Contacts of the helix formed by residues 282 - 292 (chain A) in PDB entry 5K9S
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 PRO 282 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLY* 1.3 90.1 - - - +
283A ASN* 1.3 67.1 + - - +
284A GLU* 3.1 18.4 - - + +
285A ARG* 3.0 36.8 + - + +
286A ILE* 3.3 7.4 + - - +
13C MET* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLY 4.9 0.5 - - - +
282A PRO* 1.3 73.9 - - - +
284A GLU* 1.3 70.7 + - - +
286A ILE* 3.0 13.4 + - - +
287A GLU* 2.9 21.5 + - - +
322A THR* 4.4 2.9 + - - +
323A GLY* 3.4 27.2 - - - -
324A THR* 3.2 32.1 - - + +
327A GLN* 3.5 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 6.2 4.3 - - + -
282A PRO* 4.2 15.3 - - + -
283A ASN* 1.3 84.6 - - - +
285A ARG* 1.3 64.1 + - + +
287A GLU* 3.2 9.2 + - - +
288A MET* 3.2 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ALA* 3.8 23.3 - - - +
244A PRO* 2.2 37.0 + - - +
245A PRO 4.0 0.8 - - - -
246A LEU* 3.4 38.0 - - + +
249A VAL* 4.2 14.8 - - + +
277A TYR 5.7 0.7 - - - -
278A LEU* 3.5 28.1 - - - +
279A THR* 5.3 0.2 - - - -
280A ASP 5.2 2.2 - - - -
281A GLY* 4.9 4.3 - - - -
282A PRO* 3.0 32.8 + - + +
284A GLU* 1.3 77.1 - - + +
286A ILE* 1.3 67.0 + - - +
288A MET* 3.3 19.5 + - - +
289A VAL* 3.4 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR* 3.6 32.8 - - - +
281A GLY 4.2 7.9 - - - +
282A PRO 3.3 5.5 + - - +
283A ASN* 3.0 25.6 + - - +
285A ARG* 1.3 76.2 - - - +
287A GLU* 1.3 57.9 + - - +
289A VAL* 3.3 4.0 + - - +
290A VAL* 2.9 38.3 + - + +
319A ASN 3.4 23.8 - - - +
320A ILE* 4.2 17.3 - - + -
322A THR* 3.8 10.8 - - - +
323A GLY* 4.1 7.4 - - - +
327A GLN* 3.5 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASN 2.9 12.1 + - - +
284A GLU* 3.6 10.5 - - - +
285A ARG 3.2 0.4 - - - -
286A ILE* 1.3 75.0 - - - +
288A MET* 1.3 65.9 + - - +
290A VAL* 4.1 15.0 - - - +
291A LYS* 2.9 43.1 + - + +
327A GLN* 3.0 28.4 + - - +
330A LYS* 4.3 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 3.7 32.8 - - - +
249A VAL* 3.3 33.9 - - + -
250A GLU* 3.6 38.9 - - + +
253A LEU* 3.9 8.6 - - + +
284A GLU 3.2 11.9 + - - +
285A ARG* 3.3 16.1 + - - +
287A GLU* 1.3 79.4 - - - +
289A VAL* 1.3 62.1 + - + +
291A LYS* 3.6 6.9 + - - +
292A LYS* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A VAL* 5.6 0.7 - - + -
253A LEU* 4.1 21.5 - - + -
275A ILE* 3.7 24.7 - - + -
278A LEU* 3.8 30.7 - - + -
279A THR* 3.9 15.9 - - + -
285A ARG 3.4 9.4 + - - +
286A ILE 3.3 7.0 + - - +
287A GLU 3.3 0.2 - - - -
288A MET* 1.3 74.3 - - + +
290A VAL* 1.3 68.4 + - - +
292A LYS* 3.2 17.5 + - - +
294A VAL* 3.6 29.9 - - + +
320A ILE* 5.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ILE* 2.9 35.5 + - + +
287A GLU* 4.0 14.1 - - - +
289A VAL* 1.3 76.7 - - - +
291A LYS* 1.3 63.2 + - - +
292A LYS 3.0 0.2 - - - -
293A GLY* 3.0 16.8 + - - -
294A VAL* 4.4 1.3 + - - -
295A VAL* 4.3 19.9 - - + +
320A ILE* 4.0 23.1 - - + -
327A GLN* 4.6 9.0 - - + +
330A LYS* 3.3 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 2.9 32.4 + - + +
288A MET* 4.1 4.9 - - - +
290A VAL* 1.3 78.7 - - - +
292A LYS* 1.3 62.6 + - + +
293A GLY* 3.2 0.9 + - - -
330A LYS* 5.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLU* 3.1 32.6 + - - -
253A LEU* 4.0 30.1 - - + -
254A PRO* 4.1 16.5 - - + +
257A VAL* 4.0 28.8 - - + +
288A MET 3.4 15.5 - - - +
289A VAL* 3.2 10.3 + - - +
290A VAL 3.0 1.2 + - - -
291A LYS* 1.3 80.4 - - + +
293A GLY* 1.3 59.7 + - - +
294A VAL* 3.5 5.1 + - + +
----------------------------------------------------------
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