Contacts of the strand formed by residues 330 - 334 (chain B) in PDB entry 2EWY
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 GLU 330 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A PRO* 4.3 10.7 - - - +
282B CYS* 3.4 1.9 - - - +
283B TRP* 2.9 29.2 + - - +
285B ASN 4.5 4.9 - - - +
286B SER 5.4 2.4 - - - +
287B GLU 5.7 0.9 - - - +
288B THR* 5.2 6.3 - - - +
321B PRO* 4.4 8.0 - - + +
322B MET 3.1 19.5 - - - +
324B GLY* 3.5 7.9 - - - +
328B ASN* 3.3 1.4 - - - +
329B TYR* 1.3 104.6 - - - +
331B CYS* 1.3 67.7 + - - +
332B TYR* 3.4 36.4 + - + +
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Residues in contact with CYS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 3.9 22.4 - - + -
322A MET* 4.7 0.9 - - - -
280B LEU* 4.3 6.1 - - + -
281B ALA 3.0 7.4 - - - +
282B CYS* 2.0 46.4 - - - -
321B PRO* 3.3 2.8 - - - +
322B MET* 2.6 45.9 + - + +
323B MET 4.5 2.0 - - - -
324B GLY 4.0 16.8 - - - -
328B ASN* 4.6 3.4 - - - -
330B GLU* 1.3 77.2 - - - +
332B TYR* 1.3 62.4 + - - +
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Residues in contact with TYR 332 (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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270B PHE* 5.2 5.2 - + + -
274B PHE* 3.3 10.2 - - + -
280B LEU* 3.4 6.3 - - - -
281B ALA* 2.6 42.5 + - + +
283B TRP* 3.8 25.1 - + + +
287B GLU 5.0 0.2 + - - -
288B THR* 4.0 10.2 - - - +
289B PRO* 3.1 40.2 - - + +
290B TRP* 4.4 12.1 - + - -
319B ILE* 3.7 34.1 - - + -
320B GLN 3.1 5.8 - - - +
321B PRO* 3.6 30.3 - - + -
322B MET* 5.0 0.4 - - - -
330B GLU* 3.4 30.7 + - + +
331B CYS* 1.3 76.9 - - - +
333B ARG* 1.3 60.9 + - - +
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Residues in contact with ARG 333 (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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325A ALA* 4.3 17.4 - - - +
326A GLY* 5.3 4.1 - - - +
328A ASN* 6.3 0.9 - - - +
26B SER* 3.3 28.7 + - - -
27B GLY* 4.1 11.2 - - - +
245B THR* 5.4 3.2 - - - +
246B LEU* 4.9 7.0 - - - +
274B PHE* 3.8 5.5 - - - -
277B GLY* 6.5 1.1 - - - -
279B GLN 5.0 0.9 - - - +
280B LEU* 3.4 23.6 - - + -
319B ILE* 3.7 4.5 - - - -
320B GLN* 2.8 68.3 + - - +
321B PRO 4.0 10.9 + - - -
322B MET* 3.1 39.0 - - + +
332B TYR* 1.3 75.1 - - - +
334B PHE* 1.3 64.3 + - - +
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Residues in contact with PHE 334 (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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246B LEU* 4.1 12.0 - - - +
254B PHE* 3.8 16.4 - + - -
257B VAL* 5.3 1.1 - - + -
258B VAL* 4.2 8.5 - - + -
261B VAL* 5.0 8.1 - - + -
274B PHE* 3.5 35.8 + + + +
275B TRP* 3.5 50.9 - + - +
277B GLY* 5.5 6.5 - - - +
279B GLN 5.4 0.4 + - - -
318B TYR* 3.8 22.0 - + - -
319B ILE* 4.3 3.1 - - + -
320B GLN* 4.5 0.7 - - - -
333B ARG* 1.3 74.8 - - - +
335B GLY* 1.3 61.8 + - - +
336B ILE* 3.0 67.2 + - + +
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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