Contacts of the strand formed by residues 383 - 387 (chain A) in PDB entry 3VI4
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 VAL 383 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLY* 3.4 2.6 - - - -
373A ALA* 2.8 39.0 + - + +
376A GLY* 4.2 5.6 - - - -
377A GLY* 3.8 17.9 - - - +
382A GLY* 1.3 81.3 - - - +
384A VAL* 1.3 71.7 + - - +
385A PHE* 3.5 41.7 - - + -
401A VAL* 4.5 5.6 - - + -
402A LEU 3.4 5.6 - - - +
403A GLN* 3.5 32.8 - - + +
415A PHE* 3.5 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA* 4.1 11.0 - - + -
371A ILE 3.4 9.6 - - - +
372A GLY* 4.4 2.2 - - - -
383A VAL* 1.3 80.0 - - - +
385A PHE* 1.3 72.5 + - - +
386A VAL* 5.3 0.2 - - + -
401A VAL* 3.7 4.5 - - - -
402A LEU* 2.9 52.7 + - + +
415A PHE* 3.8 4.9 - - + -
416A GLY* 3.6 28.0 - - - -
419A LEU* 3.6 22.4 - - + -
433A LEU* 5.1 1.6 - - + -
435A VAL* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLY* 5.6 2.7 - - - -
345A HIS* 5.4 16.4 - + + -
346A ASP* 5.8 5.4 - - - -
351A PHE* 3.5 33.2 - + + -
369A VAL 3.8 0.5 - - - +
370A ALA* 3.2 5.5 - - - +
371A ILE 2.6 43.3 + - - +
373A ALA* 4.6 9.9 - - + -
383A VAL* 3.5 26.0 - - + -
384A VAL* 1.3 74.3 - - - +
386A VAL* 1.3 63.5 + - - +
387A PHE* 3.4 25.3 + + + -
398A PRO* 4.1 17.3 - - + -
400A GLN 3.9 1.1 - - - -
401A VAL* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.4 9.6 - - + -
358A LEU* 3.7 29.4 - - + -
361A LEU* 3.9 14.4 - - + -
368A ASP* 4.9 5.6 - - + +
369A VAL 3.5 3.6 - - - +
370A ALA* 4.8 4.5 - - + -
384A VAL* 5.3 0.2 - - + -
385A PHE* 1.3 74.8 - - - +
387A PHE* 1.3 62.9 + - - +
398A PRO* 3.1 5.2 - - - +
399A SER* 2.7 49.9 + - - +
400A GLN* 3.1 20.7 + - + +
402A LEU* 3.7 27.6 - - + -
433A LEU* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 3.6 26.2 - - + -
351A PHE* 4.0 15.3 - + - -
368A ASP* 3.6 3.5 - - - +
369A VAL* 2.9 33.0 + - + +
371A ILE* 3.6 30.1 - - + -
385A PHE* 3.4 27.6 - + + -
386A VAL* 1.3 76.6 - - - +
388A PRO* 1.3 66.1 - - - +
394A LEU* 3.4 16.8 - - + +
395A GLY 3.2 24.5 - - - +
396A SER 4.1 4.0 - - - -
397A LYS 3.7 11.2 - - - -
398A PRO* 3.7 28.3 - - + -
----------------------------------------------------------
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