Contacts of the strand formed by residues 362 - 367 (chain B) in PDB entry 5EWL
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 LEU 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PRO* 3.5 38.8 - - + -
152B GLN* 5.4 2.7 - - + +
153B GLN* 4.7 3.4 - - + +
156B VAL* 3.8 24.7 - - + -
280B VAL* 3.7 26.9 - - + -
281B SER 3.7 6.7 - - - +
282B TYR* 3.9 21.3 - - + -
360B PRO* 3.9 16.4 - - + +
361B LYS* 1.3 76.1 - - - +
363B VAL* 1.3 64.4 + - - +
364B ILE* 4.9 0.4 - - + -
378B LYS* 3.6 4.7 - - - +
379B TRP* 2.9 44.6 + - + +
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Residues in contact with VAL 363 (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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280B VAL* 3.5 1.8 - - - -
281B SER* 2.7 43.2 + - - +
283B ASP* 3.7 26.5 - - + +
285B TRP* 3.9 14.1 - - + -
361B LYS 4.3 0.4 - - - +
362B LEU* 1.3 81.2 - - - +
364B ILE* 1.3 64.8 + - - +
365B ILE* 3.7 21.7 + - + -
375B ARG* 3.7 43.3 - - + +
377B GLY 3.7 6.1 - - - +
378B LYS* 4.6 5.6 - - + -
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Residues in contact with ILE 364 (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 VAL* 4.5 8.5 - - + -
160B ILE* 3.9 21.3 - - + -
278B ILE* 3.9 17.5 - - + -
279B SER 3.5 9.6 - - - +
280B VAL* 5.2 2.0 - - - -
362B LEU* 4.9 0.4 - - + -
363B VAL* 1.3 75.7 - - - +
365B ILE* 1.3 66.4 + - - +
375B ARG* 3.6 1.4 - - - -
376B VAL* 2.8 40.8 + - + -
377B GLY* 2.9 18.9 + - - +
378B LYS 3.8 23.8 - - - +
379B TRP* 4.0 9.2 - - + +
384B LEU* 3.5 27.1 - - + -
386B MET* 3.8 15.0 - - + -
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Residues in contact with ILE 365 (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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263B ALA* 4.1 12.1 - - + -
266B THR* 3.7 26.5 - - + -
278B ILE* 3.4 6.4 - - - +
279B SER* 2.8 49.9 + - - +
281B SER* 3.8 17.3 - - - -
285B TRP* 3.7 27.6 - - + -
363B VAL* 3.8 12.1 - - + +
364B ILE* 1.3 79.7 - - - +
366B LEU* 1.3 61.6 + - - +
373B TRP* 3.5 27.1 - - + -
374B GLU 3.1 15.7 - - - +
375B ARG* 4.2 0.4 - - - -
376B VAL* 3.8 2.9 - - - -
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLY* 3.7 27.1 - - - +
277B LEU 3.5 12.8 - - - +
278B ILE* 3.8 15.7 - - + -
365B ILE* 1.3 73.8 - - - +
367B LEU* 1.3 63.0 - - - +
368B ASN* 3.3 10.0 + - + +
373B TRP* 3.5 4.0 - - - -
374B GLU* 2.8 45.8 + - + +
376B VAL* 3.6 25.8 - - + -
388B TYR* 5.1 4.5 - - + -
391B TRP* 3.8 25.8 - - + -
392B PRO* 5.6 4.7 - - + -
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Residues in contact with LEU 367 (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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269B VAL* 3.6 22.7 - - + -
273B PHE* 3.7 27.1 - - + -
274B PRO 3.5 20.6 - - - +
275B THR* 3.7 2.4 - - - +
276B GLY* 2.9 28.9 + - - -
277B LEU* 3.0 20.3 + - + +
366B LEU* 1.3 72.1 - - - +
368B ASN* 1.4 63.1 + - - +
371B ARG* 3.6 37.2 - - - +
372B LYS 3.6 8.5 - - - +
373B TRP* 3.4 29.0 - - + +
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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