Contacts of the strand formed by residues 401 - 407 (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 GLY 401 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B VAL* 4.2 6.3 - - - -
397B HIS* 2.9 37.1 + - - +
399B THR 3.5 2.0 - - - -
400B PHE* 1.3 80.2 - - - +
402B PRO* 1.3 77.8 - - - +
403B VAL* 3.3 2.3 + - - +
424B HIS* 3.5 14.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE 3.6 7.9 - - - +
396B VAL* 4.2 17.5 - - + -
400B PHE 4.7 1.2 - - - +
401B GLY* 1.3 83.7 - - - +
403B VAL* 1.3 62.4 + - - +
418B GLY* 3.7 2.4 - - - -
419B THR* 3.0 34.1 + - - +
420B ASP* 3.7 24.4 + - + +
424B HIS* 3.7 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ASN* 3.4 6.6 - - - +
395B PHE* 2.8 74.8 + - + +
397B HIS* 4.1 6.7 - - + -
400B PHE* 4.1 8.7 - - + -
401B GLY 3.5 8.5 - - - +
402B PRO* 1.3 80.0 - - - +
404B TRP* 1.3 60.5 - - - +
416B LEU* 4.4 19.5 - - + -
417B ILE 3.2 15.5 - - - +
419B THR* 4.0 6.2 + - - -
432B LEU* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLY* 4.2 8.4 + - - -
349B LEU 4.1 3.4 - - - -
357B ILE* 3.6 55.4 - - + -
358B THR 5.2 0.2 - - - -
366B LEU* 3.7 24.7 - - + -
389B PRO* 3.4 40.2 - - + -
391B ARG 3.1 21.2 + - - -
392B GLY* 3.6 8.8 - - - -
393B ALA 3.3 11.2 - - - -
394B ASN* 3.2 31.4 - - - +
403B VAL* 1.3 76.8 - - - +
405B ALA* 1.3 63.2 + - - +
406B THR* 3.8 12.6 - - - -
415B ALA 3.8 0.6 - - - +
416B LEU* 3.5 2.3 - - - -
417B ILE* 2.9 39.8 + - + +
419B THR* 3.7 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B GLY* 3.5 5.9 - - - -
393B ALA* 2.8 37.4 + - + +
395B PHE* 4.1 9.2 - - + -
404B TRP* 1.3 81.0 - - - +
406B THR* 1.3 62.1 + - - +
414B VAL* 4.5 1.3 - - + -
415B ALA 3.3 4.9 - - - +
416B LEU* 3.5 24.5 - - + -
445B ILE* 3.4 25.9 - - + +
454B LEU* 4.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU* 4.5 2.9 - - + -
382B THR* 4.4 7.2 - - + -
387B PRO* 4.2 11.4 - - + +
388B HIS 3.6 0.9 + - - -
389B PRO* 3.2 27.8 - - - +
404B TRP* 3.8 21.1 - - + -
405B ALA* 1.3 75.3 - - - +
407B SER* 1.3 79.0 + - - +
408B HIS* 4.2 13.8 - - + -
414B VAL* 3.3 3.1 - - - +
415B ALA* 2.9 40.5 + - + +
445B ILE* 4.1 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PRO* 3.6 1.2 - - - +
388B HIS 2.9 23.4 + - - +
406B THR* 1.3 88.4 + - - +
408B HIS* 1.3 65.4 + - - +
412B ASP 6.3 0.2 - - - -
413B SER 3.5 11.9 - - - -
414B VAL* 4.3 5.4 - - - +
442B SER* 2.6 29.9 + - - -
444B PHE 4.2 11.1 + - - -
445B ILE* 4.3 8.2 - - - +
456B VAL* 3.6 21.4 - - - +
----------------------------------------------------------
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