Contacts of the strand formed by residues 363 - 368 (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 363 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203D TYR* 3.4 47.7 + - + -
204D THR 3.2 16.6 - - - +
205D PRO* 4.3 0.7 - - + -
206D ILE* 3.3 7.1 - - - +
303D GLU* 3.2 37.0 + - - +
358D ASP* 3.0 57.4 + - + +
361D GLN* 3.1 45.3 + - - +
362D LYS* 1.3 77.1 - - - +
364D VAL* 1.3 66.5 + - - +
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Residues in contact with VAL 364 (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 3.9 0.5 - - - +
203D TYR* 3.3 2.9 - - - -
204D THR* 2.7 49.4 + - + +
206D ILE* 3.6 21.5 - - + -
212D TYR* 4.6 17.9 - - + -
214D ILE* 4.1 13.7 - - + -
240D VAL* 4.5 7.9 - - + -
355D VAL* 4.0 18.4 - - + -
356D ILE 3.3 11.0 - - - +
357D PHE* 4.8 6.3 - - + -
363D ARG* 1.3 78.7 - - - +
365D GLY* 1.3 61.6 + - - +
366D PHE* 3.8 21.9 - - + -
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Residues in contact with GLY 365 (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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201D ILE* 4.6 2.7 - - - -
202D TRP 2.8 11.4 - - - -
203D TYR* 3.4 20.2 - - - -
354D TYR 3.6 0.4 - - - +
355D VAL* 3.4 6.2 - - - +
356D ILE* 2.7 43.2 + - - -
364D VAL* 1.3 74.5 - - - +
366D PHE* 1.3 65.5 + - - -
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Residues in contact with PHE 366 (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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201D ILE* 3.3 4.1 - - - -
202D TRP 2.7 33.9 + - - +
204D THR* 4.3 4.7 - - + -
214D ILE* 4.3 1.8 - - + -
240D VAL* 4.3 17.9 - - + -
300D LEU* 3.7 25.6 - - + -
309D PHE* 4.2 12.6 - + + -
311D ILE* 4.1 30.3 - - + -
345D ILE* 5.2 10.1 - - + -
349D VAL* 5.5 1.8 - - + -
350D MET* 5.8 1.6 - - + -
353D PHE* 4.4 13.2 - + + -
354D TYR 3.5 5.4 - - - +
355D VAL* 4.2 23.1 - - + -
364D VAL* 3.8 28.9 - - + -
365D GLY* 1.3 80.4 - - - -
367D ALA* 1.3 62.1 + - - +
382D ILE* 3.6 19.6 - - + +
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Residues in contact with ALA 367 (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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197D TYR* 3.8 36.6 - - + -
198D LYS 5.0 0.7 - - - +
200D ASP 4.0 8.1 - - - +
201D ILE* 4.0 12.3 - - + -
353D PHE* 3.3 8.3 - - - -
354D TYR* 2.8 36.3 + - + +
356D ILE* 6.2 0.7 - - + -
366D PHE* 1.3 77.8 - - - +
368D ALA* 1.3 66.1 + - - +
369D SER 3.1 0.7 + - - -
382D ILE* 4.4 2.2 - - - -
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Residues in contact with ALA 368 (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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197D TYR* 3.9 3.6 - - - +
198D LYS* 3.8 27.6 + - + +
199D GLY* 5.9 0.2 - - - -
200D ASP 4.8 1.2 + - - +
352D GLY 4.6 0.7 - - - -
353D PHE* 4.5 7.9 - - - -
367D ALA* 1.3 70.9 - - - +
369D SER* 1.3 59.5 + - - +
370D PRO* 3.4 10.8 - - - +
380D SER* 5.1 10.5 - - - +
381D GLU* 5.7 0.4 - - - -
382D ILE* 4.0 27.2 - - + +
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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