Contacts of the strand formed by residues 106 - 109 (chain C) in PDB entry 1L9X
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 VAL 106 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ILE* 3.4 19.5 - - + +
71C PHE* 3.6 37.0 - - + -
90C PHE 4.8 3.4 - - - +
91C TYR* 4.9 6.1 - - + -
94C SER* 3.7 31.4 - - - +
104C PHE* 4.1 2.2 - - + +
105C PRO* 1.3 77.2 - - - +
107C TRP* 1.3 64.4 + - - +
116C LEU* 4.3 14.4 - - + -
213C PRO 2.9 8.9 + - - +
214C VAL* 3.5 12.2 - - + -
215C TYR* 2.8 30.5 + - - -
251C PHE* 4.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 4.1 20.6 + + - -
69C ILE 2.9 8.2 + - - +
70C LEU* 3.2 19.4 - - + +
71C PHE* 2.7 33.4 + - - +
106C VAL* 1.3 77.7 - - - +
108C GLY* 1.3 57.7 + - - +
109C THR* 3.0 26.6 + - - -
149C MET* 3.9 27.1 - - + -
215C TYR* 3.4 31.6 - + + -
217C VAL* 3.6 30.8 - - + +
221C PRO* 4.9 0.4 - - + +
247C LEU* 4.2 20.6 - - + -
250C PHE* 4.1 17.3 - + - -
251C PHE* 3.6 43.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PHE* 3.4 9.4 - - - -
107C TRP* 1.3 79.1 + - - +
109C THR* 1.3 61.4 + - - -
112C GLY* 3.6 17.5 - - - -
113C PHE 3.6 6.0 + - - -
116C LEU* 4.1 6.3 - - - +
215C TYR 2.8 14.8 + - - -
216C GLY* 3.3 3.3 - - - -
217C VAL 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TYR* 4.0 18.3 - - - +
39C TYR* 5.6 1.9 - - - -
70C LEU* 4.8 3.6 - - - +
71C PHE 2.9 12.3 + - - -
72C PRO* 4.6 0.2 - - - -
73C GLY 3.2 11.8 + - - -
107C TRP* 3.0 25.5 + - - -
108C GLY* 1.3 69.9 - - - -
110C CYS* 1.3 66.2 + - - +
111C LEU 2.9 10.7 + - - -
112C GLY* 2.9 9.0 + - - -
217C VAL* 3.4 4.6 - - - +
219C TRP 3.4 19.7 - - - +
220C HIS* 3.7 22.2 - - - +
221C PRO* 4.3 2.9 - - + +
222C GLU* 3.7 14.9 + - - +
----------------------------------------------------------
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