Contacts of the strand formed by residues 166 - 172 (chain A) in PDB entry 1EBF
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A LEU* 4.3 17.7 - - + -
159A ILE* 5.7 0.2 - - + -
160A ILE* 3.5 26.1 - - + +
165A GLU* 1.3 77.7 - - - +
167A GLU* 1.3 64.0 + - - +
168A LYS 4.1 5.2 - - - +
169A ILE* 3.7 24.0 - - + -
230A ILE* 5.6 0.4 - - + -
231A SER* 3.4 44.6 + - - +
291A VAL* 5.7 0.4 - - + -
293A VAL* 2.9 22.0 - - + +
323A ILE* 4.9 1.8 - - + -
324A LYS 3.9 6.7 - - - +
325A THR* 4.2 9.4 - - + -
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Residues in contact with GLU 167 (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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165A GLU* 4.0 7.4 - - + +
166A VAL* 1.3 80.5 - - - +
168A LYS* 1.3 75.6 + - + +
292A ASP* 3.7 0.9 - - - +
293A VAL* 3.1 37.1 + - + +
294A ALA* 4.3 3.4 + - + +
324A LYS* 2.9 14.0 + - + +
325A THR 4.0 6.1 - - - +
326A LYS* 3.4 31.7 - - - +
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Residues in contact with LYS 168 (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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166A VAL* 4.8 0.2 - - - -
167A GLU* 1.3 90.2 - - + +
169A ILE* 1.3 67.5 + - - +
291A VAL 3.5 8.7 - - - +
292A ASP* 3.6 25.3 + - - +
294A ALA* 6.3 1.6 - - - -
322A SER 3.9 0.7 - - - +
323A ILE* 3.8 0.5 - - - -
324A LYS* 2.8 61.4 + - + +
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Residues in contact with ILE 169 (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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156A LEU* 4.2 19.3 - - + -
166A VAL* 3.7 14.6 - - + -
168A LYS* 1.3 80.1 - - - +
170A GLU* 1.3 71.8 + - - +
173A PHE* 4.6 5.4 - - + -
227A VAL* 3.4 22.9 - - + -
231A SER* 3.4 24.5 - - - +
289A GLY 5.5 0.2 - - - +
290A LYS* 3.5 2.8 - - - +
291A VAL* 2.8 44.2 + - + +
321A ILE* 3.7 23.6 - - + -
322A SER 3.3 13.7 - - - +
323A ILE* 4.2 9.4 - - + -
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Residues in contact with GLU 170 (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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169A ILE* 1.3 78.1 - - - +
171A GLY* 1.3 58.8 + - - +
173A PHE* 4.2 4.3 - - - -
288A ILE* 5.0 1.1 - - + -
289A GLY 3.2 11.0 - - - +
290A LYS* 4.1 23.8 + - + -
303A GLU* 4.1 2.8 - - - +
305A TYR* 3.3 31.1 + - - +
309A HIS* 3.8 23.4 + - - -
311A PHE* 3.7 5.5 - - + -
321A ILE* 3.7 1.0 - - - +
322A SER* 2.8 47.1 + - - +
324A LYS* 5.8 2.3 + - - -
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Residues in contact with GLY 171 (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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170A GLU* 1.3 76.2 - - - +
172A ILE* 1.3 62.3 + - - -
173A PHE* 3.0 18.5 - - - -
288A ILE* 3.2 6.7 - - - +
289A GLY 2.7 38.0 + - - -
311A PHE* 4.0 9.3 - - - -
320A VAL 3.1 13.5 - - - -
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Residues in contact with ILE 172 (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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171A GLY* 1.3 73.4 - - - -
173A PHE* 1.3 59.7 + - - +
174A SER* 4.0 7.6 - - - +
177A LEU* 5.2 0.7 - - + -
178A SER* 3.4 37.0 - - - +
286A ARG* 4.0 26.2 - - + -
287A PHE* 3.7 22.7 - - + +
288A ILE* 4.2 8.7 - - + -
311A PHE* 4.2 19.7 - - + +
314A LEU* 3.3 27.1 - - + -
318A ASP 4.3 2.0 - - - +
319A ASN* 3.2 26.3 - - - +
320A VAL* 3.0 15.6 + - + +
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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