Contacts of the strand formed by residues 343 - 348 (chain B) in PDB entry 1LEI
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 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B ILE* 3.5 41.6 + - + +
251B VAL 5.5 1.8 + - - -
252B ARG* 4.9 5.3 - - - +
253B MET* 3.8 30.3 - - - +
256B THR* 4.3 18.3 - - - +
328B PHE* 3.1 3.7 - - - -
329B VAL* 2.4 56.8 + - + +
341B GLU 4.4 2.2 - - - +
342B PRO* 1.3 74.9 - - - +
344B PRO* 1.3 72.9 - - + +
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Residues in contact with PRO 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B MET* 5.9 0.7 - - - +
256B THR* 4.2 15.9 - - - +
326B SER* 5.0 7.0 - - - +
327B VAL 3.3 8.5 - - - +
328B PHE* 3.5 20.8 - - + -
329B VAL* 4.3 0.9 - - - +
342B PRO 4.2 2.5 - - - +
343B LYS* 1.3 101.7 - - + +
345B PHE* 1.3 59.0 + - - +
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Residues in contact with PHE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B MET* 5.0 4.0 - - + -
255B ARG 4.5 1.8 - - - -
256B THR* 3.3 17.5 - - - -
257B ALA 3.5 10.8 - - - -
258B GLY* 3.3 23.8 - - - -
266B ILE* 3.7 25.1 - - + -
282B PHE* 3.5 24.7 - + + -
313B THR* 3.8 15.5 - - + -
326B SER* 3.7 2.2 + - - -
327B VAL* 2.7 46.6 + - + +
329B VAL* 3.0 25.6 - - + -
343B LYS 3.6 0.4 + - - -
344B PRO* 1.3 72.3 - - - +
346B LEU* 1.3 71.6 + - - +
347B TYR* 3.7 29.7 + + - -
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR 2.9 10.2 + - - +
257B ALA* 3.0 22.9 - - + +
258B GLY 2.8 31.4 + - - +
324B PRO* 3.7 20.4 - - + -
325B ALA 3.3 30.5 - - - +
326B SER* 3.4 13.0 - - - +
345B PHE* 1.3 76.4 - - - +
347B TYR* 1.3 67.5 + - - +
348B TYR* 5.2 5.8 - - + -
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Residues in contact with TYR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLY 3.5 11.4 - - - -
259B CYS 3.5 20.4 - - - -
260B VAL* 3.7 17.0 - - + -
282B PHE* 4.5 5.1 - + - -
292B TRP* 4.2 10.4 - + - -
313B THR* 4.5 4.9 - - - -
314B PRO* 2.5 45.6 + - - +
315B LYS 4.4 0.2 - - - -
316B TYR* 3.6 35.2 + + + -
321B ILE* 3.9 1.6 - - - +
324B PRO* 3.1 4.7 - - - +
325B ALA* 2.7 50.2 + - + +
327B VAL* 4.2 20.6 - - + -
345B PHE* 3.7 27.9 - + - -
346B LEU* 1.3 72.3 - - - +
348B TYR* 1.3 60.0 + - - +
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Residues in contact with TYR 348 (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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255B ARG* 4.0 17.7 + - - -
257B ALA* 3.9 18.7 + - + -
258B GLY* 3.0 34.8 + - - -
259B CYS* 3.4 21.7 + - + -
260B VAL* 3.2 21.4 + - - -
264B GLU* 4.2 4.5 + - - -
324B PRO* 4.3 10.3 - - + -
346B LEU* 4.4 6.7 - - + -
347B TYR* 1.3 74.8 - - - +
349B PRO* 1.3 86.3 - - + +
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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