Contacts of the strand formed by residues 194 - 200 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A VAL 4.1 2.7 - - - -
145A ALA* 3.6 28.9 - - - -
146A GLY* 3.9 2.0 - - - -
147A ILE* 3.6 31.0 - - + -
179A LEU* 3.8 18.8 - - + -
180A ALA 3.1 11.4 - - - +
181A ARG* 3.5 35.9 - - + -
182A SER* 3.2 4.8 + - - -
190A ALA* 3.2 35.3 + - + -
192A LYS 3.3 0.4 - - - -
193A ALA* 1.3 81.6 - - + +
195A THR* 1.3 56.5 + - - +
242A GLY* 2.8 44.5 + - - +
244A GLY* 4.1 0.7 - - - -
245A PHE* 3.7 26.9 - + + +
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Residues in contact with THR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA* 4.3 6.5 - - + -
158A TYR* 4.4 8.0 - - + -
179A LEU* 4.5 0.2 - - - -
180A ALA 2.9 26.6 + - - +
182A SER* 3.7 20.9 - - - -
194A PHE* 1.3 77.6 - - - +
196A GLY* 1.3 60.2 + - - +
197A PHE* 3.5 32.5 - - + -
237A VAL* 3.8 13.2 - - - +
240A GLY 3.3 17.7 + - - -
241A ASP* 3.5 7.7 - - - -
242A GLY 4.0 3.6 - - - -
244A GLY* 3.7 6.7 - - - +
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Residues in contact with GLY 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PHE* 4.2 9.4 - - - -
178A LEU 2.9 15.0 - - - -
179A LEU* 4.4 3.8 - - - -
195A THR* 1.3 73.3 + - - +
197A PHE* 1.3 62.3 + - - +
237A VAL* 3.8 2.9 - - - +
238A LEU* 3.0 34.2 + - - +
239A ILE 4.8 0.2 + - - -
240A GLY 5.4 0.2 + - - -
244A GLY* 3.3 18.3 - - - -
247A VAL* 5.4 1.2 - - - +
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Residues in contact with PHE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA* 3.9 17.7 - - + -
158A TYR* 3.6 22.0 - + + -
160A ILE* 3.9 17.9 - - + -
177A PHE* 3.7 3.6 - - - -
178A LEU* 3.0 56.4 + - + +
180A ALA* 4.5 2.2 - - + -
195A THR* 3.5 33.9 - - + -
196A GLY* 1.3 71.2 - - - -
198A ILE* 1.3 65.6 + - - +
199A VAL* 4.4 8.1 - - + -
232A VAL* 4.2 11.2 - - + -
236A ASN 3.1 18.2 - - - +
237A VAL* 3.3 32.3 - - + -
238A LEU* 3.6 10.0 - - - +
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Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ILE* 3.6 27.1 - - + -
116A GLN* 4.3 15.3 - - + +
120A TYR* 3.6 44.6 - - + +
175A TRP* 4.1 20.0 - - + -
176A TYR 3.4 10.1 - - - +
177A PHE* 5.8 1.3 - - - -
197A PHE* 1.3 76.5 - - - +
199A VAL* 1.3 65.4 + - - +
232A VAL* 3.4 23.4 - - - +
236A ASN* 2.9 41.3 + - - +
238A LEU* 4.0 20.6 - - + -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TRP* 3.2 3.5 - - - -
176A TYR* 2.7 42.7 + - + +
178A LEU* 4.1 32.3 - - + -
197A PHE* 4.4 3.1 - - + +
198A ILE* 1.3 81.2 - - - +
200A GLU* 1.3 73.4 + - - +
201A ALA 3.6 0.5 + - - -
203A THR* 4.6 2.5 - - - +
206A ILE* 4.0 9.0 - - + -
227A PHE* 4.1 11.2 - - + -
230A VAL* 3.8 27.6 - - + -
232A VAL* 3.7 21.1 - - + -
236A ASN* 5.1 1.1 - - - +
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Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS* 3.8 8.5 + - - -
120A TYR* 3.3 41.9 + - + +
123A ARG* 3.4 21.8 + - - +
174A ASN* 3.6 6.1 - - - +
175A TRP* 4.1 4.3 - - + +
199A VAL* 1.3 74.2 - - - +
201A ALA* 1.3 65.6 + - - +
202A ASP* 4.4 9.9 - - + +
203A THR* 3.1 31.3 + - - +
206A ILE* 3.4 6.6 - - - +
236A ASN* 5.3 4.1 - - - +
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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