Contacts of the strand formed by residues 399 - 405 (chain A) in PDB entry 5V8V
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 399 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A TYR* 3.5 55.6 + - + +
259A ILE 3.3 18.2 - - - +
260A ASN* 3.8 15.5 - - - +
261A LEU* 4.1 3.5 - - - +
267A TRP* 3.8 1.6 - - - -
392A GLU* 5.1 0.4 + - - -
394A ASP* 2.8 64.3 + - + +
397A ASN* 3.7 26.2 - - - +
398A ASN* 1.3 79.7 - - - +
400A ILE* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A HIS 3.7 2.1 - - - +
258A TYR* 3.4 3.4 - - - -
259A ILE* 2.8 37.4 + - - +
261A LEU* 3.8 22.4 - - + -
267A TRP* 3.9 19.5 - - + +
269A ILE* 4.2 10.3 - - + -
291A VAL* 3.6 30.1 - - + -
391A THR* 3.7 19.5 - - + -
392A GLU 3.4 3.6 - - - +
393A PHE* 4.0 13.0 - - + -
399A ARG* 1.3 79.1 - - - +
401A GLY* 1.3 61.0 + - - +
402A PHE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PHE* 3.8 9.9 - - - -
257A HIS 3.5 2.7 - - - -
258A TYR* 3.4 27.8 - - - -
390A TYR 3.6 0.2 - - - +
391A THR* 3.3 8.0 - - - +
392A GLU* 2.7 36.9 + - - -
400A ILE* 1.3 74.2 - - - +
402A PHE* 1.3 64.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASN 3.9 1.2 - - - +
256A PHE* 3.3 4.9 - - - -
257A HIS* 2.8 33.0 + - - +
259A ILE* 3.6 32.1 - - + -
269A ILE* 4.1 10.3 - - + -
291A VAL* 4.2 18.8 - - + -
338A LEU* 4.3 8.5 - - + -
343A TYR* 3.5 35.3 + + + +
381A LEU* 5.0 0.9 - - + -
385A PHE* 3.6 27.1 - + - -
389A PHE* 4.2 5.2 - - + -
390A TYR 3.5 3.6 - - - -
391A THR* 3.4 33.9 - - + -
400A ILE* 3.6 20.4 - - + -
401A GLY* 1.3 75.9 - - - -
403A ALA* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR* 3.8 25.4 - - + -
253A GLU 4.0 4.5 - - - +
255A ASN 3.9 14.4 - - - +
256A PHE* 3.6 21.3 - - + -
389A PHE* 3.4 6.9 - - - +
390A TYR* 2.8 32.7 + - - +
402A PHE* 1.3 75.7 - - - +
404A LEU* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR* 3.2 5.5 - - - -
253A GLU* 3.1 63.3 + - + +
388A LYS* 3.8 24.7 - - + +
389A PHE* 3.7 27.9 - - + -
403A ALA* 1.3 70.8 - - - +
405A ALA* 1.3 70.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TYR* 4.5 14.6 - - + -
230A ARG* 4.9 10.7 + - - +
251A HIS 3.6 9.0 - - - +
253A GLU* 5.0 0.3 - - - +
386A ILE 4.7 1.1 - - - +
387A ARG 3.6 19.5 - - - +
388A LYS 2.7 25.2 + - - +
389A PHE 4.3 0.2 - - - -
390A TYR* 3.7 15.0 - - + +
403A ALA 3.3 0.8 + - - -
404A LEU* 1.3 84.3 - - - +
406A ARG* 1.3 61.5 + - - +
----------------------------------------------------------
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