Contacts of the strand formed by residues 270 - 276 (chain E) in PDB entry 1LWU
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 TRP 270 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E CYS* 3.9 1.8 - - - -
261E CYS* 3.4 4.2 - - - -
262E ASP* 2.8 46.5 + - + +
263E MET* 3.6 0.2 - - - +
265E SER* 3.5 23.4 + - - -
266E HIS* 3.1 25.6 + - + +
268E GLY* 3.5 9.2 - - - -
269E GLY* 1.3 77.6 - - - +
271E THR* 1.3 62.6 + - - +
272E VAL 3.5 1.2 + - - -
329E GLN* 3.3 37.7 - - + -
330E VAL 4.3 1.3 - - - -
331E LEU* 3.5 35.0 - - + -
345E GLN* 4.0 10.3 - - - -
473E LYS* 3.4 31.6 - - + -
474E LEU 3.4 19.1 - - - -
475E ARG* 3.3 39.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E HIS* 3.0 24.9 + - - -
232E CYS* 3.2 28.2 + - - -
248E ILE* 4.3 10.5 - - + -
259E VAL* 3.6 30.7 - - + -
269E GLY 3.6 0.2 + - - -
270E TRP* 1.3 68.4 - - - +
272E VAL* 1.3 63.7 + - - +
273E VAL* 3.3 5.5 + - + +
314E LEU* 4.9 7.2 - - + -
322E LEU* 4.9 9.4 - - + -
473E LYS* 4.2 0.7 - - - -
474E LEU* 2.8 40.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E VAL* 3.5 12.5 - - - +
260E PHE* 3.0 36.7 + - + +
262E ASP* 4.3 9.0 - - + -
271E THR* 1.3 69.4 - - - +
273E VAL* 1.3 58.9 + - - +
274E GLN 3.3 23.8 - - - +
275E ASN* 3.7 20.0 - - + -
312E TYR* 2.6 36.3 + - + +
314E LEU* 4.5 0.3 - - - +
471E ALA* 4.8 1.8 - - + -
472E MET 3.5 5.4 - - - +
473E LYS* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E THR* 3.6 15.0 - - + +
272E VAL* 1.3 74.6 - - - +
274E GLN* 1.3 62.4 + - + +
312E TYR* 4.1 2.2 - - - -
313E TRP* 3.5 11.2 - - + -
314E LEU* 2.8 46.4 + - + +
319E VAL* 3.1 36.3 - - + -
322E LEU* 5.0 0.4 - - + -
472E MET* 2.8 20.3 + - + +
474E LEU* 3.4 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 274 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E VAL* 3.3 7.1 - - - +
273E VAL* 1.3 77.6 - - - +
275E ASN* 1.3 71.5 + - - +
276E ARG* 3.3 19.3 - - - +
283E PHE* 4.3 3.4 - - + -
312E TYR* 3.2 10.5 - - - +
313E TRP* 3.3 27.6 - - + -
432E PRO* 3.3 19.7 - - + +
433E ASN* 3.1 28.3 - - - +
470E MET* 3.9 2.4 - - - +
471E ALA* 3.1 14.8 - - - +
472E MET* 2.8 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 275 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E PHE* 6.2 0.2 - - - -
272E VAL* 3.7 16.6 - - + -
274E GLN* 1.3 80.6 - - - +
276E ARG* 1.3 74.8 + - - +
277E VAL* 4.5 6.9 - - - +
283E PHE* 4.1 0.2 - - - -
309E PRO* 3.7 25.0 - - - +
310E GLY 2.9 26.4 + - - +
311E GLU* 3.1 26.3 - - - +
312E TYR* 3.1 15.6 + - + -
470E MET 3.4 7.4 - - - +
471E ALA* 3.3 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 276 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E GLN* 3.3 21.5 - - - +
275E ASN* 1.3 78.8 - - - +
277E VAL* 1.3 65.0 + - - +
279E GLY* 5.0 0.4 - - - -
281E SER 4.4 3.6 + - - -
283E PHE* 3.3 37.0 - - - +
311E GLU* 2.9 28.9 + - - +
433E ASN* 3.3 24.0 - - - +
434E GLY 2.7 29.9 + - - +
436E TYR* 3.5 32.6 - - + +
455E VAL* 3.6 14.2 - - + +
468E ARG 4.5 0.2 - - - -
469E GLN* 3.6 4.9 - - - +
470E MET* 2.5 47.2 + - + +
----------------------------------------------------------
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