Contacts of the strand formed by residues 380 - 387 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312C THR 3.1 13.5 - - - -
314C LEU* 4.7 1.6 - - - +
317C LEU* 4.3 2.7 - - - -
352C GLY* 2.7 40.6 + - - -
353C PHE* 3.9 9.0 - - - -
368C ALA* 5.1 7.4 - - - +
369C SER 4.5 5.5 + - - -
372C ALA* 4.1 8.3 + - - +
378C ALA* 3.5 12.2 - - - +
379C VAL* 1.3 83.1 + - - +
381C GLU* 1.3 69.9 + - - +
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Residues in contact with GLU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLU* 3.8 18.9 - - - +
295C LYS* 2.9 36.4 + - - +
310C ARG* 5.5 1.6 + - - -
312C THR* 2.7 49.4 + - - +
314C LEU* 4.2 13.9 - - + +
353C PHE* 3.3 8.4 - - - -
368C ALA* 5.7 2.5 - - - -
378C ALA* 5.5 5.9 - - + +
380C SER* 1.3 81.8 - - - +
382C ILE* 1.3 62.4 + - - +
383C SER* 6.3 0.2 - - - -
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Residues in contact with ILE 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C ASP 4.9 5.6 - - - +
202C TRP* 3.5 35.6 + - + +
309C PHE* 4.3 3.8 - - + -
310C ARG* 3.3 13.7 - - - +
311C ILE* 4.1 9.4 - - + -
353C PHE* 4.2 7.0 - - + -
366C PHE* 3.6 37.5 - - + +
367C ALA* 4.4 1.6 - - - +
368C ALA* 4.0 27.5 - - + +
381C GLU* 1.3 78.6 - - - +
383C SER* 1.3 67.8 + - - +
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Residues in contact with SER 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ASP* 4.2 0.9 - - - -
119A PHE* 4.0 30.6 - - - -
202C TRP* 4.5 7.0 - - - +
309C PHE* 3.5 3.9 - - - +
310C ARG* 2.9 45.9 + - - +
381C GLU* 6.3 0.4 - - - -
382C ILE* 1.3 79.1 - - - +
384C GLY* 1.3 60.2 - - - +
386C PHE* 3.3 19.0 - - - -
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Residues in contact with GLY 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ASP* 3.0 21.7 + - - +
95A PHE* 5.6 1.7 - - - -
202C TRP* 3.3 21.7 - - - -
309C PHE* 4.3 3.1 - - - -
383C SER* 1.3 78.5 - - - +
385C PRO* 1.3 72.8 - - - +
386C PHE* 3.8 6.5 - - - -
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Residues in contact with PRO 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY 3.8 21.8 - - - +
81A PHE* 3.6 7.8 - - + +
82A ASP* 3.0 25.0 + - - +
202C TRP* 3.5 22.9 - - + -
307C ARG* 3.6 42.2 - - + +
308C SER 3.1 10.3 - - - +
384C GLY* 1.3 85.9 - - - +
386C PHE* 1.3 61.5 + - - +
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Residues in contact with PHE 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 5.2 2.0 - - - -
82A ASP* 3.9 29.4 - - + -
83A VAL* 4.5 1.8 - - - -
84A THR* 4.4 13.0 - - + -
93A THR* 3.8 22.9 - - + -
299C TYR* 3.7 28.5 - + + -
307C ARG* 3.3 8.4 - - - -
308C SER* 2.6 44.7 + - - +
309C PHE* 4.3 2.7 - - - -
310C ARG* 3.8 26.5 - - + -
383C SER* 3.3 41.5 - - - -
384C GLY* 3.8 2.7 - - - -
385C PRO* 1.3 76.1 - - - +
387C SER* 1.3 65.9 + - - +
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Residues in contact with SER 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 5.3 8.7 - - - +
82A ASP 4.8 3.6 + - - -
145A PRO* 4.6 23.6 - - - +
218C LYS* 5.5 4.7 + - - -
306C SER 3.8 5.2 + - - -
307C ARG* 4.9 1.3 - - - +
308C SER* 4.8 1.4 + - - -
386C PHE* 1.3 77.4 - - - +
388C THR* 1.3 60.0 + - - +
389C GLU* 3.4 24.6 + - - +
390C ASP* 3.2 13.5 + - - +
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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