Contacts of the strand formed by residues 216 - 223 (chain E) in PDB entry 4JRX
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 HIS 216 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169E TRP* 4.8 1.6 - - + -
170E VAL* 3.3 7.6 - - - +
171E ASN* 2.8 48.6 + - - +
172E GLY* 4.6 9.6 - - - -
214E ARG* 3.5 2.7 + - - +
215E ASN* 1.3 71.9 - - - +
217E PHE* 1.3 61.7 + - - +
218E ARG* 3.7 25.2 + - + +
247E GLU* 3.1 42.3 + - + -
248E ALA 3.8 4.5 + - - -
249E TRP* 3.3 40.5 - + + +
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Residues in contact with PHE 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E VAL* 5.4 0.9 - - - +
152E LEU* 3.8 24.5 - - + -
168E TRP* 4.8 4.5 - - + -
169E TRP 3.5 3.8 - - - -
170E VAL* 3.7 9.9 - - + -
203E LEU* 3.7 24.7 - - + -
205E VAL* 4.3 12.3 - - + -
209E PHE* 3.7 43.1 - + - -
210E TRP* 3.7 36.8 - + - -
215E ASN* 3.7 25.1 - - + -
216E HIS* 1.3 75.4 - - - +
218E ARG* 1.3 59.5 + - - +
247E GLU* 3.2 4.7 - - - +
248E ALA 2.8 45.7 + - - +
250E GLY* 3.9 5.8 - - - -
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Residues in contact with ARG 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E SER 3.8 0.5 - - - +
168E TRP* 3.4 9.6 - - - -
169E TRP* 2.8 71.2 + - + +
172E GLY* 6.4 0.2 - - - -
216E HIS* 3.7 21.4 + - - +
217E PHE* 1.3 73.7 - - - +
219E CYS* 1.3 62.9 + - - +
220E GLN* 2.8 48.0 + - - +
243E ILE* 4.8 3.6 - - - +
245E SER* 3.8 24.8 + - - +
246E ALA 3.5 10.1 - - - +
247E GLU* 4.4 12.3 - - + -
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Residues in contact with CYS 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E VAL* 4.0 5.4 - - + +
136E VAL* 3.6 17.8 - - + +
154E CYS* 2.1 52.7 - - + -
166E LEU* 3.7 25.8 - - - -
167E SER 3.7 2.2 - - - -
168E TRP* 3.9 10.3 - - + -
218E ARG* 1.3 72.8 - - - +
220E GLN* 1.3 58.2 + - - +
221E VAL* 4.5 0.9 - - - -
245E SER* 3.1 7.0 - - - -
246E ALA 2.7 32.0 + - - -
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Residues in contact with GLN 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E GLU 3.5 1.4 - - - +
166E LEU* 3.4 3.5 - - - +
167E SER* 2.8 51.5 + - - +
169E TRP* 3.6 22.4 + - + +
218E ARG* 2.8 45.4 + - - +
219E CYS* 1.3 71.8 - - - +
221E VAL* 1.4 66.2 + - - +
222E GLN* 4.7 5.5 - - - +
243E ILE* 3.6 36.2 - - + +
244E VAL 3.7 3.1 - - - -
245E SER* 4.1 0.7 - - - -
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Residues in contact with VAL 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E PRO* 3.8 18.2 - - + -
134E VAL* 3.7 28.9 - - + -
156E ALA* 3.9 10.3 - - + -
164E VAL* 3.8 30.7 - - + -
165E GLU 3.5 5.4 - - - +
166E LEU* 3.8 27.6 - - + -
199E LEU* 6.1 0.2 - - + -
219E CYS* 4.5 0.9 - - - -
220E GLN* 1.4 76.8 - - - +
222E GLN* 1.3 62.2 + - - +
223E PHE* 3.6 1.6 + - - +
242E GLN 3.8 0.3 - - - +
243E ILE* 3.4 2.8 - - - -
244E VAL* 2.8 43.3 + - - +
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Residues in contact with GLN 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E VAL* 3.2 8.0 - - - +
165E GLU* 2.9 44.4 + - + +
220E GLN* 4.1 6.9 - - - +
221E VAL* 1.3 70.1 - - - +
223E PHE* 1.3 71.8 + - - +
224E TYR* 3.6 34.6 + - + +
241E THR* 3.7 16.1 - - - +
242E GLN* 3.1 29.5 + - - +
243E ILE* 3.3 27.3 - - + +
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Residues in contact with PHE 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E VAL* 4.0 3.4 - - + -
130E PHE 3.3 25.6 - - - -
131E PRO* 3.8 17.3 - - + -
132E PRO* 3.5 30.7 - - + -
159E PHE* 4.4 0.7 - - + -
160E TYR 3.6 13.0 - - - -
161E PRO* 3.6 22.2 - - + -
163E HIS 3.7 2.9 - - - -
164E VAL* 3.8 14.6 - - + -
221E VAL 3.6 1.0 + - - +
222E GLN* 1.3 81.3 + - - +
224E TYR* 1.3 75.2 + - - +
225E GLY* 3.6 20.2 - - - -
239E PRO 3.8 12.6 - - - -
240E VAL 3.6 15.5 - - - -
241E THR* 3.3 2.8 - - - -
242E GLN* 2.7 40.9 + - + +
244E VAL* 5.5 0.4 - - + -
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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