Contacts of the strand formed by residues 352 - 358 (chain D) in PDB entry 5ED1
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 LEU 352 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D VAL* 3.9 20.0 - - + -
332D LEU* 3.6 35.0 - - + -
335D PHE* 3.8 14.4 - - + -
349D ARG* 4.0 21.0 - - - +
351D VAL* 1.3 75.0 - - - +
353D ALA* 1.3 66.2 + - - +
371D VAL* 3.7 23.8 - - + -
372D SER 3.4 16.8 - - - +
373D THR* 3.7 12.3 - - + -
445D TYR* 4.1 11.6 - - + +
446D ILE* 3.6 0.5 - - - -
447D SER* 2.8 40.4 + - - +
588D GLU* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D VAL* 4.1 6.4 - - - +
352D LEU* 1.3 81.3 - - - +
354D GLY* 1.3 56.4 + - - +
371D VAL* 3.4 3.8 - - - +
372D SER* 2.7 31.6 + - - +
395D ALA* 3.6 26.9 - - + +
396D GLU* 3.8 9.4 - - + +
399D SER* 3.4 14.1 - - - +
444D LEU* 5.0 0.7 - - + -
445D TYR* 3.1 14.1 - - - +
446D ILE* 4.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D VAL* 3.9 16.6 - - - +
353D ALA* 1.3 77.4 - - - +
355D VAL* 1.3 64.6 + - - -
370D SER 2.9 14.1 - - - -
371D VAL* 4.1 0.2 - - - -
399D SER* 3.3 7.5 + - - -
443D HIS 3.8 0.2 - - - +
444D LEU* 3.6 4.6 - - - +
445D TYR* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D VAL* 4.4 0.4 - - - +
354D GLY* 1.3 77.1 - - - +
356D VAL* 1.3 74.9 + - - +
368D VAL* 3.8 1.6 - - - +
369D ILE* 2.8 38.5 + - + -
370D SER* 2.8 30.8 + - - +
399D SER* 4.0 20.4 - - - +
403D LEU* 4.2 16.8 - - + -
442D PHE* 4.3 9.0 - - + -
443D HIS 3.4 9.0 - - - +
444D LEU* 4.4 1.6 - - + -
542D PHE* 4.0 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D VAL* 3.9 37.7 - - + +
330D LEU* 4.5 6.5 - - + -
331D VAL* 3.9 19.1 - - + -
354D GLY 5.4 0.2 - - - -
355D VAL* 1.3 82.8 - - - +
357D MET* 1.3 65.0 + - - +
358D THR* 4.7 4.0 - - + -
366D ALA* 3.8 26.5 - - + -
367D LYS 3.4 10.1 - - - +
368D VAL* 4.1 15.5 - - + -
369D ILE* 4.4 0.2 - - - -
442D PHE* 3.4 2.3 - - - +
443D HIS* 2.8 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D VAL* 1.3 73.7 - - - +
358D THR* 1.3 66.0 + - - +
359D THR* 3.7 24.9 - - + -
365D ASP 4.0 1.4 - - - +
366D ALA* 3.1 6.8 - - - +
367D LYS* 2.9 55.7 + - + +
369D ILE* 3.6 18.3 - - + +
406D PHE* 4.0 13.5 - - + -
425D ILE* 3.8 28.9 - - + -
440D VAL* 4.1 14.1 - - + -
441D GLN 3.3 8.5 - - - +
442D PHE* 3.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D LEU* 5.6 0.5 - - - +
318D HIS* 3.4 34.3 - - + +
323D LEU* 4.7 8.1 - - + -
356D VAL* 4.1 2.8 + - + -
357D MET* 1.3 79.5 - - - +
359D THR* 1.3 64.5 + - - +
360D GLY 3.8 0.9 - - - -
362D ASP 5.8 0.9 - - - +
363D VAL* 5.3 4.3 - - + +
365D ASP 4.5 3.6 - - - -
366D ALA* 3.9 19.7 - - + +
439D ASN 3.7 1.9 + - - +
440D VAL* 3.3 4.3 - - - +
441D GLN* 2.9 38.7 + - - +
443D HIS* 2.8 32.8 + - + +
----------------------------------------------------------
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