Contacts of the strand formed by residues 155 - 161 (chain E) in PDB entry 4JFF
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 155 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123E PRO* 4.5 1.8 - - + -
147E ALA* 4.8 2.2 - - + -
150E PHE* 3.5 44.0 - - + -
154E HIS* 1.3 95.5 + - - +
156E GLU* 1.3 67.4 + - - +
157E LEU 4.1 1.4 + - - +
190E LEU* 3.7 30.9 - - + +
212E VAL* 3.5 27.8 - - + -
213E GLN 3.3 8.5 - - - +
214E PHE* 4.0 14.4 - - + -
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Residues in contact with GLU 156 (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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9E ALA* 5.7 3.3 - - - +
10E THR* 4.5 3.1 + - - -
154E HIS* 3.4 28.2 + - + +
155E VAL* 1.3 71.2 - - - +
157E LEU* 1.3 62.6 + - - +
158E SER* 4.8 2.3 - - - -
211E GLN 3.7 1.2 - - - +
212E VAL* 3.5 2.2 - - - -
213E GLN* 2.9 42.9 + - + +
215E TYR* 3.2 34.3 + - + -
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Residues in contact with LEU 157 (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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145E CYS* 4.1 20.0 - - - +
147E ALA* 5.0 3.8 - - + -
155E VAL 3.9 2.6 + - - -
156E GLU* 1.3 75.0 - - - +
158E SER* 1.3 92.1 + - - +
159E TRP* 3.9 9.9 - - + +
165E GLU* 5.4 0.3 - - - +
172E THR* 4.1 20.6 + - + +
190E LEU* 4.5 20.6 - - + +
191E SER* 4.6 4.7 - - - -
192E SER* 3.2 42.6 - - - +
210E CYS* 4.0 11.9 - - - -
211E GLN 3.3 4.9 - - - +
212E VAL* 4.3 14.1 - - + +
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Residues in contact with SER 158 (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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156E GLU 4.8 2.2 - - - -
157E LEU* 1.3 83.8 - - - +
159E TRP* 1.3 61.7 + - - +
160E TRP* 2.9 28.8 + - - -
165E GLU* 3.0 27.8 + - - -
210E CYS* 3.5 2.6 - - - -
211E GLN* 2.7 48.5 + - - +
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Residues in contact with TRP 159 (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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127E VAL* 4.4 9.6 - - + -
143E LEU* 3.9 28.3 - - + -
144E VAL 4.1 1.3 - - - -
145E CYS* 3.4 41.3 - - + -
157E LEU* 3.9 8.0 - - + +
158E SER* 1.3 72.6 + - - +
160E TRP* 1.3 63.5 + - - +
165E GLU* 3.3 9.5 - - - +
166E VAL* 2.9 47.8 + - + +
170E VAL* 3.8 26.0 - - + -
192E SER* 2.7 31.4 + - - -
193E ARG 3.8 6.3 + - - -
194E LEU* 3.6 34.1 - - + -
208E PHE* 5.0 0.2 - - + -
209E ARG 3.5 23.3 - - - -
210E CYS* 4.0 13.2 - - + -
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Residues in contact with TRP 160 (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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158E SER* 2.9 28.6 + - - -
159E TRP* 1.3 80.0 - - - +
161E VAL* 1.3 62.5 + - - +
162E ASN 4.0 1.0 + - - -
163E GLY* 3.0 33.7 - - - +
164E LYS* 3.5 4.7 - - - +
165E GLU* 3.5 36.6 - - + -
207E HIS 3.6 2.6 - - - +
208E PHE* 3.6 1.4 - - - -
209E ARG* 2.8 52.3 + - + +
211E GLN* 3.6 40.8 - - + +
304E SO4 4.4 14.9 + - - +
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Residues in contact with VAL 161 (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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160E TRP* 1.3 73.4 - - - +
162E ASN* 1.3 82.8 + - - +
163E GLY 3.4 0.2 - - - -
164E LYS* 2.9 20.7 + - - +
166E VAL* 3.3 37.4 - - + +
194E LEU* 4.1 18.4 - - + -
196E VAL* 5.7 2.0 - - + -
200E PHE* 3.6 35.9 - - + -
206E ASN* 5.2 0.7 - - + -
207E HIS 3.3 7.0 - - - +
208E PHE* 4.1 11.9 - - + -
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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