Contacts of the strand formed by residues 401 - 407 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A VAL* 4.1 7.0 - - - -
397A HIS* 2.8 38.7 + - - +
399A THR 3.5 2.2 + - - -
400A PHE* 1.3 78.3 - - - +
402A PRO* 1.3 77.8 - - - +
403A VAL* 3.2 2.1 + - - +
424A HIS* 3.7 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE 3.5 9.6 - - - +
396A VAL* 4.3 16.4 - - + -
400A PHE 4.6 1.7 - - - +
401A GLY* 1.3 83.7 - - - +
403A VAL* 1.3 62.0 + - - +
418A GLY* 3.6 2.8 - - - -
419A THR* 3.0 34.4 + - - +
420A ASP* 3.9 22.1 + - + +
424A HIS* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ALA 3.8 0.2 - - - +
394A ASN* 3.3 5.7 - - - +
395A PHE* 2.9 76.0 + - + +
397A HIS* 4.1 5.6 - - + -
400A PHE* 4.1 9.6 - - + -
401A GLY 3.4 10.1 - - - +
402A PRO* 1.3 77.6 - - - +
404A TRP* 1.3 63.0 + - - +
416A LEU* 4.4 14.6 - - + -
417A ILE 3.2 15.7 - - - +
419A THR* 3.7 7.0 + - - -
432A LEU* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLY 4.2 7.7 + - - -
349A LEU 4.0 6.2 + - - -
357A ILE* 3.6 52.5 - - + -
366A LEU* 3.7 25.8 - - + -
389A PRO* 3.4 40.4 - - + -
391A ARG 3.1 20.9 + - - -
392A GLY* 3.6 9.0 - - - -
393A ALA 3.2 11.7 - - - -
394A ASN* 3.2 33.4 - - - +
403A VAL* 1.3 72.9 - - - +
405A ALA* 1.3 63.2 + - - +
406A THR* 3.8 12.8 - - + -
415A ALA 3.9 0.6 - - - +
416A LEU* 3.5 2.2 - - - -
417A ILE* 2.9 40.8 + - + +
419A THR* 3.7 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLY* 3.6 6.2 - - - -
393A ALA* 2.8 36.1 + - + +
395A PHE* 4.1 9.9 - - + -
404A TRP* 1.3 81.0 - - - +
406A THR* 1.3 61.2 - - - +
414A VAL* 4.5 1.6 - - + -
415A ALA 3.3 5.6 - - - +
416A LEU* 3.5 23.8 - - + -
445A ILE* 3.4 25.7 - - + +
454A LEU* 4.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 4.4 10.8 - - + -
382A THR* 4.5 0.9 - - + -
387A PRO* 4.3 9.6 - - + -
388A HIS 3.6 0.9 + - - -
389A PRO* 3.2 27.5 - - - +
404A TRP* 3.8 21.1 - - + -
405A ALA* 1.3 76.1 - - - +
407A SER* 1.3 77.9 + - - +
408A HIS* 4.1 13.0 + - + -
413A SER 4.1 0.3 - - - +
414A VAL* 3.3 3.1 - - - +
415A ALA* 2.9 40.4 + - + +
445A ILE* 4.1 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PRO* 3.6 0.3 - - - +
388A HIS 3.0 22.4 + - - +
406A THR* 1.3 88.7 + - - +
408A HIS* 1.3 65.8 + - - +
412A ASP 6.3 0.2 - - - -
413A SER 3.4 11.0 - - - -
414A VAL* 4.2 5.2 - - - +
442A SER* 2.6 28.7 + - - -
444A PHE 4.2 13.2 + - - -
445A ILE* 4.2 8.0 - - - +
456A VAL* 3.6 21.9 - - - +
----------------------------------------------------------
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