Contacts of the strand formed by residues 322 - 326 (chain A) in PDB entry 4L0D
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 322 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ARG* 4.3 16.2 - - - +
277A ILE 3.3 2.4 + - - -
278A ILE* 3.4 19.1 - - + -
279A GLY 2.9 23.9 + - - -
320A VAL* 3.3 4.6 - - - +
321A ASP* 1.3 81.8 - - - +
323A TRP* 1.3 77.9 + - - +
324A PHE* 3.5 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 3.9 37.5 - - + -
279A GLY* 3.6 17.5 - - - -
280A VAL 4.4 0.2 - - - -
281A ASP* 4.2 16.4 - - + -
287A LEU* 3.8 21.1 - - + -
288A ALA* 3.5 34.3 - - + -
289A GLU* 3.4 49.8 + - + +
293A LEU* 4.2 11.3 - - + +
315A LEU* 4.7 7.6 - - + -
317A ARG* 4.4 14.1 + - + -
320A VAL* 3.5 39.4 + - + +
322A LYS* 1.3 91.5 - - - +
324A PHE* 1.3 71.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ILE* 3.7 19.1 - - + -
279A GLY 2.9 8.1 + - - +
280A VAL* 3.4 3.5 - - - +
281A ASP* 2.9 27.0 + - - +
293A LEU* 5.5 0.9 - - - -
322A LYS* 3.5 42.0 - - + -
323A TRP* 1.3 83.4 - - - +
325A LYS* 1.3 66.4 + - - +
326A SER 3.9 0.2 + - - -
356A VAL* 3.6 33.7 - - + -
359A LYS* 4.3 22.4 - - + -
360A ALA* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASP* 3.1 38.4 - - + +
282A PRO 3.2 16.6 + - - +
283A GLU* 3.3 34.9 - - + +
284A GLY 3.8 2.6 - - - +
285A SER 3.3 10.7 + - - -
288A ALA* 4.0 5.4 - - + -
293A LEU* 4.0 36.1 + - + +
294A ASN* 3.4 26.9 + - - +
296A THR* 5.5 0.8 - - - +
324A PHE* 1.3 79.8 - - - +
326A SER* 1.3 59.5 + - - +
330A GLU* 4.0 7.6 - - - +
356A VAL* 4.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 3.8 22.8 - - - +
281A ASP 2.9 13.6 + - - -
282A PRO* 3.3 9.9 - - - +
283A GLU* 2.9 29.6 + - - +
306A ILE* 4.6 1.2 - - - +
324A PHE 3.9 0.2 + - - -
325A LYS* 1.3 75.4 - - - +
327A ASN* 1.3 63.1 + - - +
330A GLU* 3.1 13.5 - - - -
352A SER* 3.8 24.0 + - - -
356A VAL* 4.4 7.2 - - - -
----------------------------------------------------------
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