Contacts of the strand formed by residues 194 - 200 (chain D) in PDB entry 1EGE
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 PHE 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D VAL 4.3 1.1 - - - -
145D ALA* 3.4 46.0 - - + -
147D ILE* 4.2 20.2 - - + -
179D LEU* 3.4 17.7 - - + -
180D ALA 3.2 22.9 - - - +
181D ARG* 3.9 28.7 - - + -
190D ALA* 3.4 31.0 + - + +
193D ALA* 1.3 80.7 - - + +
195D THR* 1.3 66.4 + - - +
242D GLY 3.3 11.8 - - - +
244D GLY 2.9 19.4 + - - -
245D PHE* 3.5 31.4 - + + +
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Residues in contact with THR 195 (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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179D LEU* 4.5 0.9 - - - -
180D ALA 2.9 28.3 + - - +
182D SER* 3.3 17.8 + - - +
193D ALA 4.2 0.4 + - - -
194D PHE* 1.3 72.6 + - - +
196D GLY* 1.3 62.0 + - - +
197D PHE* 3.3 31.7 - - + -
237D VAL* 3.5 23.8 - - + -
240D GLY 4.0 2.0 - - - +
241D ASP* 2.7 35.9 + - + -
242D GLY 2.9 10.7 + - - -
243D ALA 4.5 0.7 - - - -
244D GLY* 3.8 6.7 - - - +
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Residues in contact with GLY 196 (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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177D PHE* 4.4 11.4 - - - -
178D LEU 3.0 10.5 - - - -
179D LEU* 4.3 6.5 - - - -
195D THR* 1.3 74.1 - - - +
197D PHE* 1.3 66.1 + - - -
237D VAL* 3.4 11.6 - - - +
238D LEU* 3.3 28.3 + - - +
243D ALA 4.4 3.0 + - - -
244D GLY* 3.8 9.9 - - - -
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Residues in contact with PHE 197 (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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151D ALA* 3.5 24.9 - - + -
158D TYR* 3.3 45.3 - + + -
160D ILE* 3.9 14.4 - - + -
177D PHE* 4.7 1.7 - - - -
178D LEU* 2.8 38.4 + - + +
180D ALA* 4.2 2.0 - - + -
195D THR* 3.3 35.2 - - + -
196D GLY* 1.3 74.1 - - - -
198D ILE* 1.3 64.1 + - - +
199D VAL* 3.1 9.7 + - + -
232D VAL* 3.5 31.4 - - + -
236D ASN 4.0 4.5 - - - -
237D VAL* 3.3 29.6 - - + -
238D LEU* 4.3 1.5 - - - +
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Residues in contact with ILE 198 (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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108D ILE* 3.3 22.0 - - + -
116D GLN* 5.3 6.1 - - + +
120D TYR* 3.7 37.2 - - + -
175D TRP* 3.1 45.8 - - + -
176D TYR 3.7 4.9 - - - +
177D PHE* 4.8 3.1 - - - +
197D PHE* 1.3 71.3 - - - +
199D VAL* 1.3 61.9 + - - +
200D GLU 4.2 0.2 - - - -
232D VAL* 4.5 0.5 - - - +
233D PRO* 5.4 0.3 - - - +
236D ASN* 3.0 55.9 + - + +
238D LEU* 3.6 16.5 - - + +
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Residues in contact with VAL 199 (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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175D TRP* 4.2 1.8 - - - -
176D TYR* 2.8 58.2 + - + +
178D LEU* 3.6 32.1 - - + -
197D PHE* 3.5 9.6 - - + +
198D ILE* 1.3 80.9 - - - +
200D GLU* 1.3 69.9 - - - +
201D ALA 3.5 0.2 + - - -
203D THR* 5.5 1.3 - - - +
227D PHE* 5.2 4.5 - - + -
230D VAL* 5.8 4.9 - - + -
232D VAL* 3.4 41.3 - - + -
233D PRO* 5.5 2.2 - - + -
236D ASN* 5.6 0.2 - - - -
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Residues in contact with GLU 200 (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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119D LYS* 3.1 26.7 + - - -
120D TYR* 3.4 25.2 + - + +
174D ASN 3.9 8.5 - - - +
175D TRP* 4.0 5.3 - - + +
198D ILE 4.2 0.4 - - - -
199D VAL* 1.3 77.7 - - - +
201D ALA* 1.3 61.7 - - - +
202D ASP* 3.3 22.8 - - - +
203D THR* 2.7 29.1 + - - +
206D ILE* 3.8 5.7 - - - +
236D ASN* 5.1 1.4 + - - +
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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