Contacts of the strand formed by residues 322 - 325 (chain H) in PDB entry 1R4N
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 LEU 322 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496G PHE* 5.8 2.0 - - + -
522G TYR* 5.7 2.9 - - + -
527G GLN* 3.9 36.8 - - - +
188H ASN* 3.0 9.6 - - - +
189H ALA* 2.9 40.0 + - + +
299H ILE* 5.5 2.2 - - + -
302H VAL* 4.2 18.8 - - + -
318H LEU* 4.0 7.6 - - + -
321H TYR* 1.3 83.1 - - - +
323H VAL* 1.3 103.1 + - - +
324H PHE* 4.1 3.6 - - + +
332H THR* 3.6 23.6 - - + -
333H TYR 3.3 11.2 - - - +
334H THR* 4.5 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H LYS* 6.0 1.3 - - + -
187H GLY 3.5 9.4 - - - +
321H TYR* 3.5 19.7 - - + -
322H LEU* 1.3 93.4 - - - +
324H PHE* 1.3 66.5 + - - +
331H TYR* 5.9 1.7 - - + -
332H THR* 3.0 17.3 - - - -
333H TYR* 2.9 14.1 + - + +
335H PHE* 4.8 0.2 - - + -
108L LEU* 3.9 28.7 - - + -
170L VAL* 3.3 30.7 - - + -
171L LEU* 3.7 20.2 - - + +
173L LEU* 5.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 324 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496G PHE* 4.4 9.6 - + - -
500G ALA* 4.5 6.5 - - + -
520G TYR* 4.8 4.9 - - - -
185H PHE 3.7 13.5 - - - -
186H LYS* 3.3 5.4 - - - +
187H GLY 2.7 43.6 + - - +
295H THR* 4.9 8.7 - - + -
298H VAL* 3.5 43.7 - - + -
299H ILE* 4.3 10.3 - - + -
322H LEU* 4.7 2.9 - - + -
323H VAL* 1.3 80.0 - - - +
325H ASN* 1.3 68.3 + - - +
326H ASP* 3.1 39.5 - - - -
330H LEU* 4.5 10.8 - - + -
331H TYR* 3.4 4.3 - - - -
332H THR* 3.3 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 325 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G ASP* 3.4 15.9 - - - +
185H PHE* 3.7 7.2 + - - +
186H LYS* 3.6 24.9 - - - +
324H PHE* 1.3 81.3 - - - +
326H ASP* 1.3 67.5 + - - +
327H VAL* 2.8 30.7 - - - +
328H ASP 4.6 2.0 - - - +
329H GLY 3.2 12.6 - - - +
330H LEU* 3.8 0.9 - - - -
331H TYR* 3.0 32.5 + - + +
108L LEU* 3.2 34.1 - - + +
109L THR* 3.8 5.6 - - + +
----------------------------------------------------------
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