Contacts of the strand formed by residues 387 - 393 (chain C) in PDB entry 5U07
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 ASP 387 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C TRP* 3.2 24.1 - - + -
379C PHE* 4.0 15.9 - - + -
381C GLN* 3.3 13.0 - - + +
382C ASP 4.7 0.4 - - - +
385C ALA 4.4 5.6 - - - +
386C ARG* 1.3 79.3 - - - +
388C LYS* 1.3 61.4 + - - +
21N PHE* 3.1 47.4 - - + +
22N GLY 4.5 2.1 + - - -
23N GLU* 4.4 1.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
329C GLU* 5.3 1.4 - - - +
330C ALA* 3.8 18.2 - - - +
331C GLU* 5.3 1.8 - - - +
380C ASP* 3.0 49.4 + - + +
381C GLN* 4.1 7.9 - - - -
382C ASP 5.3 1.6 - - - +
387C ASP* 1.3 76.1 - - - +
389C GLN* 1.3 74.7 + - + +
19N SER* 4.6 0.3 + - - -
21N PHE* 3.7 17.7 - - - +
23N GLU* 3.1 45.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C ALA* 3.8 25.6 - - + +
379C PHE* 3.5 9.2 - - - -
380C ASP* 2.5 50.1 + - - +
388C LYS* 1.3 82.6 + - + +
390C TRP* 1.3 72.1 + - - +
391C PHE* 5.0 3.1 - - + -
18N HIS* 3.5 6.5 - - - +
19N SER* 2.9 39.2 + - - -
20N MET 4.6 1.0 + - - -
21N PHE* 4.8 4.0 - - - -
23N GLU* 3.6 15.5 + - + +
25N ASP* 2.9 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PRO 4.6 4.7 + - - -
61C LEU* 4.5 20.6 - - + -
62C PRO* 3.1 38.4 - - + +
63C PRO* 4.6 6.1 - - + -
153C TRP* 4.8 12.6 - - + -
378C GLY 3.2 8.7 - - - +
379C PHE* 3.2 42.2 - + + -
389C GLN* 1.3 77.8 + - - +
391C PHE* 1.3 69.8 + - - +
392C THR 5.4 0.2 - - - -
18N HIS* 2.9 53.2 + - + +
20N MET* 3.6 48.2 - - + -
21N PHE* 3.5 25.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO* 4.2 6.5 - - - +
219C VAL* 4.6 11.4 - - + -
221C TYR* 5.9 0.4 - - - -
328C ALA* 4.1 18.4 - - + -
329C GLU 4.2 19.3 - - - -
330C ALA* 4.6 7.0 - - - -
332C ARG* 5.7 5.4 - - - -
334C ILE* 5.5 9.6 - - + -
376C ALA* 3.6 3.2 - - + +
377C PHE* 3.6 1.2 - - - -
378C GLY* 2.9 68.6 + - - -
380C ASP* 4.3 10.5 - - - -
389C GLN* 4.9 3.4 - - + -
390C TRP* 1.3 87.3 - - - +
392C THR* 1.3 69.9 + - - +
393C ALA* 4.8 9.6 - - + -
18N HIS* 4.4 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO* 4.9 4.1 - - - +
375C ARG* 3.8 14.5 + - - +
376C ALA 3.1 9.6 + - - -
377C PHE* 3.6 25.5 - - - -
390C TRP* 5.4 0.4 - - - -
391C PHE* 1.3 80.2 - - - +
393C ALA* 1.3 71.0 + - - +
394C THR* 4.4 3.3 - - - +
18N HIS* 6.1 0.4 - - - +
199N VAL* 4.6 22.7 - - + +
200N LEU* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ILE* 3.3 34.5 - - + -
375C ARG* 3.5 1.6 - - - -
376C ALA* 2.9 34.5 + - + +
391C PHE* 4.8 7.9 - - + -
392C THR* 1.3 81.4 + - - +
394C THR* 1.3 61.1 + - - +
395C THR* 3.0 14.0 + - + +
----------------------------------------------------------
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