Contacts of the strand formed by residues 297 - 300 (chain J) in PDB entry 3LUE
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 THR 297 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J ILE* 3.4 11.0 - - + +
153J MET* 5.5 2.9 - - + -
278J THR* 3.9 26.8 - - + +
282J ILE* 5.1 2.1 - - - +
293J LEU 3.2 15.2 + - - -
294J TYR* 3.8 9.4 + - - -
296J ASN* 1.3 72.6 - - - +
298J VAL* 1.3 53.4 + - - +
299J LEU* 4.7 12.3 - - + -
313J MET* 5.2 1.1 - - + -
317J ILE* 4.2 6.3 - - + +
327J ILE* 5.3 0.9 - - - +
328J LYS 3.2 11.8 + - - -
329J ILE* 3.2 25.1 - - + +
330J ILE* 2.5 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H MET* 4.9 0.2 - - - -
45H VAL* 3.0 38.8 - - + +
46H GLY* 4.2 0.4 - - - -
142J LEU* 4.6 0.2 - - + -
145J SER* 5.2 4.3 - - - +
147J ARG* 4.2 18.6 - - - +
151J ILE 2.9 11.5 + - - +
152J VAL* 3.2 8.6 - - + -
153J MET* 2.8 27.9 + - - +
296J ASN 4.3 6.1 - - - +
297J THR* 1.3 76.2 - - - +
299J LEU* 1.3 74.6 - - - +
300J SER* 5.4 1.6 - - - -
330J ILE* 3.4 28.9 - - + +
332J PRO* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153J MET* 3.5 14.6 - - + -
297J THR* 4.7 10.1 - - + -
298J VAL* 1.3 89.8 - - - +
300J SER* 1.3 63.3 + - - +
304J THR* 3.8 21.1 - - + +
309J ILE* 3.8 35.0 - - + +
310J ALA* 4.4 14.8 - - - -
313J MET* 3.9 32.3 - - + -
329J ILE* 4.6 7.6 - - + -
330J ILE 3.1 15.2 + - - +
331J ALA* 4.6 7.4 - - + -
332J PRO* 4.2 3.3 - - - +
335J ARG* 3.9 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 300 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J SER* 2.8 31.1 + - - -
152J VAL* 3.5 9.9 - - - +
153J MET 2.9 8.1 + - - +
154J ASP* 2.6 30.8 + - - -
155J SER 3.0 22.7 + - - -
298J VAL* 5.4 2.2 - - - -
299J LEU* 1.3 77.9 - - - +
301J GLY* 1.3 59.3 + - - +
304J THR* 3.1 9.5 - - - +
335J ARG* 3.8 9.2 - - - -
338J SER* 5.0 2.2 - - - -
----------------------------------------------------------
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