Contacts of the strand formed by residues 307 - 313 (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 ARG 307 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D TRP* 6.1 0.2 - - - -
301D ARG* 4.0 0.7 - - - +
302D ASP* 3.1 25.7 + - + -
304D ASN* 2.6 38.7 + - - +
305D SER 3.2 5.4 - - - +
306D SER* 1.3 82.3 + - - +
308D SER* 1.3 59.6 + - - +
385D PRO* 3.6 35.8 - - + +
386D PHE 3.3 8.7 - - - +
387D SER* 5.5 0.7 - - - -
388D THR* 2.9 14.4 - - - +
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Residues in contact with SER 308 (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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217D LEU* 4.0 13.7 - - - -
299D TYR* 3.9 13.4 - - - +
300D LEU 3.3 17.3 - - - -
302D ASP* 3.6 6.7 - - - +
307D ARG* 1.3 77.0 - - - +
309D PHE* 1.3 62.8 + - - +
385D PRO* 3.1 6.1 - - - +
386D PHE* 2.6 45.9 + - - +
387D SER 4.8 1.7 + - - -
388D THR* 3.5 12.7 - - - +
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Residues in contact with PHE 309 (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* 3.6 57.2 - + + -
203D TYR 3.4 29.4 - - - -
204D THR* 4.1 11.9 - - - -
299D TYR* 3.6 4.0 - - - -
300D LEU* 3.0 64.2 + - + +
301D ARG 4.2 1.6 - - - -
302D ASP* 4.2 7.0 - - - -
308D SER* 1.3 75.2 - - - +
310D ARG* 1.3 70.9 + - - +
311D ILE* 4.1 14.1 - - + -
366D PHE* 4.2 8.7 - + - -
382D ILE* 4.3 6.7 - - + -
383D SER 3.5 12.8 - - - +
384D GLY* 4.3 0.7 - - - -
386D PHE* 4.3 4.3 - - - -
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Residues in contact with ARG 310 (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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220D GLU* 3.0 14.3 + - - -
297D SER* 4.2 13.7 + - - -
298D ILE 3.4 12.3 - - - +
299D TYR* 2.9 48.1 + - + -
309D PHE* 1.3 80.0 - - - +
311D ILE* 1.3 61.8 + - - +
312D THR* 4.0 11.8 + - - +
381D GLU* 5.5 4.8 + - - -
382D ILE* 3.3 5.2 - - - +
383D SER* 2.9 44.5 + - - +
386D PHE* 3.8 21.3 - - + -
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Residues in contact with ILE 311 (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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297D SER* 3.4 0.5 - - - -
298D ILE* 3.0 56.8 + - + +
300D LEU* 4.4 11.7 - - + -
309D PHE* 4.1 11.9 - - + -
310D ARG* 1.3 73.0 - - - +
312D THR* 1.3 67.0 + - - +
345D ILE* 5.1 4.0 - - + -
349D VAL* 4.3 20.0 - - + -
353D PHE* 3.5 21.8 - - + -
366D PHE* 4.1 35.2 - - + -
381D GLU 3.5 4.0 - - - -
382D ILE* 4.1 15.5 - - + +
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Residues in contact with THR 312 (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* 4.0 23.8 - - + -
296D ILE 3.3 10.8 - - - +
297D SER* 2.6 28.2 + - - +
310D ARG* 4.0 14.2 + - - +
311D ILE* 1.3 76.4 - - - +
313D ILE* 1.3 75.0 + - - +
314D LEU* 4.7 3.1 - - + -
353D PHE* 3.4 2.2 - - - -
380D SER* 3.1 8.8 - - - -
381D GLU* 2.7 52.7 + - + +
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Residues in contact with ILE 313 (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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247D LEU* 4.8 5.4 - - + -
295D LYS* 3.9 1.4 - - - -
296D ILE* 3.1 45.0 + - + +
312D THR* 1.3 81.4 - - - +
314D LEU* 1.3 66.1 + - - +
317D LEU* 3.5 26.2 - - + -
318D TYR* 4.0 29.5 - - + -
348D THR* 4.2 6.7 - - - +
349D VAL* 4.1 35.4 - - + +
353D PHE* 4.1 16.6 - - + -
379D VAL 3.8 3.4 - - - -
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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