Contacts of the strand formed by residues 130 - 134 (chain D) in PDB entry 1T9G
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 MET 130 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR* 3.4 24.5 - - + +
53D ILE* 3.7 32.3 - - + -
62D MET* 4.3 6.5 - - - +
97D ALA 3.6 13.0 - - - +
101D ASN* 3.2 25.6 - - - +
124D MET* 3.8 2.2 - - - -
128D PRO 4.5 6.7 - - - +
129D LEU* 1.3 82.7 - - - +
131D CYS* 1.3 57.9 + - - +
169D ASN* 3.5 23.8 - - - +
172D LYS* 3.2 28.5 + - + +
173D ALA* 3.7 1.8 - - - -
174D ASN* 2.6 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLY 3.4 9.5 - - - +
101D ASN* 2.7 48.3 + - - +
104D GLY* 4.1 3.1 - - - -
105D GLN* 3.7 17.0 - - - -
124D MET* 3.7 21.5 - - + -
130D MET* 1.3 75.7 - - - +
132D ALA* 1.3 64.4 + - - +
169D ASN* 3.8 9.6 + - - +
173D ALA* 3.6 3.1 - - - -
175D TRP* 3.3 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLY 4.4 4.0 - - - -
104D GLY* 4.1 6.1 - - - -
131D CYS* 1.3 79.9 - - - +
133D TYR* 1.3 59.7 + - - +
134D CYS 3.7 1.1 + - - -
167D ILE* 3.9 12.3 - - + -
168D THR 3.1 26.7 - - - +
169D ASN 4.1 11.0 - - - +
173D ALA* 4.2 0.4 - - + -
175D TRP 3.2 4.8 + - - -
176D TYR* 3.4 19.5 - - + -
177D PHE 3.0 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLY 4.9 1.0 + - - -
103D LEU* 3.7 53.4 - - + -
104D GLY* 4.1 7.9 - - - +
107D PRO* 4.6 6.1 - - + -
132D ALA* 1.3 71.7 - - - +
134D CYS* 1.3 58.4 + - - +
135D VAL* 3.1 34.9 - - + +
144D VAL* 5.9 0.9 - - - +
167D ILE* 3.6 7.1 - - - +
168D THR 4.8 1.0 + - - -
177D PHE* 3.7 28.0 - + - +
248D ALA* 4.0 17.4 + - - +
251D ALA* 5.1 2.0 - - + -
252D PHE* 3.1 37.4 - + - -
399D FAD 2.8 47.5 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D TYR* 1.3 69.8 - - - +
135D VAL* 1.3 67.8 + - - +
164D LYS* 3.2 15.9 - - + -
167D ILE* 3.7 21.1 - - - -
176D TYR* 3.6 37.2 - - - -
177D PHE 2.6 16.6 + - - +
178D LEU* 3.5 17.2 - - + -
179D LEU 3.2 18.2 + - - -
225D ILE* 4.0 14.6 - - - -
227D PHE* 4.8 3.8 - - - -
----------------------------------------------------------
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