Contacts of the strand formed by residues 253 - 257 (chain B) in PDB entry 2CT8
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 LEU 253 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 4.3 12.8 - - + -
8B TYR 3.3 3.1 + - - +
9B VAL* 3.4 17.0 - - + +
10B THR* 3.0 26.3 + - - +
34B ILE* 4.4 17.5 - - + -
251B ALA* 3.5 1.6 - - - +
252B ASP* 1.3 81.7 - - - +
254B HIS* 1.3 77.7 + - - +
255B LEU* 3.8 26.2 - - + +
282B LYS* 3.4 22.0 - - + +
284B PHE* 4.0 27.1 - - + +
396B VAL* 4.2 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 2.8 25.9 + - + +
237B TYR* 3.3 42.0 - + + +
249B TRP* 4.2 1.8 - - - -
251B ALA* 3.8 19.4 - - + +
253B LEU* 1.3 73.8 + - - +
255B LEU* 1.3 61.6 + - - +
256B VAL* 3.6 8.2 + - + -
264B HIS* 4.8 2.7 - + + -
268B TRP* 3.4 23.1 + + - -
280B PRO* 3.6 33.2 - - + +
282B LYS 2.9 9.5 + - - -
283B VAL* 3.3 26.6 - - + +
284B PHE 2.9 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.0 9.6 - - + -
10B THR 3.2 14.7 + - - +
11B THR* 3.8 0.7 - - - -
12B PRO* 3.1 22.9 - - - +
27B THR* 4.2 13.5 - - + +
30B ALA* 3.9 7.4 - - + +
31B ALA* 3.2 46.0 - - + +
34B ILE* 4.4 1.6 - - + -
253B LEU* 3.9 24.7 - - + -
254B HIS* 1.3 71.6 - - - +
256B VAL* 1.3 62.1 + - - +
284B PHE* 3.7 12.8 - - + +
286B HIS* 5.3 1.1 - - - +
328B PHE* 3.6 33.4 - - + -
396B VAL* 4.3 6.5 - - + -
398B PHE* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PRO* 3.8 13.5 - - + -
237B TYR* 4.5 2.7 - - - +
254B HIS* 4.1 8.7 - - + +
255B LEU* 1.3 80.6 - - - +
257B GLY* 1.3 69.1 + - - +
260B ILE* 3.9 13.0 - - + -
261B LEU* 4.6 5.8 - - - -
264B HIS* 3.6 38.8 - - + +
283B VAL* 4.0 15.5 - - + -
284B PHE 3.1 13.0 + - - +
285B ALA* 3.8 10.8 - - + -
286B HIS* 2.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B VAL* 1.3 80.1 - - - +
258B LYS* 1.3 65.4 + - - -
259B ASP* 2.8 8.5 + - - -
260B ILE* 3.0 15.2 + - - +
261B LEU 3.6 4.5 + - - -
285B ALA* 4.5 0.2 - - - -
286B HIS* 3.6 16.1 - - - -
288B TRP* 4.6 0.7 - - - -
1501B MSP 2.9 32.5 + - - -
----------------------------------------------------------
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