1.9 - - - -
91F GLN* 5.2 0.2 - - - +
92F SER 5.5 0.4 - - - +
93F VAL* 4.0 4.3 - - + -
212F PHE* 3.8 39.7 - - + -
213F LEU 4.4 10.4 - - - +
214F LEU* 5.4 6.4 - - + +
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Residues in contact with PHE 220 (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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135D GLY* 3.3 0.2 - - - -
136D TYR* 2.8 71.6 + + + -
218D LEU* 3.5 5.8 - - - -
219D ILE* 1.3 95.6 - - + +
221D PRO* 1.3 84.2 - - + +
222D SER* 5.1 2.9 - - - -
89F LYS* 4.2 15.7 - - + -
91F GLN* 3.4 60.1 - - + +
92F SER 4.7 1.3 - - - -
93F VAL* 4.2 17.7 - - + -
120F GLN* 4.3 4.7 - - - -
213F LEU 5.8 0.4 - - - -
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Residues in contact with PRO 221 (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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91D PRO* 4.5 14.4 - - + -
133D VAL* 4.0 18.4 - - + -
134D PRO 3.3 13.5 - - - +
135D GLY* 3.9 0.7 - - - -
218D LEU* 3.8 10.5 - - + -
220D PHE* 1.3 102.7 - - + +
222D SER* 1.3 64.4 + - - +
91F GLN* 6.0 0.2 - - - +
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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