Contacts of the strand formed by residues 247 - 252 (chain G) in PDB entry 4KYI
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 GLU 247 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LEU* 4.0 8.2 - - - +
242G ASN* 2.9 31.3 + - + +
245G LYS* 3.2 53.4 + - + +
246G HIS* 1.3 75.7 - - - +
248G LEU* 1.3 71.0 + - - +
249G GLU* 3.2 3.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LEU* 3.8 28.9 - - + +
239G VAL* 3.9 14.4 - - + -
240G VAL 3.4 8.5 - - - +
241G THR* 3.3 25.6 - - - +
247G GLU* 1.3 73.4 - - - +
249G GLU* 1.3 60.3 + - - +
250G ARG* 4.1 1.7 + - - +
289G GLY 4.4 8.3 - - - +
292G LEU 5.9 0.2 - - - +
294G ASN* 3.4 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G VAL 4.4 0.3 - - - +
239G VAL* 3.8 2.8 - - - +
240G VAL* 2.9 46.3 + - + +
242G ASN* 3.2 31.7 + - + +
245G LYS* 4.6 9.9 - - - -
247G GLU* 3.2 9.5 + - + +
248G LEU* 1.3 73.6 - - - +
250G ARG* 1.3 65.6 + - - +
251G TYR* 2.7 35.5 + - + -
280G ASN* 5.4 0.3 + - - -
284G GLU* 4.2 5.5 - - - +
286G ILE* 5.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 250 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G VAL 3.9 9.2 - - - +
239G VAL* 4.7 14.6 - - + +
248G LEU 4.1 2.2 + - - +
249G GLU* 1.3 82.1 - - - +
251G TYR* 1.3 70.7 + - - +
252G SER* 3.7 11.6 + - - +
255G THR* 3.8 24.9 + - - +
256G THR* 4.3 9.5 - - - +
297G GLU 5.4 2.2 - - - -
299G GLU* 2.8 28.5 + - - +
601G EDO 2.3 53.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 251 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G LEU* 4.9 7.2 - - + +
237G SER* 3.4 1.0 - - - -
238G VAL* 3.1 38.5 + - + +
240G VAL* 3.7 25.1 - - + -
249G GLU* 2.7 33.7 + - + -
250G ARG* 1.3 78.7 - - - +
252G SER* 1.3 65.7 + - - +
256G THR* 3.3 22.9 - - + +
259G GLN* 3.5 43.3 + - + -
264G VAL* 3.4 31.2 - - + -
267G TRP* 3.5 21.7 - + - -
280G ASN* 4.8 2.8 + - - -
286G ILE* 3.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G LEU* 3.4 7.6 - - - +
235G ASN* 5.0 1.1 - - - -
236G LEU 3.6 9.6 - - - -
237G SER* 3.2 17.0 - - - -
250G ARG* 3.7 9.5 + - - +
251G TYR* 1.3 75.7 + - - +
253G GLU* 1.3 61.8 + - - +
254G ASP* 3.2 16.4 - - - -
255G THR* 3.2 19.0 + - - -
256G THR* 2.9 37.6 + - - +
601G EDO 3.6 11.3 + - - -
----------------------------------------------------------
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