Contacts of the strand formed by residues 110 - 115 (chain B) in PDB entry 3TJK
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 110 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LYS* 1.3 77.8 - - - +
111B LEU* 1.3 58.9 + - - +
142B ASN* 3.0 10.4 + - - +
143B THR* 3.2 26.3 - - + +
144B GLU* 2.9 25.3 + - - +
204B ILE* 3.9 22.0 - - + -
205B ILE 3.4 12.3 - - - -
206B ASP* 3.3 14.8 - - + +
207B ASP* 3.4 28.9 - - + +
212B ARG* 3.4 18.0 + - + -
232B VAL* 4.3 10.5 - - + -
235B PHE* 3.4 22.2 - - + +
236B GLN* 3.7 28.0 - - + -
239B ASP* 2.6 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TRP* 4.1 11.9 - - + -
103B LEU* 3.7 29.6 - - + -
106B TYR* 4.0 34.1 - - + -
109B LYS 4.8 1.1 - - - +
110B TYR* 1.3 74.5 - - - +
112B VAL* 1.3 76.0 + - - +
113B PHE* 3.8 12.1 + - + -
143B THR* 4.7 0.2 - - - -
144B GLU 3.5 22.2 - - - +
146B VAL* 3.9 21.3 - - + -
203B PHE 3.5 3.1 - - - +
204B ILE* 3.5 3.4 - - - +
205B ILE* 2.8 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 1.3 74.7 - - - +
113B PHE* 1.3 59.5 + - - +
114B PHE* 4.4 4.3 - - + -
131B PHE* 4.1 11.0 - - + -
138B PHE* 4.0 10.3 - - + -
143B THR* 3.9 19.5 - - + -
144B GLU 2.9 10.3 + - - +
145B VAL* 3.3 13.2 - - + +
146B VAL 2.9 26.3 + - - +
202B LEU* 3.8 32.8 - - + -
203B PHE 3.5 4.0 - - - -
204B ILE* 4.7 5.2 - - + -
228B THR* 3.9 23.3 - - + -
232B VAL* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TRP* 3.4 50.5 - + - -
111B LEU* 3.8 13.4 - - + -
112B VAL* 1.3 72.7 - - - +
114B PHE* 1.3 60.4 + - - +
115B PHE* 3.4 37.9 - + - -
146B VAL* 3.5 23.3 - - + -
148B CYS* 4.2 8.7 - - + -
177B LEU* 3.9 15.9 - - + -
184B ILE* 3.9 9.9 - - + -
188B TYR* 3.8 23.3 - + - -
203B PHE* 2.9 41.3 + - + +
205B ILE* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 4.4 8.5 - - + -
113B PHE* 1.3 76.9 - - - +
115B PHE* 1.3 63.5 + - - +
116B TYR* 4.5 4.7 - + + -
127B GLU* 4.6 10.3 - - + -
128B ILE* 4.2 25.6 - - + -
131B PHE* 4.0 26.2 - + + -
145B VAL* 3.6 29.8 - - + -
146B VAL 3.0 14.5 + - - -
147B ALA* 3.3 33.2 - - + -
148B CYS* 2.9 25.4 + - - +
174B ILE* 4.8 2.5 - - + -
201B GLY 3.3 4.3 - - - +
202B LEU* 3.9 15.5 - - + -
223B ARG* 3.6 35.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 3.4 33.9 - + - -
114B PHE* 1.3 76.3 - - - +
116B TYR* 1.3 54.7 + - - +
148B CYS* 3.1 36.8 - - + -
149B SER* 5.4 0.4 - - - -
184B ILE* 3.8 10.5 - - + -
185B SER* 3.9 22.0 - - - -
188B TYR* 3.7 31.6 - + + -
190B VAL* 3.7 15.9 - - + -
198B THR* 3.6 17.5 - - + +
199B LEU 4.1 5.8 - - - +
200B ARG* 3.8 0.3 - - - -
201B GLY 2.8 23.0 + - - +
203B PHE* 3.7 13.9 - + - -
223B ARG* 2.7 31.6 + - - -
----------------------------------------------------------
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