Contacts of the strand formed by residues 158 - 161 (chain D) in PDB entry 1TLF
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 SER 158 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D LEU* 4.4 0.4 - - - -
147D PHE 3.1 13.2 - - - +
150D VAL* 3.7 23.3 - - - +
151D SER 4.6 1.6 + - - -
154D THR 4.3 3.1 + - - -
156D ILE* 3.6 14.4 + - - +
157D ASN* 1.3 73.9 - - - +
159D ILE* 1.3 62.5 - - - +
160D ILE* 4.3 2.7 - - - -
303D ARG* 2.8 20.8 + - - +
315D GLY 3.2 4.6 + - - -
316D ASN* 3.4 27.0 + - - +
317D GLN 2.9 18.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D LEU* 3.5 26.7 - - + -
147D PHE 3.1 5.5 + - - -
148D LEU* 3.5 27.2 - - + +
158D SER* 1.3 80.2 - - - +
160D ILE* 1.3 65.3 + - - +
296D LEU* 3.7 21.5 - - + +
299D THR* 3.5 34.1 - - - +
300D SER* 3.7 7.0 - - - -
303D ARG* 3.7 12.1 - - - +
317D GLN* 3.6 23.8 - - + +
319D LEU* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D LEU 4.1 19.1 - - - +
149D ASP* 4.8 0.2 - - - -
150D VAL* 3.4 39.9 - - + +
151D SER* 4.5 0.9 - - - -
152D ASP* 3.5 30.1 - - + +
158D SER* 4.1 3.3 - - - -
159D ILE* 1.3 85.5 - - - +
161D PHE* 1.3 70.7 + - - +
163D HIS* 4.6 8.7 - - + -
196D LEU* 4.6 4.0 - - + -
316D ASN* 3.7 11.4 - - - +
317D GLN 2.9 19.2 + - - +
318D LEU* 3.1 12.5 - - + -
319D LEU* 3.1 15.8 + - - -
998D IPT 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D ILE* 1.3 89.8 - - - +
162D SER* 1.3 61.4 + - - +
163D HIS* 2.9 12.0 + - - +
291D GLN* 3.5 54.7 - - + +
292D ASP* 3.2 31.6 - - + -
293D PHE* 3.7 21.5 - + - -
295D LEU* 5.3 1.1 - - + -
296D LEU* 3.7 30.1 - - + -
318D LEU* 4.2 0.6 - - - +
319D LEU* 3.5 22.4 - - + +
320D PRO 3.3 20.9 - - - +
321D VAL* 5.0 0.7 - - + -
998D IPT 5.0 11.9 - - + -
----------------------------------------------------------
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