Contacts of the strand formed by residues 351 - 357 (chain A) in PDB entry 5J3S
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 351 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 5.2 0.2 - - - -
118A THR 3.4 8.3 - - - -
119A TRP* 3.5 26.1 - - - +
333A ASP 3.6 0.3 - - - +
334A LEU* 3.2 9.0 - - - +
335A LEU* 2.5 48.7 + - - +
350A TRP* 1.3 72.8 - - - +
352A LEU* 1.3 61.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.5 1.1 - - - -
117A ILE* 3.1 11.1 - - - +
118A THR* 2.7 45.6 + - + +
293A CYS* 4.6 6.7 - - + +
296A THR* 4.5 8.3 - - + -
316A ASP* 3.4 33.4 - - + +
317A ARG* 4.8 0.9 - - - -
318A ILE* 3.8 24.5 - - + -
332A LEU* 3.6 30.5 - - + -
333A ASP 3.7 7.4 - - - +
334A LEU* 3.6 26.9 - - + -
335A LEU* 4.4 0.4 - - - -
350A TRP 3.8 0.8 + - - +
351A GLY* 1.3 73.7 - - - -
353A LEU* 1.3 58.5 + - - +
354A CYS 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 4.4 10.3 - - - -
116A LEU 3.2 23.3 - - - +
117A ILE* 3.7 15.0 - - + -
143A TYR* 3.6 37.9 - - + -
145A PRO* 5.2 2.2 - - + -
331A SER 3.8 0.9 - - - +
332A LEU* 3.2 7.2 + - - -
333A ASP* 3.0 39.9 + - + +
335A LEU* 3.5 21.8 - - + -
352A LEU* 1.3 76.6 - - - +
354A CYS* 1.3 60.3 + - - +
355A ASN* 3.9 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 3.4 2.3 - - - -
116A LEU* 3.1 48.4 + - + +
283A VAL* 3.6 30.3 - - - -
318A ILE* 4.0 5.8 - - + -
329A PRO* 3.8 7.2 - - - -
331A SER 3.2 15.7 - - - +
332A LEU* 3.7 11.0 - - + -
353A LEU* 1.3 73.5 - - - +
355A ASN* 1.3 71.6 + - - +
356A LEU* 3.6 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE 3.4 7.5 - - - +
115A SER* 4.2 12.2 - - - +
329A PRO* 3.6 0.9 - - - +
330A ARG* 2.6 41.3 + - + +
331A SER* 2.5 30.9 + - - +
333A ASP* 5.5 1.4 + - - -
353A LEU* 3.9 28.0 + - - +
354A CYS* 1.3 77.0 - - - +
356A LEU* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A MET* 3.6 1.0 - - - +
114A PHE* 2.7 51.5 + - + +
115A SER* 4.9 1.1 - - - +
116A LEU* 4.9 9.2 - - + -
258A ILE* 4.5 10.8 - - + -
320A PHE* 4.0 25.4 - - + -
327A ILE* 4.6 4.9 - - + -
328A ILE 3.6 13.9 - - - +
329A PRO* 3.6 26.9 - - + -
330A ARG* 4.1 4.2 - - - +
354A CYS* 3.6 25.1 - - + +
355A ASN* 1.3 83.4 - - - +
357A ASP* 1.3 76.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A HIS 3.0 42.7 - - - +
113A MET* 3.6 12.1 - - - +
114A PHE* 5.1 2.7 - - - -
327A ILE* 3.8 26.2 - - - +
328A ILE* 3.7 9.8 + - + +
330A ARG* 5.0 15.7 + - - +
356A LEU* 1.3 92.0 - - - +
----------------------------------------------------------
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