Contacts of the strand formed by residues 242 - 245 (chain I) in PDB entry 5TJ4
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 TYR 242 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I ILE* 4.3 7.9 - - + -
117I TYR 3.2 12.3 - - - +
118I ASN* 4.4 0.2 - - - +
119I LYS* 4.4 4.7 - - - +
217I PHE* 4.3 14.4 - - + -
232I TRP* 4.0 12.9 - + + +
235I ILE* 3.2 35.4 - - + -
236I ASP* 2.7 26.6 + - - -
240I VAL* 4.0 8.7 - - + -
241I ASN* 1.3 81.1 + - - +
243I GLY* 1.3 61.9 + - - +
244I VAL* 3.8 27.6 - - + -
316I ARG* 2.6 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 243 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I ILE* 3.4 6.8 - - - +
117I TYR* 2.8 59.5 + - - -
119I LYS* 5.3 0.4 - - - +
242I TYR* 1.3 75.2 - - - +
244I VAL* 1.3 64.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I SER* 3.5 28.0 - - - +
115I LEU 3.5 3.6 - - - +
116I ILE* 4.5 5.4 - - + +
117I TYR* 4.0 0.8 - - - -
232I TRP* 3.8 33.9 - - + +
242I TYR* 3.8 14.4 - - + -
243I GLY* 1.3 76.4 - - - +
245I THR* 1.3 62.9 + - - +
315I PRO 4.8 2.9 - - - +
316I ARG* 3.7 33.4 - - + +
319I ALA* 3.4 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 245 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I SER* 3.9 1.2 - - - -
115I LEU* 2.8 49.6 + - + +
117I TYR* 3.6 27.8 - - + -
125I PRO* 4.1 14.5 - - + +
244I VAL* 1.3 73.9 - - - +
246I VAL* 1.3 84.8 + - - +
319I ALA* 4.0 7.2 - - - -
323I ASN* 3.3 10.9 + - - -
----------------------------------------------------------
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