Contacts of the helix formed by residues 1276 - 1279 (chain G) in PDB entry 4PKI
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 LEU1276 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248G LEU* 5.1 3.1 - - + -
1272G LEU 4.8 0.4 - - - +
1273G VAL* 2.9 34.9 + - + +
1275G ALA* 1.3 78.1 - - - +
1277G PRO* 1.3 60.9 - - + +
1279G ASN* 2.8 39.8 + - + +
1282G LEU* 4.4 15.9 - - + +
1285G MET* 3.7 26.5 - - + -
1305G MET 4.8 4.7 - - - +
1306G LEU* 3.8 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1277 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1274G GLU 3.5 8.5 - - - +
1275G ALA 3.5 2.7 - - - -
1276G LEU* 1.3 93.6 - - + +
1278G TYR* 1.3 68.5 + - + +
1279G ASN 3.2 3.4 + - - +
1280G THR* 5.4 3.3 - - - +
1305G MET* 3.3 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1278 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248G LEU 4.0 2.3 - - - +
1249G LYS* 3.7 56.9 + - + +
1252G LYS* 3.7 13.5 + - - -
1274G GLU 3.8 23.1 - - - -
1275G ALA 2.8 10.6 + - - +
1277G PRO* 1.3 88.2 - - + +
1279G ASN* 1.3 57.9 + - - +
1280G THR* 5.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1279 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248G LEU* 2.9 42.2 + - + +
1251G ASN* 3.6 9.3 + - - -
1252G LYS* 5.4 2.2 - - - +
1254G LEU* 5.4 0.8 + - - +
1275G ALA 3.9 7.2 - - - +
1276G LEU* 2.8 28.4 + - + +
1277G PRO 3.2 2.1 + - - -
1278G TYR* 1.3 79.1 - - - +
1280G THR* 1.3 68.2 + - - +
1281G SER* 3.0 19.3 + - - -
1282G LEU* 2.6 41.0 + - - +
----------------------------------------------------------
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