Contacts of the strand formed by residues 369 - 374 (chain D) in PDB entry 4L28
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
----------------------------------------------------------
76B ILE* 4.1 17.7 - - - +
103D CYS* 4.5 0.4 - - - -
104D GLU* 2.9 45.4 + - + +
106D LEU* 3.7 18.8 - - + +
244D CYS* 3.0 33.7 + - - +
247D LYS* 2.9 44.1 + - - +
248D LEU* 4.0 12.3 - - + +
249D ASP* 3.1 31.1 + - - +
250D MET 3.3 6.4 + - - -
364D LEU* 4.4 3.4 - - - -
367D GLY 5.4 0.9 - - - +
368D GLN* 1.3 75.3 - - - +
370D CYS* 1.3 59.9 + - - +
371D VAL* 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D CYS* 4.2 6.9 - - - -
104D GLU 2.7 9.7 + - - +
105D LEU* 3.4 24.8 - - + +
106D LEU* 2.6 34.5 + - - +
250D MET* 3.4 20.4 - - - +
252D VAL* 3.8 30.3 - - - -
357D ALA* 4.6 1.3 - - - -
361D ALA* 4.3 6.3 - - + -
364D LEU* 4.0 16.2 - - + -
369D ARG* 1.3 74.3 - - - +
371D VAL* 1.3 60.4 + - - +
372D VAL* 4.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D MET* 4.1 20.4 - - + -
106D LEU* 3.3 19.1 - - + -
108D LYS* 4.6 1.8 - - + -
240D ILE* 4.4 5.4 - - + -
244D CYS* 3.9 20.6 - - - -
248D LEU* 3.6 25.4 - - + -
250D MET 2.9 7.9 + - - +
251D LEU* 3.3 23.6 - - + +
252D VAL 2.9 25.3 + - - +
369D ARG* 4.7 0.7 - - - -
370D CYS* 1.3 75.7 - - - +
372D VAL* 1.3 72.2 + - - +
373D ILE* 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ILE* 6.3 0.4 - - + -
105D LEU* 4.0 16.4 - - + -
106D LEU 2.7 14.9 + - - +
107D ALA* 3.5 3.6 - - + -
108D LYS* 2.8 26.9 + - - +
252D VAL* 3.6 11.0 - - + -
353D THR* 3.7 14.1 - - + -
354D VAL* 3.8 14.1 - - + -
357D ALA* 3.6 31.0 - - + -
370D CYS* 4.4 1.1 - - - -
371D VAL* 1.3 78.5 - - - +
373D ILE* 1.3 65.5 + - - +
374D LEU* 3.6 26.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LYS* 3.7 28.7 - - + +
110D GLU* 4.8 10.5 - - + +
118D VAL* 5.5 3.4 - - + -
236D THR* 5.6 2.2 - - + -
240D ILE* 4.2 17.5 - - + -
251D LEU* 4.2 11.0 - - + -
252D VAL 3.0 17.3 + - - +
253D ALA* 4.0 18.4 - - + -
254D SER* 5.1 1.1 + - - +
260D THR* 4.5 15.5 - - + -
264D ILE* 4.2 13.5 - - + -
353D THR* 3.7 15.9 + - - +
371D VAL* 4.6 0.9 - - + -
372D VAL* 1.3 76.5 - - - +
374D LEU* 1.3 70.7 + - - +
375D PRO* 3.3 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ALA* 3.8 20.2 - - + -
108D LYS 3.3 11.9 + - - +
109D CYS* 4.3 3.8 - - - -
110D GLU* 3.2 20.4 + - - -
111D PHE* 3.8 25.8 - - + -
338D LEU* 5.1 2.5 - - + -
344D LEU* 3.7 29.6 - - + -
346D CYS* 4.5 8.5 - - - -
350D ALA* 3.5 28.9 - - + +
354D VAL* 4.0 7.4 - - + -
372D VAL* 3.6 19.3 - - + -
373D ILE* 1.3 82.8 - - - +
375D PRO* 1.3 67.6 - - - +
376D ASP 3.3 3.4 + - - -
----------------------------------------------------------
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