Contacts of the strand formed by residues 394 - 399 (chain C) in PDB entry 5VOT
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 THR 394 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C LYS* 1.3 79.2 - - - +
395C VAL* 1.3 66.5 + - - +
396C VAL* 3.9 5.3 + - + +
439C LYS* 3.1 16.3 - - + +
440C TYR* 3.4 30.5 - - - +
441C LYS* 4.0 10.8 - - + -
473C ASP* 3.8 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C LYS 4.3 5.6 - - - +
394C THR* 1.3 72.2 - - - +
396C VAL* 1.3 67.3 + - - +
397C VAL* 3.3 2.1 + - + -
438C PHE* 3.4 34.5 - - + -
439C LYS 2.3 29.8 + - - +
440C TYR* 2.9 4.2 - - - +
441C LYS* 2.9 26.9 + - - -
473C ASP* 3.3 21.8 - - + +
474C ILE* 4.1 16.4 - - + -
742C LEU* 4.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C THR* 4.8 5.6 - - + +
395C VAL* 1.3 64.2 - - - +
397C VAL* 1.3 59.9 + - - +
398C THR 3.9 0.2 + - - -
441C LYS* 4.5 6.1 - - + +
443C THR* 4.2 20.2 - - + +
471C LYS 3.7 10.8 - - - +
472C ALA* 3.6 23.3 - - + -
473C ASP* 2.4 63.4 + - - +
474C ILE* 3.1 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C VAL* 3.8 3.8 - - + +
396C VAL* 1.3 73.4 - - - +
398C THR* 1.3 64.0 + - - +
399C THR* 4.9 0.8 - - - +
429C ALA* 4.8 5.2 - - + -
438C PHE* 5.1 2.7 - - + -
440C TYR* 3.6 33.2 - - + -
441C LYS 2.8 31.5 + - - +
442C LEU* 3.7 17.7 - - + -
443C THR* 2.6 28.6 + - - -
474C ILE* 3.6 20.4 - - + +
476C ILE* 4.5 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C VAL 3.9 0.8 + - - -
397C VAL* 1.3 75.4 - - - +
399C THR* 1.3 69.1 + - - +
443C THR* 3.3 13.5 + - - -
444C ILE 5.1 0.2 - - - -
445C VAL* 4.4 3.5 + - - +
463C MET* 3.7 23.2 - - + +
466C GLU* 3.9 14.2 - - + +
467C LEU* 4.7 3.1 - - + -
472C ALA* 3.8 24.0 - - + -
474C ILE 3.0 16.9 + - - +
475C ALA* 3.6 18.4 - - + +
476C ILE 3.4 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C VAL* 4.9 2.5 - - - +
398C THR* 1.3 78.5 + - - +
400C ILE* 1.3 69.7 + - - +
406C VAL* 3.3 26.6 - - + +
421C TYR* 6.1 0.7 - - + -
425C CYS* 5.7 0.2 - - - -
442C LEU* 5.1 13.9 - - + -
443C THR 2.9 23.1 + - - +
444C ILE* 3.5 16.7 - - + -
445C VAL* 3.1 24.3 + - - +
463C MET* 3.5 16.7 - - - +
476C ILE 3.4 17.4 + - - -
477C ALA* 3.5 8.6 - - - +
478C PRO* 4.9 0.2 - - - +
----------------------------------------------------------
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