Contacts of the strand formed by residues 383 - 388 (chain P) in PDB entry 1VYH
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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342P ARG* 3.2 25.3 - - - +
356P CYS* 3.5 29.2 - - + -
357P ALA 3.2 13.6 + - - +
358P ASP* 4.2 0.3 - - - +
360P LYS* 4.1 3.1 - - - +
361P THR 3.9 25.8 - - - +
362P LEU* 5.6 0.9 - - + -
378P ALA* 3.9 10.1 - - + -
379P HIS* 3.4 24.2 - - + -
382P PHE* 1.3 72.0 - - - +
384P THR* 1.3 63.3 + - - +
385P SER 3.8 3.4 - - - +
397P THR* 3.6 15.7 - - + -
398P GLY 3.4 10.3 - - - +
399P SER* 3.3 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 384 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110P PRO* 5.9 0.2 - - - +
111P VAL 3.2 27.3 + - - +
112P THR* 3.2 25.3 - - + +
113P ARG* 5.6 1.9 + - - -
342P ARG* 3.6 49.7 + - - +
356P CYS* 3.9 3.1 - - - -
382P PHE 3.4 10.1 + - - -
383P VAL* 1.3 73.2 - - - +
385P SER* 1.3 57.2 + - - +
398P GLY 2.7 14.5 + - - -
399P SER* 3.9 4.2 - - - -
400P VAL* 4.0 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 385 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P VAL* 4.7 0.5 + - - +
112P THR 3.7 15.6 + - - -
113P ARG* 3.7 25.8 - - - -
114P VAL* 3.7 20.8 - - - +
342P ARG 5.2 1.6 - - - -
343P GLY* 5.3 1.1 - - - -
356P CYS* 3.6 10.0 - - - -
383P VAL* 3.8 3.8 - - - +
384P THR* 1.3 82.3 - - - +
386P LEU* 1.3 61.9 + - - +
397P THR* 3.5 2.3 - - - -
398P GLY* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 386 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P ARG* 6.0 0.7 - - - -
114P VAL* 4.3 8.2 - - - +
343P GLY* 3.6 37.2 - - - +
344P VAL 3.9 2.9 - - - +
345P LEU* 3.9 19.5 - - + +
354P LEU* 3.8 24.5 - - + +
355P SER 4.0 8.5 - - - +
356P CYS* 4.1 8.7 - - + -
362P LEU* 3.5 28.0 - - + -
385P SER* 1.3 75.2 - - - +
387P ASP* 1.3 65.4 + - - +
395P VAL* 4.8 6.7 - - + -
396P VAL 3.4 10.8 - - - +
397P THR* 4.1 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 387 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P VAL* 3.8 22.7 - - + +
115P ILE* 3.9 3.9 - - - +
116P PHE* 2.8 66.8 + - + +
345P LEU* 4.0 12.2 - - - +
386P LEU* 1.3 77.8 - - - +
388P PHE* 1.3 63.9 + - - +
395P VAL* 3.6 3.5 - - - -
396P VAL 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 388 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P TRP* 3.5 31.0 - + + -
95P ILE 5.0 5.4 - - - -
96P PRO* 4.9 12.3 - - + -
116P PHE* 3.8 0.8 - - - -
345P LEU* 3.3 23.0 - - + +
346P PHE 4.6 9.6 - - - +
347P HIS* 3.4 39.3 - + - -
348P SER 4.8 8.3 - - - -
354P LEU* 4.3 23.3 - - + -
387P ASP* 1.3 82.5 - - - +
389P HIS* 1.3 88.3 + - - +
390P LYS* 3.4 2.8 + - - -
392P ALA 4.5 0.2 - - - -
393P PRO 5.5 1.6 - - - -
394P TYR 4.0 7.0 - - - -
395P VAL* 3.3 29.9 - - + +
----------------------------------------------------------
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