Contacts of the strand formed by residues 387 - 394 (chain C) in PDB entry 5E9W
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 MET 387 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C CYS* 3.7 31.4 - - + -
308C LEU* 3.7 19.5 - - + -
314C PHE* 3.9 5.8 - - + -
379C ASN 5.3 0.5 - - - +
382C ALA* 3.3 31.4 + - + +
383C LYS* 3.9 23.1 + - - +
385C TYR 3.8 10.8 - - - +
386C ASN* 1.3 78.1 - - - +
388C LYS* 1.3 59.5 + - - +
472C PHE* 3.7 30.7 - - + +
473C GLU 3.3 27.6 - - - -
474C LYS* 3.4 21.5 - - - +
475C GLN* 4.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C MET* 1.3 74.6 - - - +
389C LEU* 1.3 66.9 + - - +
390C VAL 3.3 0.2 + - - -
472C PHE* 3.3 4.7 - - - -
473C GLU* 2.7 38.8 + - + +
475C GLN* 3.4 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C PHE* 3.8 33.0 - - + -
379C ASN* 3.6 20.6 + - - +
388C LYS* 1.3 76.5 - - - +
390C VAL* 1.3 62.2 + - - +
391C TYR* 3.4 29.8 - - - +
392C LYS* 4.3 13.7 - - + +
471C ALA 3.4 10.5 - - - +
472C PHE* 3.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C PHE* 4.2 13.2 - - + -
190C LYS* 5.4 5.8 - - + -
313C TYR* 4.1 13.7 - - + -
389C LEU* 1.3 76.7 - - - +
391C TYR* 1.3 78.6 + - + +
471C ALA* 2.7 23.4 + - + +
472C PHE 3.8 3.1 - - - -
473C GLU* 3.6 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C LEU* 3.4 11.4 - - + +
186C GLU* 2.8 40.6 + - - -
187C PHE* 3.3 24.8 - + - -
190C LYS* 5.7 0.2 - - - -
389C LEU* 3.4 15.3 - - - +
390C VAL* 1.3 93.5 - - + +
392C LYS* 1.3 64.6 + - - +
393C LYS* 3.2 40.8 - - + +
398C PHE* 3.4 7.5 - + - -
402C LYS* 5.5 1.8 - - - -
469C VAL* 3.7 23.6 - - + -
470C PHE* 3.5 0.3 - - - -
471C ALA* 3.1 30.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C ASN* 5.1 7.7 + - - +
322C PHE* 5.0 15.1 - - - -
375C PHE* 3.7 45.2 - - + +
389C LEU* 4.2 8.0 - - + +
391C TYR* 1.3 76.1 - - - +
393C LYS* 1.3 70.9 + - - +
394C THR* 5.6 5.7 - - - +
397C GLU* 4.3 3.1 - - - +
468C LEU* 4.1 27.8 - - + -
469C VAL 3.5 8.7 - - - +
470C PHE* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C TYR* 3.2 46.4 - - + +
392C LYS* 1.3 80.8 - - - +
394C THR* 1.3 66.7 + - - +
397C GLU* 3.3 14.8 - - + +
398C PHE* 4.1 23.1 - - + +
401C GLU* 3.0 35.0 + - - +
402C LYS* 5.6 0.2 - - - +
468C LEU* 3.3 4.6 - - - -
469C VAL* 2.7 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C ASN* 4.0 22.4 - - - +
392C LYS* 5.6 6.7 - - - +
393C LYS* 1.3 74.9 - - - +
395C PHE* 1.3 65.5 + - - +
396C LEU* 3.4 11.3 + - - +
397C GLU* 2.9 45.5 + - - +
398C PHE* 3.0 21.3 + - - +
465C SER 5.1 6.1 - - - +
467C TYR 3.8 7.9 - - - -
468C LEU* 4.1 4.0 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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