Contacts of the strand formed by residues 369 - 377 (chain D) in PDB entry 5DWQ
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 ARG 369 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D TYR* 5.6 0.2 + - - -
365D GLY 4.6 1.4 + - - -
366D ASP 3.6 11.0 + - - +
368D HIS* 1.3 81.4 - - + +
370D ILE* 1.3 62.0 + - - +
371D GLU* 2.7 46.7 + - - +
439D LEU* 4.0 23.7 - - + +
440D LEU 3.5 5.2 - - - +
441D ILE* 4.8 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D PHE* 3.4 44.2 - - + -
355D TYR* 3.5 37.7 - - + +
366D ASP 4.0 3.4 - - - +
367D LEU* 3.9 35.7 - - + +
369D ARG* 1.3 74.2 - - - +
371D GLU* 1.3 59.1 + - - +
372D ILE* 4.0 16.4 - - + +
438D CYS 3.6 2.9 - - - +
439D LEU* 3.5 4.1 - - - -
440D LEU* 2.8 48.8 + - + +
448D TYR* 4.0 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D TYR* 3.6 16.8 + - - -
369D ARG* 2.7 40.7 + - - +
370D ILE* 1.3 72.4 - - - +
372D ILE* 1.3 60.8 + - - +
373D PRO* 3.4 18.2 - - + +
437D THR* 3.8 29.3 + - + +
438D CYS 3.9 0.2 - - - -
439D LEU* 3.8 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D PHE* 4.9 2.0 - - + -
292D VAL* 4.8 7.6 - - + -
294D LEU* 3.9 34.1 - - + -
353D VAL* 4.9 7.4 - - + -
354D LYS 5.6 0.7 - - - -
355D TYR* 3.8 44.2 - - + +
370D ILE* 4.0 14.6 - - + +
371D GLU* 1.3 75.8 - - - +
373D PRO* 1.3 70.2 - - + +
374D PHE* 3.7 3.1 + - - -
389D PHE* 5.2 1.1 - - + -
437D THR* 3.6 1.7 - - - -
438D CYS* 2.8 49.3 + - + +
440D LEU* 4.6 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D VAL* 4.5 4.9 - - - +
355D TYR* 5.3 3.4 - - + -
371D GLU* 3.4 19.2 - - + +
372D ILE* 1.3 92.2 - - + +
374D PHE* 1.3 61.0 + - - +
436D GLY 3.6 9.9 - - - +
437D THR* 4.4 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D LEU* 4.1 11.7 - - + -
353D VAL* 4.0 13.9 - - + -
372D ILE 3.8 10.3 - - - -
373D PRO* 1.3 74.7 - - - +
375D LYS* 1.3 62.4 + - - +
376D PHE* 3.3 40.6 - + + -
387D LEU* 3.8 22.7 - - + -
434D LEU* 3.7 9.2 - - + -
435D SER* 3.4 8.5 - - - -
436D GLY* 3.0 48.8 + - - +
437D THR 3.4 23.8 - - - -
438D CYS* 3.6 2.0 - - + -
452D ILE* 4.5 0.7 - - + -
453D VAL 3.3 20.4 - - - -
454D ALA* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D VAL* 4.5 10.3 - - - +
374D PHE* 1.3 76.9 - - - +
376D PHE* 1.3 62.1 + - - +
377D HIS* 3.7 27.2 + - + +
433D THR* 3.4 27.6 - - + -
434D LEU 3.5 4.5 - - - -
435D SER* 4.4 7.9 - - - -
457D ASP* 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D LEU* 3.4 35.2 - - + -
295D ALA* 3.8 4.5 - - - -
296D PRO* 3.5 28.0 - - + -
350D ALA* 4.0 12.1 - - + -
351D LYS 3.5 20.0 - - - -
353D VAL* 3.6 19.5 - - + -
374D PHE* 3.3 40.6 - + + -
375D LYS* 1.3 72.2 - - - +
377D HIS* 1.3 61.2 + - - +
378D MET* 3.8 4.8 + - - -
387D LEU* 3.9 12.8 - - + -
432D ASP 3.7 0.2 - - - +
433D THR* 3.2 7.3 - - - +
434D LEU* 2.8 53.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D ALA* 3.5 11.7 - - - +
351D LYS 4.8 1.2 + - - -
375D LYS* 4.0 28.5 + - + +
376D PHE* 1.3 71.6 - - - +
378D MET* 1.3 65.0 + - - +
379D LEU* 3.4 9.7 + - - +
431D GLY* 5.3 7.0 - - - +
432D ASP 3.6 5.2 - - - +
433D THR* 3.7 20.5 + - - -
----------------------------------------------------------
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