Contacts of the helix formed by residues 270 - 278 (chain A) in PDB entry 4UHX
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 SER 270 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ASN* 4.4 0.2 - - - +
269A THR* 1.3 80.2 + - - +
271A VAL* 1.3 69.0 + - - +
272A GLY 3.4 0.9 - - - -
273A PRO* 3.7 3.2 - - - +
274A GLU* 3.3 35.5 + - - +
357A GLY 5.3 1.6 - - - -
361A SER* 3.4 22.5 - - - -
363A HIS* 2.7 34.4 + - - -
1231A ARG* 5.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PRO* 4.5 9.9 - - + -
264A VAL 5.9 1.1 - - - +
265A ILE* 4.1 24.9 - - + -
268A ASN* 3.6 17.1 + - - +
270A SER* 1.3 77.2 - - - +
272A GLY* 1.3 66.6 + - - +
274A GLU* 3.2 13.0 + - - +
275A VAL* 3.0 27.7 + - + +
282A HIS* 3.7 33.2 - - + +
285A ILE* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 6.3 0.2 - - - -
75A LEU* 4.2 8.3 - - - -
268A ASN* 3.0 35.5 + - - -
271A VAL* 1.3 76.8 - - - +
273A PRO* 1.3 61.6 - - - +
275A VAL* 3.2 11.7 - - - +
276A LYS* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY 5.7 0.7 - - - +
46A GLY* 4.7 10.1 - - - +
75A LEU* 3.8 20.6 - - + -
268A ASN 3.5 10.1 - - - +
269A THR 3.5 23.8 - - - +
270A SER 3.7 5.2 - - - +
272A GLY* 1.3 88.5 - - - +
274A GLU* 1.3 60.4 + - - +
276A LYS* 4.1 6.5 - - + -
277A PHE* 3.2 51.1 + - + -
278A LYS* 4.6 0.8 - - - +
1231A ARG* 4.8 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A SER* 3.3 31.1 + - - +
271A VAL* 3.2 15.7 + - - +
272A GLY 3.2 1.0 - - - -
273A PRO* 1.3 77.4 - - - +
275A VAL* 1.3 58.3 + - + +
278A LYS* 2.7 62.0 + - + +
280A VAL* 4.3 21.1 - - + +
282A HIS* 5.4 2.8 + - - -
361A SER 5.7 0.2 - - - +
363A HIS* 4.4 7.3 + - - -
1231A ARG* 5.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 5.9 8.1 - - + -
271A VAL* 3.0 17.8 + - + +
272A GLY* 3.2 20.2 - - - +
274A GLU* 1.3 75.8 - - + +
276A LYS* 1.3 61.6 + - + +
279A GLY* 4.6 7.1 + - - -
280A VAL* 3.3 37.5 + - + +
281A PHE* 4.5 3.1 - - + +
282A HIS* 4.1 23.6 - - + +
691A LYS* 5.0 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 5.6 4.6 - - - -
45A GLY* 4.2 17.5 - - - +
75A LEU* 6.0 1.6 - - + -
272A GLY 3.0 17.9 + - - +
273A PRO* 3.7 9.0 - - + +
274A GLU 3.2 0.2 - - - -
275A VAL* 1.3 81.2 - - + +
277A PHE* 1.3 79.7 + - + +
683A GLU* 5.8 1.6 + - - -
691A LYS* 4.5 12.2 + - - -
837A GLU* 3.6 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A CYS 5.0 5.4 - - - -
45A GLY 4.1 16.6 - - - -
46A GLY* 4.7 7.6 - - - -
273A PRO* 3.2 39.6 + - + -
276A LYS* 1.3 99.0 - - + +
278A LYS* 1.3 72.7 + - + +
279A GLY 3.8 2.5 - - - +
691A LYS* 6.0 0.7 - - - +
837A GLU* 5.3 5.4 - - - -
1231A ARG* 4.4 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PRO 4.6 2.0 - - - +
274A GLU* 2.7 42.2 + - + +
277A PHE* 1.3 81.6 - - + +
279A GLY* 1.3 62.5 - - - +
280A VAL* 3.2 15.8 + - + +
1231A ARG* 3.7 50.6 - - - +
----------------------------------------------------------
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