Contacts of the strand formed by residues 380 - 387 (chain D) 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 SER 380 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312D THR 3.1 13.9 - - - -
314D LEU* 4.7 1.5 - - - +
317D LEU* 4.3 2.5 - - - -
352D GLY* 2.7 40.8 + - - -
353D PHE* 3.9 9.0 - - - -
368D ALA* 5.1 7.7 - - - +
369D SER 4.5 5.4 + - - -
372D ALA* 4.1 8.8 + - - +
378D ALA* 3.5 11.9 - - - +
379D VAL* 1.3 83.2 + - - +
381D GLU* 1.3 70.6 + - - +
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Residues in contact with GLU 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D LYS* 2.9 36.3 + - - +
310D ARG* 4.5 5.6 + - - -
312D THR* 2.7 48.6 + - - +
314D LEU* 4.2 13.9 - - + +
353D PHE* 3.3 9.1 - - - -
368D ALA* 5.7 2.5 - - - -
378D ALA* 5.5 6.4 - - + +
380D SER* 1.3 80.4 - - - +
382D ILE* 1.3 60.5 + - - +
383D SER* 6.3 0.7 - - - -
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Residues in contact with ILE 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D ASP 4.9 5.4 - - - +
202D TRP* 3.5 35.6 + - + +
309D PHE* 4.3 4.3 - - + -
310D ARG 3.3 13.2 - - - +
311D ILE* 4.1 11.7 - - + -
353D PHE* 4.2 7.0 - - + -
366D PHE* 3.6 37.2 - - + +
367D ALA* 4.4 1.6 - - - +
368D ALA* 4.0 26.2 - - + +
381D GLU* 1.3 79.8 - - - +
383D SER* 1.3 68.2 + - - +
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Residues in contact with SER 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D TRP* 4.5 7.2 - - - +
309D PHE* 3.5 4.3 - - - +
310D ARG* 2.9 47.2 + - - -
381D GLU* 6.3 0.2 - - - -
382D ILE* 1.3 78.7 - - - +
384D GLY* 1.3 59.3 + - - +
386D PHE* 3.3 20.9 - - - -
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Residues in contact with GLY 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D TRP* 3.3 22.5 - - - -
309D PHE* 4.3 2.9 - - - -
383D SER* 1.3 78.3 - - - +
385D PRO* 1.3 74.8 - - - +
386D PHE* 3.8 10.0 - - - -
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Residues in contact with PRO 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D TRP* 3.5 22.9 - - + -
302D ASP* 5.5 0.2 - - - +
307D ARG* 3.6 45.3 - - + +
308D SER 3.1 11.4 - - - +
384D GLY* 1.3 85.8 - - - +
386D PHE* 1.3 62.9 + - - +
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Residues in contact with PHE 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D TYR* 3.7 26.7 - + + -
307D ARG* 3.3 8.3 - - - -
308D SER* 2.6 43.9 + - - +
309D PHE* 4.3 2.9 - - - -
310D ARG* 3.8 31.9 - - + -
383D SER* 3.3 42.4 - - - -
384D GLY* 3.8 3.6 - - - -
385D PRO* 1.3 78.0 - - - +
387D SER* 1.3 66.6 + - - +
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Residues in contact with SER 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D LYS* 5.5 4.9 + - - -
306D SER 3.8 5.2 + - - -
307D ARG* 5.5 1.3 - - - -
308D SER* 4.8 1.0 + - - -
386D PHE* 1.3 76.1 - - - +
388D THR* 1.3 60.2 + - - +
389D GLU* 3.4 25.8 + - - +
390D ASP* 3.2 12.8 + - - +
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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