Contacts of the strand formed by residues 166 - 172 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B LEU* 4.9 5.6 - - + -
159B ILE* 5.9 1.5 - - + +
160B ILE* 5.0 14.4 - - + +
165B GLU* 1.3 75.6 - - - +
167B GLU* 1.3 64.2 + - - +
168B LYS 3.8 9.9 - - - +
169B ILE* 3.7 25.4 - - + -
231B SER* 3.2 54.4 - - - +
291B VAL* 6.4 0.2 - - + -
293B VAL* 3.1 19.5 - - + +
323B ILE* 4.4 5.6 - - + -
324B LYS 3.8 5.4 - - - +
325B THR* 4.1 8.5 - - + +
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLU* 3.6 4.5 + - + +
166B VAL* 1.3 75.5 - - - +
168B LYS* 1.3 73.0 + - + +
292B ASP* 4.5 1.4 - - - +
293B VAL* 3.1 38.2 + - + +
294B ALA* 4.5 2.1 + - + +
324B LYS* 2.8 15.3 + - + +
325B THR* 3.9 8.5 + - - +
326B LYS* 3.2 34.5 + - - +
329B THR* 6.0 0.7 - - - -
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 3.8 1.7 - - - +
167B GLU* 1.3 89.0 - - + +
169B ILE* 1.3 71.0 + - - +
291B VAL* 3.6 9.4 - - - +
292B ASP* 3.1 28.6 + - + +
293B VAL* 5.4 0.4 - - - -
322B SER 4.2 0.9 - - - -
324B LYS* 2.9 62.1 + - + +
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Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 4.0 20.0 - - + -
166B VAL* 3.7 11.9 - - + -
168B LYS* 1.3 86.5 - - - +
170B GLU* 1.3 72.7 + - - +
173B PHE* 4.6 6.1 - - + -
227B VAL* 3.4 30.3 - - + -
231B SER* 3.3 26.0 - - - +
290B LYS* 3.6 2.7 - - - +
291B VAL* 3.0 41.8 + - + +
321B ILE* 3.8 20.6 - - + -
322B SER 3.1 10.3 - - - +
323B ILE* 4.1 7.9 - - + -
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ILE* 1.3 87.4 - - - +
171B GLY* 1.3 55.9 + - - +
288B ILE* 5.0 1.6 - - + -
289B GLY 3.1 14.6 - - - +
290B LYS* 3.5 27.2 + - + +
303B GLU* 4.1 5.1 - - - +
305B TYR* 3.0 35.1 + - - -
309B HIS* 4.8 4.2 + - - -
311B PHE* 3.3 15.2 - - + -
321B ILE* 4.4 0.4 - - - -
322B SER* 2.7 38.1 + - - -
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLU* 1.3 75.8 - - - +
172B ILE* 1.3 64.3 + - - -
173B PHE* 3.9 12.4 - - - -
288B ILE* 3.2 7.3 - - - +
289B GLY* 2.8 32.6 + - - -
311B PHE* 3.7 10.5 - - - -
320B VAL 2.8 15.7 - - - -
321B ILE* 4.0 1.6 - - - -
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B GLY* 1.3 75.3 - - - -
173B PHE* 1.3 56.4 + - - +
174B SER* 4.2 5.4 - - - +
177B LEU* 5.3 1.1 - - + -
178B SER* 3.6 37.0 - - - +
286B ARG* 3.8 31.6 - - + -
287B PHE 3.8 15.9 - - - +
288B ILE* 3.8 16.2 - - + -
311B PHE* 4.0 13.7 - - + +
314B LEU* 3.6 20.6 - - + -
319B ASN* 2.5 31.3 - - + +
320B VAL* 2.8 26.5 + - + +
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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