Contacts of the strand formed by residues 267 - 275 (chain B) in PDB entry 4LUD
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 267 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE* 4.0 11.0 - - + -
264B ARG* 3.1 16.8 + - - +
265B GLU* 3.9 4.5 - - - +
266B SER* 1.3 81.3 - - - +
268B LYS* 1.3 66.4 + - - +
269B LEU* 3.9 12.0 + - + +
284B ALA* 5.0 0.7 - - + -
285B THR 3.5 4.5 - - - +
286B TYR* 3.9 30.7 - - + -
292B VAL* 4.2 5.8 - - + -
294B VAL* 4.1 17.9 - - + -
329B VAL* 4.0 13.9 - - + -
335B TYR* 4.2 13.5 - - + -
337B ILE* 3.6 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLU 5.3 4.9 - - - +
266B SER 5.5 1.1 - - - +
267B LEU* 1.3 76.6 - - - +
269B LEU* 1.3 63.9 + - - +
270B GLU* 3.1 17.1 + - + +
284B ALA* 3.9 2.9 - - - -
285B THR* 3.0 38.1 + - + +
288B LYS* 3.7 37.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 3.9 16.3 + - + +
268B LYS* 1.3 67.9 - - - +
270B GLU* 1.3 63.8 + - - +
282B TRP* 3.7 38.4 - - + +
283B MET 4.2 0.2 - - - -
284B ALA* 3.6 21.5 - - + -
294B VAL* 3.8 21.3 - - + -
296B THR* 3.8 29.4 - - + -
335B TYR* 4.1 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LYS* 3.2 21.6 - - + +
269B LEU* 1.3 74.6 - - - +
271B LYS* 1.3 60.4 + - + +
282B TRP* 3.9 7.1 - - - -
283B MET* 2.8 39.3 + - + +
284B ALA* 4.4 1.1 - - - -
285B THR* 3.0 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU* 1.3 80.5 - - + +
272B LYS* 1.3 73.4 + - - +
273B LEU* 3.2 14.6 + - + +
282B TRP* 3.4 4.7 - - - -
283B MET* 2.8 52.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LYS* 1.3 79.1 - - - +
273B LEU* 1.3 62.5 + - - +
274B GLY* 3.8 13.9 - - - +
275B ALA* 4.4 11.9 - - + +
280B GLU* 3.7 37.1 + - + +
281B VAL 3.6 10.1 - - - +
282B TRP* 3.3 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LYS* 3.6 26.5 - - + +
272B LYS* 1.3 76.1 - - - +
274B GLY* 1.3 52.8 + - - +
281B VAL* 2.6 21.9 + - + +
282B TRP 4.1 2.7 - - - -
283B MET* 3.7 31.6 - - + +
340B PHE* 4.1 6.5 - - + -
601B SK8 3.6 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LYS* 3.5 7.2 - - - +
273B LEU* 1.3 80.9 - - - +
275B ALA* 1.3 60.1 + - - +
280B GLU* 3.4 3.5 - - - +
281B VAL* 2.7 36.0 + - - +
601B SK8 6.0 1.3 - - - -
605B GOL 4.1 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LYS* 4.4 16.2 - - + +
274B GLY* 1.3 75.4 - - - +
276B GLY* 1.3 59.5 + - - +
279B GLY 3.7 4.7 - - - -
280B GLU* 4.1 16.8 - - + +
605B GOL 3.6 13.3 - - - -
----------------------------------------------------------
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