Contacts of the strand formed by residues 130 - 139 (chain R) in PDB entry 1UW9
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 130 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H ARG* 2.8 48.7 + - - +
42R MET* 5.4 0.2 - - + -
43R THR 3.7 11.4 - - - +
45R GLN* 3.9 5.5 + - - +
53R CYS* 3.9 17.3 - - - -
56R ALA* 6.4 0.9 - - + -
57R VAL* 3.9 26.5 - - + -
124R VAL 3.5 24.2 - - - +
125R PHE 3.9 5.6 - - - +
127R PHE* 3.0 14.7 - - + +
128R LYS 3.1 2.3 - - - +
129R ALA* 1.3 80.3 - - + +
131R ARG* 1.3 54.2 + - - +
132R ALA* 4.0 19.3 - - - +
133R LEU* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H ARG* 4.7 2.9 - - - +
304H GLN* 3.0 18.4 + - - +
470H ASP* 2.9 30.1 + - - +
471H THR 5.7 0.2 + - - -
472H ILE* 3.5 40.5 - - + +
43R THR* 2.7 24.3 + - + +
44R PRO 4.0 12.3 - - - +
45R GLN* 3.1 40.1 + - + +
46R PRO* 4.1 12.6 - - - +
95R ASN* 4.7 6.7 - - - +
130R LEU* 1.3 75.9 - - - +
132R ALA* 1.3 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304H GLN* 3.7 9.4 - - - +
41R ARG 4.5 0.2 - - - -
42R MET* 3.9 0.5 - - - -
43R THR* 2.9 43.2 + - + +
130R LEU* 3.6 9.7 - - - +
131R ARG* 1.3 81.4 - - + +
133R LEU* 1.3 63.0 + - - +
306R ASN* 3.4 32.1 - - + +
307R HIS* 3.7 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R PHE* 3.8 33.4 - - + -
41R ARG 3.3 14.1 - - - +
42R MET* 3.9 20.9 - - + -
57R VAL* 4.3 10.8 - - + -
124R VAL* 3.7 39.0 - - + +
125R PHE* 3.1 34.6 - - + -
130R LEU* 4.0 15.0 - - + -
132R ALA* 1.3 75.7 - - - +
134R ARG* 1.3 61.6 + - - +
306R ASN 3.8 2.0 - - - -
307R HIS* 3.2 10.0 + - - -
308R GLY 2.9 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R PHE* 3.4 3.8 - - - -
41R ARG* 2.7 47.7 + - + +
125R PHE* 4.4 0.9 - - - -
133R LEU* 1.3 76.8 - - - +
135R LEU* 1.3 63.3 + - - +
136R GLU* 3.0 36.6 + - - -
302R ASP 3.0 24.7 + - - -
304R GLN 3.2 17.1 + - - -
305R ARG* 3.4 24.6 + - - +
306R ASN 3.8 11.9 - - - +
307R HIS 3.7 3.1 + - - +
308R GLY 3.1 24.7 - - - +
309R ILE 4.1 2.7 - - - +
310R HIS* 3.4 27.8 - - - +
473R ASP* 2.8 29.7 + - - -
474R LYS 5.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R ALA* 3.9 21.1 - - + -
39R ALA 3.7 10.3 - - - +
40R PHE* 4.1 13.9 - - + -
117R PHE* 5.8 1.6 - - + -
120R ILE* 4.1 3.6 - - + -
121R VAL* 3.7 22.4 - - + -
125R PHE* 4.0 17.6 - - + -
134R ARG* 1.3 71.6 - - - +
136R GLU* 1.3 58.9 + - - +
137R ASP 3.5 21.1 - - - +
138R LEU* 3.9 15.0 - - + -
308R GLY 2.9 9.1 + - - -
309R ILE* 3.4 10.6 - - + +
310R HIS 2.9 27.2 + - - -
313R VAL* 3.8 31.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R ALA 2.8 14.0 + - - +
41R ARG* 2.8 56.0 + - + +
98R ILE* 4.9 0.9 - - + -
134R ARG* 3.0 31.1 + - - +
135R LEU* 1.3 75.8 - - - +
137R ASP* 1.3 60.8 + - - +
310R HIS* 3.8 5.6 - - - +
312R ARG* 2.8 54.6 + - - +
313R VAL* 3.6 3.4 - - - +
363R TYR* 3.7 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R ALA* 3.5 0.5 - - - -
39R ALA* 3.0 24.6 + - + -
135R LEU* 3.5 9.6 - - - +
136R GLU* 1.3 79.0 - - - +
138R LEU* 1.3 73.5 + - - +
312R ARG* 4.0 14.0 - - - +
313R VAL* 3.5 8.2 - - - +
316R LYS* 3.2 25.4 + - - +
348R LEU* 5.2 0.3 - - - +
362R ILE* 3.8 6.6 - - - +
363R TYR* 2.9 46.7 + - + -
364R PHE* 3.4 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R ILE* 4.6 1.6 - - + -
37R LEU 3.1 15.9 - - - +
38R ALA* 3.7 17.3 - - + -
116R MET* 3.8 35.7 - - + -
117R PHE* 4.9 3.1 - - + -
120R ILE* 3.8 21.3 - - + -
135R LEU* 3.9 17.9 - - + -
137R ASP* 1.3 86.8 + - - +
139R ARG* 1.3 56.5 + - - +
140R ILE* 3.6 14.4 + - + -
313R VAL* 3.9 23.1 - - + +
316R LYS* 2.6 39.6 + - + +
364R PHE* 3.7 4.5 - - - -
366R GLN* 3.5 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R VAL* 4.8 4.4 - - - +
32R ARG 3.0 23.8 + - - -
33R ASP* 4.0 19.8 + - - +
35R ASP 2.8 29.9 + - - +
36R ILE* 3.5 3.8 - - - +
37R LEU* 2.8 60.3 + - + +
138R LEU* 1.3 71.9 - - - +
140R ILE* 1.3 70.9 + - - +
141R PRO* 3.3 17.7 - - - +
142R PRO* 5.5 1.7 - - - +
364R PHE* 3.5 24.2 - - + -
365R THR 3.4 24.6 + - - +
366R GLN* 3.9 2.9 - - - +
367R ASP 5.9 0.9 - - - +
----------------------------------------------------------
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