Contacts of the strand formed by residues 318 - 325 (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 ASP 318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ASN* 4.0 17.7 - - - +
331A PRO* 4.3 5.2 - - - +
178B SER* 2.3 36.7 + - - -
314B LEU* 3.8 16.4 - - + +
315B LYS* 2.7 52.5 + - - +
316B GLY 3.2 0.8 - - - -
317B SER* 1.3 72.4 - - - +
319B ASN* 1.3 57.5 - - - +
335B GLN* 5.0 4.2 + - - -
336B GLY* 3.6 18.3 + - - +
337B ALA* 2.9 23.3 + - - +
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Residues in contact with ASN 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLY* 4.0 11.5 - - - -
150B LEU* 3.5 16.4 - - - +
152B ILE* 5.5 1.4 - - - +
172B ILE* 2.5 31.4 - - + +
173B PHE* 3.8 20.8 - - - +
174B SER 4.7 2.5 - - - +
175B GLY 4.7 2.1 + - - -
314B LEU* 3.5 6.5 - - - -
317B SER 4.6 1.1 - - - +
318B ASP* 1.3 75.0 - - - +
320B VAL* 1.3 68.6 + - - +
334B ILE 4.1 0.2 - - - +
335B GLN* 3.4 1.6 - - - -
336B GLY 3.2 26.7 + - - -
338B GLY* 3.3 27.1 - - - +
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Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 5.7 0.7 - - - -
152B ILE* 5.7 1.6 - - - -
171B GLY* 2.8 23.0 - - - -
172B ILE* 2.8 19.8 + - + +
173B PHE* 4.5 3.4 - - - -
310B PRO 4.7 1.6 - - - +
311B PHE* 3.3 42.2 - - + -
314B LEU* 3.1 29.6 - - + +
319B ASN* 1.3 74.6 - - - +
321B ILE* 1.3 62.4 + - - +
333B VAL* 4.7 5.2 - - + -
334B ILE 3.3 7.9 - - - +
335B GLN* 2.9 34.5 - - + +
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Residues in contact with ILE 321 (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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152B ILE* 3.7 44.6 - - + -
156B LEU* 4.6 1.3 - - + -
169B ILE* 3.8 33.0 - - + -
170B GLU 3.6 2.9 - - - +
171B GLY* 4.0 0.2 - - - -
173B PHE* 4.2 21.5 - - + -
227B VAL* 4.4 6.5 - - + -
311B PHE* 4.9 0.2 - - - -
320B VAL* 1.3 78.8 - - - +
322B SER* 1.3 63.0 + - - +
323B ILE* 3.9 21.5 - - + +
332B VAL 3.7 2.1 - - - +
333B VAL* 3.5 6.5 - - - +
334B ILE* 3.1 41.5 + - + +
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Residues in contact with SER 322 (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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168B LYS 3.7 0.9 - - - +
169B ILE* 3.1 26.5 - - - +
170B GLU* 2.7 26.4 + - - +
309B HIS* 6.0 1.2 - - - -
311B PHE* 3.9 18.4 - - - -
321B ILE* 1.3 72.7 - - - +
323B ILE* 1.3 61.7 + - - +
324B LYS* 4.1 2.0 + - - +
331B PRO* 3.1 26.2 - - - +
332B VAL 3.7 3.8 - - - -
333B VAL* 4.0 9.8 - - - +
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Residues in contact with ILE 323 (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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152B ILE* 5.4 2.9 - - + +
155B PHE* 4.0 22.9 - - + -
156B LEU* 3.9 32.3 - - + -
159B ILE* 4.9 2.7 - - + -
166B VAL* 4.4 2.5 - - + -
168B LYS 3.6 1.8 - - - -
169B ILE* 4.1 11.0 - - + -
321B ILE* 3.9 32.5 - - + +
322B SER* 1.3 78.7 + - - +
324B LYS* 1.3 59.2 + - - +
325B THR* 3.4 28.1 + - + +
328B TYR* 4.3 3.6 - - - +
331B PRO* 3.2 6.4 - - - +
332B VAL* 3.0 42.8 + - + +
334B ILE* 5.2 2.7 - - + -
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Residues in contact with LYS 324 (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 0.7 - - - +
167B GLU* 2.8 31.1 + - + +
168B LYS* 2.9 48.2 + - + +
322B SER* 4.1 2.2 + - - +
323B ILE* 1.3 72.1 - - - +
325B THR* 1.3 63.6 + - - +
328B TYR 3.6 7.2 - - - +
329B THR 3.8 14.6 - - - +
331B PRO* 3.4 35.8 - - + +
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Residues in contact with THR 325 (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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155B PHE* 6.1 0.2 - - + -
159B ILE* 3.9 15.7 - - + -
164B ASP* 2.7 26.2 + - - +
165B GLU 3.1 14.6 - - - +
166B VAL* 4.1 6.5 - - - -
167B GLU* 3.9 11.5 - - - +
323B ILE* 3.4 26.5 - - + +
324B LYS* 1.3 79.9 - - - +
326B LYS* 1.3 66.2 + - - +
328B TYR* 2.8 43.3 + - + +
329B THR* 3.7 3.1 + - - -
332B VAL* 6.4 0.2 - - + -
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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