Contacts of the strand formed by residues 36 - 44 (chain O) 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 ILE 36 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O THR 3.8 7.0 - - - +
35O ASP* 1.3 71.4 - - - +
37O LEU* 1.3 67.4 + - - +
102O ALA* 3.5 0.9 - - - -
103O TYR* 2.8 41.4 + - + -
105O ILE* 4.1 8.7 - - - -
108O PHE* 3.6 37.9 - - + -
116O MET* 4.9 8.7 - - - -
120O ILE* 3.8 28.7 - - + -
138O LEU* 4.7 3.8 - - + -
139O ARG 3.5 9.9 - - - +
140O ILE* 4.9 2.7 - - + -
141O PRO* 3.7 27.1 - - + -
144O TYR* 4.2 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O VAL* 4.0 22.2 - - + -
35O ASP* 3.8 13.5 - - + -
36O ILE* 1.3 77.7 - - - +
38O ALA* 1.3 60.4 - - - +
85O TYR* 3.8 15.3 - - - +
101O VAL 3.3 3.6 - - - +
102O ALA* 3.7 28.0 - - + -
138O LEU* 3.1 11.0 - - - +
139O ARG* 2.8 77.2 + - + +
364O PHE* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O ILE 4.3 0.2 + - - -
37O LEU* 1.3 74.6 - - - +
39O ALA* 1.3 60.3 + - - +
40O PHE* 3.6 27.1 - - + -
99O ALA 3.6 1.6 - - - +
100O TYR* 3.3 5.9 - - - +
101O VAL* 2.8 33.8 + - + +
103O TYR* 3.8 16.6 - - + -
120O ILE* 4.2 1.6 - - + -
135O LEU* 3.8 4.0 - - + -
137O ASP 3.5 4.0 - - - -
138O LEU* 3.7 16.8 - - + -
364O PHE* 3.7 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O ALA* 1.3 71.0 - - - +
40O PHE* 1.3 61.2 + - - +
41O ARG 4.1 0.2 - - - -
98O ILE* 4.0 4.3 - - + -
99O ALA 3.8 3.4 - - - -
100O TYR* 3.8 10.8 - - + -
135O LEU* 3.7 2.8 - - - +
136O GLU* 2.8 29.9 + - - +
137O ASP 3.0 13.4 + - - +
363O TYR* 3.8 31.4 - - + -
364O PHE* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O ALA* 3.6 17.0 - - + -
39O ALA* 1.3 71.7 - - - +
41O ARG* 1.3 59.2 + - - +
42O MET* 3.4 1.3 + - + -
57O VAL* 3.7 22.0 - - + -
97O TYR 3.2 1.9 - - - +
98O ILE* 3.2 5.7 - - - -
99O ALA* 2.7 55.6 + - + +
101O VAL* 3.9 10.3 - - + -
103O TYR* 3.6 18.8 - - - -
120O ILE* 3.5 37.0 - - + -
124O VAL* 4.5 0.4 - - + -
125O PHE* 4.1 9.4 - + - -
133O LEU* 3.8 42.8 - - + -
134O ARG 3.5 1.8 - - - -
135O LEU* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O ALA 4.0 1.2 + - - -
40O PHE* 1.3 68.8 - - - +
42O MET* 1.3 60.1 + - - +
43O THR* 5.2 0.6 + - - +
90O VAL* 3.8 13.3 - - + +
96O GLN* 3.0 43.8 + - + +
97O TYR 3.4 4.0 - - - +
98O ILE* 3.9 17.3 - - + +
132O ALA 4.1 0.2 - - - +
133O LEU* 3.3 6.2 - - - +
134O ARG* 2.7 45.9 + - + +
136O GLU* 2.8 33.5 + - + +
305O ARG* 3.2 48.1 + - - +
306O ASN* 4.3 6.7 - - - +
363O TYR* 3.6 15.7 + - - -
474O LYS 5.0 0.2 + - - -
475O LEU* 3.2 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 42 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O PHE* 4.1 5.4 - - - +
41O ARG* 1.3 74.6 - - - +
43O THR* 1.3 63.9 + - - +
44O PRO* 3.6 6.9 - - + +
50O PRO* 3.4 31.4 - - + +
53O CYS* 3.7 25.4 - - + +
54O GLY* 3.5 26.2 - - - +
57O VAL* 4.7 5.2 - - - -
87O ILE* 4.6 2.9 - - + -
96O GLN* 3.4 4.8 - - - -
97O TYR* 2.7 59.6 + - + +
99O ALA* 3.9 18.2 - - + -
130O LEU* 5.3 0.9 - - + -
132O ALA 3.9 2.9 - - - +
133O LEU* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O ARG 5.2 0.5 + - - -
42O MET* 1.3 73.7 - - - +
44O PRO* 1.3 56.9 - - - +
95O ASN* 3.4 28.3 - - + +
96O GLN* 3.6 22.4 + - + +
130O LEU* 3.7 3.2 - - - -
131O ARG* 2.7 47.7 + - + -
132O ALA* 2.9 33.4 + - + +
306O ASN* 4.8 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 44 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O MET* 3.6 9.9 - - + +
43O THR* 1.3 85.2 - - - +
45O GLN* 1.3 64.4 + - - +
46O PRO 3.8 0.2 - - - -
48O VAL* 3.6 24.0 - - + +
50O PRO* 4.4 5.4 - - + -
53O CYS* 3.9 33.4 - - + -
95O ASN* 2.9 46.1 + - - +
97O TYR* 3.9 22.4 - - + -
129O ALA 4.0 0.7 - - - +
130O LEU* 4.3 0.2 - - - -
131O ARG* 3.9 5.2 - - - +
----------------------------------------------------------
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