Contacts of the strand formed by residues 254 - 259 (chain B) in PDB entry 1EF1
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 LYS 254 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LYS* 5.0 2.8 - - - +
250B PHE* 3.1 6.8 - - - +
251B ASN* 2.7 47.7 + - + +
253B LYS* 1.3 80.3 - - - +
255B PHE* 1.3 61.5 + - - +
256B VAL* 3.9 20.6 - - + +
268B VAL* 3.7 18.0 - - + +
269B PHE 3.8 4.5 - - - -
270B TYR* 3.6 37.5 + - + -
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Residues in contact with PHE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 4.0 24.7 - - + -
249B SER 3.5 5.6 - - - -
250B PHE* 3.7 17.0 - + + -
254B LYS* 1.3 73.9 - - - +
256B VAL* 1.3 64.4 + - - +
257B ILE* 3.7 24.9 - - + -
267B PHE 4.0 0.2 - - - +
268B VAL* 2.9 21.0 - - - +
269B PHE* 2.9 56.1 + + + +
277B ASN* 3.2 46.9 - - - +
280B ILE* 3.7 20.6 - - + -
281B LEU* 4.1 13.5 - - + -
284B CYS* 5.0 2.2 - - - -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ASN* 4.6 0.7 - - - +
248B ILE* 3.4 4.0 - - - -
249B SER* 2.8 44.9 + - - +
250B PHE* 5.8 0.9 - - - -
251B ASN 6.1 0.4 - - - +
254B LYS* 3.9 22.4 - - + +
255B PHE* 1.3 78.8 - - - +
257B ILE* 1.3 67.0 + - - +
258B LYS* 4.0 17.9 + - + +
266B ASP* 3.3 37.9 - - + +
267B PHE 3.6 2.5 - - - -
268B VAL* 3.7 11.0 - - + -
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Residues in contact with ILE 257 (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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218B LEU* 5.9 0.2 - - + -
225B LEU* 3.7 17.0 - - + -
240B PHE* 6.1 0.4 - - + -
245B ILE* 3.4 41.1 - - + -
247B ASN 3.6 2.7 - - - -
248B ILE* 3.8 7.9 - - + -
255B PHE* 3.7 16.8 - - + -
256B VAL* 1.3 80.0 - - - +
258B LYS* 1.3 62.8 + - - +
259B PRO* 3.5 4.6 - - - +
266B ASP* 3.6 0.9 - - - -
267B PHE* 2.7 73.0 + - + +
269B PHE* 3.5 27.6 - - + -
280B ILE* 6.3 0.2 - - + -
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Residues in contact with LYS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 3.9 1.9 - - - +
246B ARG* 2.9 43.4 + - + +
247B ASN* 2.8 40.7 + - + +
249B SER* 4.4 7.7 + - - -
256B VAL* 4.2 16.2 - - + +
257B ILE* 1.3 75.2 - - - +
259B PRO* 1.4 64.1 - - + +
266B ASP* 3.5 23.7 + - - +
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Residues in contact with PRO 259 (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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244B GLU 3.3 13.0 - - - +
245B ILE* 4.7 1.3 - - + -
246B ARG* 3.6 10.9 - - - +
257B ILE* 3.5 7.4 - - + +
258B LYS* 1.4 87.7 - - + +
260B ILE* 1.3 59.7 + - - +
261B ASP* 3.2 22.6 + - - +
262B LYS* 4.9 0.8 + - - +
264B ALA* 3.1 28.7 - - + +
265B PRO 3.4 17.9 - - - +
266B ASP* 3.9 6.7 - - - +
267B PHE* 4.8 0.4 - - + +
567D THR* 3.8 24.0 - - + +
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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