Contacts of the strand formed by residues 395 - 399 (chain G) 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 395 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G PRO 4.0 16.4 - - - +
116G PHE* 4.5 0.2 - - - -
354G LEU* 4.5 13.0 - - + -
362G LEU* 5.2 7.9 - - + -
386G LEU* 4.6 11.7 - - + -
387G ASP 3.0 20.6 - - - +
388G PHE* 3.2 34.5 - - + -
394G TYR* 1.3 72.3 - - - +
396G VAL* 1.3 64.9 + - - +
406G VAL* 3.6 1.0 - - - +
407G TRP* 2.9 59.9 + - + +
408G GLU 5.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 396 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G VAL* 3.6 24.2 - - + +
115G ILE 4.8 0.9 - - - +
116G PHE* 3.7 35.6 - - + -
123G MET* 3.7 24.9 - - + -
137G TYR* 4.9 0.9 - - + -
386G LEU* 3.1 6.6 - - - +
387G ASP* 3.0 41.6 + - + +
395G VAL* 1.3 76.8 - - - +
397G THR* 1.3 61.7 + - - +
404G VAL* 5.0 1.3 - - + -
405G LYS 3.6 3.1 - - - +
406G VAL* 4.5 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 397 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G VAL* 4.1 3.4 - - - -
362G LEU* 4.0 18.2 - - - +
378G ALA* 4.6 1.0 - - + +
379G HIS* 2.7 36.8 - - + +
383G VAL* 4.1 11.8 - - - +
385G SER 3.2 7.7 + - - -
386G LEU* 4.4 5.1 - - - +
395G VAL* 5.7 0.4 - - - -
396G VAL* 1.3 76.3 - - - +
398G GLY* 1.3 58.8 + - - +
404G VAL* 3.4 5.9 - - - +
405G LYS* 2.9 36.3 + - + -
407G TRP* 3.0 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 398 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G VAL* 4.5 7.4 - - - -
114G VAL* 3.8 15.7 - - - +
379G HIS* 3.9 2.0 + - - -
383G VAL* 4.6 0.8 - - - +
384G THR* 2.6 33.1 + - - -
385G SER* 2.6 25.6 + - - -
397G THR* 1.3 77.2 + - - +
399G SER* 1.3 56.0 + - - -
403G THR 3.7 8.3 - - - -
404G VAL* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 399 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G VAL* 3.0 27.5 + - - +
379G HIS* 2.9 39.8 + - - -
381G HIS 3.9 0.4 - - - -
382G PHE 3.1 17.5 - - - -
383G VAL* 3.7 2.7 - - - -
384G THR* 3.5 6.3 - - - +
398G GLY* 1.3 72.7 - - - -
400G VAL* 1.3 63.2 + - - +
401G ASP* 2.0 29.8 + - - -
402G GLN* 3.7 4.3 + - - -
403G THR* 3.4 6.4 + - - -
----------------------------------------------------------
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