Contacts of the strand formed by residues 393 - 397 (chain B) in PDB entry 1DY7
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 ALA 393 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B GLY* 1.3 75.2 - - - +
394B ASN* 1.3 62.9 - - - +
395B PHE* 4.0 3.0 - - - -
403B VAL 3.9 0.3 - - - +
404B TRP* 3.3 5.2 - - - +
405B ALA* 2.8 38.0 + - + +
445B ILE* 4.0 14.6 - - + -
446B LYS* 4.2 0.9 - - - -
447B THR* 3.9 18.2 - - + +
454B LEU* 3.7 29.8 - - + -
567B TYR 3.4 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LEU 2.9 23.8 + - - -
350B ASP* 3.3 10.1 + - - +
351B GLY* 3.3 29.0 + - - +
393B ALA* 1.3 73.0 - - - +
395B PHE* 1.3 62.4 + - - +
403B VAL 3.4 6.7 - - - +
404B TRP* 3.2 27.0 - - - +
419B THR* 4.7 0.5 + - - +
447B THR* 3.2 16.8 - - - +
448B HIS 5.6 2.1 - - - -
449B PRO* 5.7 2.3 - - - +
567B TYR* 2.8 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ALA 4.0 5.2 - - - -
394B ASN* 1.3 79.8 - - - +
396B VAL* 1.3 65.3 + - - +
397B HIS* 3.8 13.9 - - + -
402B PRO* 3.6 1.7 - - - +
403B VAL* 2.8 58.2 + - + +
405B ALA* 4.1 5.8 - - + -
416B LEU* 3.8 21.5 - - + -
447B THR* 4.3 4.7 - - + -
454B LEU* 4.0 31.6 - - + -
475B ILE* 3.6 47.1 - - + -
478B MET* 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 1.3 76.3 - - - +
397B HIS* 1.3 71.0 + - - +
398B PRO* 3.5 6.6 - - + +
401B GLY* 3.9 14.4 - - - -
402B PRO* 4.4 17.3 - - + -
475B ILE* 3.9 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.5 14.2 + + + -
396B VAL* 1.3 76.2 - - - +
398B PRO* 1.3 72.7 - - + +
399B THR* 3.1 30.8 + - - -
400B PHE* 3.0 50.9 + + + -
401B GLY* 2.9 36.7 + - - +
403B VAL* 4.1 5.8 - - + -
416B LEU* 3.7 20.3 - - + +
433B ASP* 5.0 2.8 + - - -
478B MET* 3.5 35.3 - - + +
479B THR 4.1 1.3 - - - -
480B GLY* 3.7 14.2 + - - -
----------------------------------------------------------
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