Contacts of the strand formed by residues 357 - 362 (chain A) in PDB entry 5E9W
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 LYS 357 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PHE* 4.1 6.1 - - - -
346A GLN* 3.4 32.3 + - + +
355A GLY 3.2 6.5 + - - +
356A CYS* 1.3 74.5 - - - +
358A TYR* 1.3 68.2 + - - +
359A ASP* 5.1 4.5 - - - +
369A PRO* 3.8 28.0 - - + +
370A GLU 3.4 11.4 - - - +
371A PHE* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A HIS* 4.8 0.5 - - - -
319A PRO* 3.3 23.6 - - + +
324A LEU* 3.6 21.0 - - + +
343A VAL* 3.8 19.3 - - + -
344A LYS 3.3 12.6 - - - +
345A PHE* 4.0 33.0 - + + -
346A GLN 4.7 0.4 - - - +
356A CYS 4.1 6.1 - - - -
357A LYS* 1.3 79.4 - - - +
359A ASP* 1.3 70.6 + - - +
360A PHE* 4.1 10.3 - + + -
369A PRO* 3.8 0.9 - - - +
370A GLU* 2.5 71.1 + - + +
371A PHE 3.7 25.9 + - - -
372A LEU* 3.7 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A THR 3.7 0.3 - - - +
343A VAL* 3.3 6.2 - - - -
344A LYS* 2.7 55.9 + - + +
357A LYS* 5.1 5.5 - - - +
358A TYR* 1.3 80.4 - - - +
360A PHE* 1.3 60.4 + - - +
361A ASN* 4.2 11.9 - - - +
367A ASP* 5.3 4.0 - - - +
368A VAL 5.3 0.9 - - - -
369A PRO* 4.1 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 6.1 0.7 - - + -
341A TYR* 4.6 20.6 - + + -
342A THR 3.7 0.9 - - - -
343A VAL* 4.0 25.1 - - + -
358A TYR* 3.9 6.0 + + + -
359A ASP* 1.3 75.7 - - - +
361A ASN* 1.3 64.4 + - - +
362A LEU* 4.1 31.3 + - + -
367A ASP* 3.7 4.7 + - - +
368A VAL 3.4 32.5 + - - +
370A GLU* 3.4 38.6 - - + +
463A ALA* 5.8 2.5 - - + -
466A ILE* 4.7 15.0 - - + -
467A TYR* 3.9 27.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ILE 4.0 0.2 - - - +
341A TYR* 3.3 9.5 - - - +
342A THR* 2.6 66.1 + - - +
343A VAL* 4.5 0.4 - - - +
344A LYS* 4.7 3.8 - - - +
359A ASP* 4.0 15.0 + - - +
360A PHE* 1.3 79.8 + - - +
362A LEU* 1.3 60.5 + - - +
363A GLU* 3.9 16.7 + - - +
367A ASP* 2.7 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 4.3 24.0 - - + -
172A LEU* 4.3 15.9 - - + -
173A ARG* 6.2 1.3 - - + -
176A ASN* 6.2 2.2 - - - +
340A ILE* 3.8 31.9 - - + +
341A TYR* 4.1 11.7 - - + -
360A PHE* 4.1 24.7 + - + -
361A ASN* 1.3 73.9 - - - +
363A GLU* 1.3 69.0 + - - +
367A ASP 5.0 9.7 + - - +
463A ALA* 5.2 1.3 - - + -
----------------------------------------------------------
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