Contacts of the helix formed by residues 273 - 281 (chain B) in PDB entry 6L9F
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 GLY 273 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PRO* 3.1 20.6 - - - -
269B GLU* 3.6 15.7 + - - -
271B LYS 2.9 10.7 + - - -
272B GLY* 1.3 80.9 - - - +
274B LEU* 1.3 66.6 + - - -
275B LYS 3.2 2.5 - - - -
276B GLU 3.3 3.3 + - - -
277B LEU* 3.0 22.9 + - - +
326B LYS* 5.8 0.4 - - - -
389B LEU* 5.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ILE* 4.1 23.8 - - + -
263B ILE* 4.0 21.1 - - + +
264B TYR* 4.2 8.5 - - + -
267B PHE* 3.9 36.3 - - + -
268B PRO 3.2 7.7 + - - -
269B GLU* 3.4 11.2 + - - +
273B GLY* 1.3 72.7 - - - -
275B LYS* 1.3 58.6 + - - +
277B LEU* 3.4 3.5 + - + -
278B PHE* 2.9 26.7 + - - +
286B PHE* 4.2 8.5 - - + -
389B LEU* 4.3 18.1 - - + +
403B CYS* 4.1 26.2 - - - -
405B ALA* 5.1 2.2 - - + -
424B LEU* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ARG* 6.2 1.4 - - - +
264B TYR* 3.6 47.4 + - + +
269B GLU* 2.8 20.7 + - + +
274B LEU* 1.3 76.0 - - - +
276B GLU* 1.3 65.4 + - - +
278B PHE* 3.4 1.4 + - - +
279B GLU* 3.0 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLU* 4.5 0.2 + - - -
270B LYS 5.0 3.1 - - - +
271B LYS 3.5 24.2 - - - +
272B GLY* 4.7 3.8 - - - -
273B GLY* 3.3 6.4 + - - +
275B LYS* 1.3 79.1 - - - +
277B LEU* 1.3 63.6 + - - +
279B GLU* 3.3 10.9 + - - +
280B ARG* 3.0 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLY* 3.6 24.9 - - - +
273B GLY 3.0 14.5 + - - +
274B LEU* 3.8 7.9 - - - +
276B GLU* 1.3 76.8 - - - +
278B PHE* 1.3 62.4 + - - +
280B ARG* 3.3 16.5 + - - +
281B GLY 3.1 15.4 + - - +
286B PHE* 3.1 21.8 - - + -
326B LYS* 6.0 1.3 - - - +
389B LEU* 5.1 4.7 - - + -
391B VAL* 3.9 37.2 - - + -
400B THR* 3.7 26.2 - - + +
403B CYS* 5.1 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ILE* 3.4 34.3 - - + -
264B TYR* 3.9 14.4 - - - +
274B LEU 2.9 18.8 + - - +
275B LYS 3.9 3.4 - - - +
277B LEU* 1.3 76.6 - - - +
279B GLU* 1.3 69.4 + - + +
281B GLY* 2.9 16.3 + - - -
283B SER* 3.6 33.3 - - - -
286B PHE* 3.5 27.7 - + + -
424B LEU 3.6 24.5 - - - -
425B VAL* 4.0 14.6 - - - -
426B LYS* 4.0 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR* 5.4 1.8 - - - +
275B LYS* 3.0 49.1 + - + +
276B GLU* 3.8 10.1 - - - +
278B PHE* 1.3 84.5 - - + +
280B ARG* 1.3 61.1 + - - +
281B GLY* 4.5 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU 3.0 17.5 + - - +
277B LEU* 3.5 15.0 - - + +
278B PHE 3.1 0.2 - - - -
279B GLU* 1.3 78.9 - - - +
281B GLY* 1.3 63.9 + - - +
282B PRO* 4.8 0.2 - - - +
397B THR 5.0 0.4 + - - -
398B GLN* 2.3 43.0 + - - +
399B GLU* 3.8 8.7 - - - +
400B THR* 4.2 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU 3.1 7.4 + - - +
278B PHE 2.9 16.0 + - - -
279B GLU 4.5 0.4 - - - -
280B ARG* 1.3 86.8 + - - +
282B PRO* 1.3 76.5 - - - +
283B SER 3.6 1.6 - - - -
286B PHE* 4.3 6.1 - - - -
400B THR* 3.9 17.7 + - - -
----------------------------------------------------------
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