Contacts of the strand formed by residues 104 - 111 (chain W) 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 TYR 104 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W PHE* 3.4 35.0 - + - -
44W PHE* 3.1 8.3 - - - +
45W ALA 2.8 35.0 + - - +
47W ALA* 3.8 20.8 - - + +
50W ALA* 3.5 25.6 - - + -
51W TYR* 4.1 4.9 + + - -
73W TRP* 3.5 20.2 - - + -
103W ALA* 1.3 72.3 - - - +
105W VAL* 1.3 59.5 + - - +
122W LEU* 4.0 7.0 - - + -
124W GLN 3.3 4.7 - - - -
125W ARG* 3.5 29.8 + - + -
126W PRO* 3.5 23.1 - - + -
129W ALA* 3.7 19.1 - - - +
131W ASP* 3.8 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42W LEU* 4.0 13.0 - - + -
43W GLU 3.4 10.3 - - - +
44W PHE* 3.9 10.8 - - + -
73W TRP* 4.2 0.2 - - - -
93W ILE 5.7 0.2 - - - +
96W CYS* 3.7 26.9 - - + -
97W THR* 4.2 10.3 - - + -
100W PHE* 4.5 5.2 - - + +
103W ALA* 4.1 3.1 - - + +
104W TYR* 1.3 80.9 - - - +
106W ARG* 1.3 63.9 + - - +
122W LEU* 3.4 6.6 - - - +
123W VAL* 2.8 37.6 + - + -
124W GLN* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H LYS* 5.9 0.4 - - - +
187H ARG* 5.8 0.6 - - - +
163V ASN* 3.9 21.1 + - - +
12W PHE* 5.3 5.0 - - + -
42W LEU* 3.5 9.2 - - - +
43W GLU* 2.8 61.5 + - + +
70W ASN 5.3 0.2 + - - -
71W ARG 3.0 24.0 + - - -
73W TRP* 3.3 61.6 - - + +
105W VAL* 1.3 74.1 - - - +
107W LEU* 1.3 60.3 + - - +
108W VAL* 4.0 16.3 + - + +
117W GLN* 5.7 2.0 + - - +
120W GLY* 6.4 0.4 - - - -
121W PHE 3.4 20.4 - - - +
122W LEU* 4.1 4.9 - - + +
123W VAL* 4.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W ILE* 5.4 0.2 - - + -
30W VAL* 3.8 28.9 - - + -
33W ILE* 3.8 18.2 - - + -
40W PRO* 4.6 0.9 - - + -
41W CYS 3.6 20.6 - - - +
42W LEU* 3.9 16.8 - - + -
89W VAL* 3.8 22.7 - - + -
93W ILE* 4.5 7.2 - - + -
106W ARG* 1.3 72.3 - - - +
108W VAL* 1.3 68.2 + - - +
119W MET* 4.3 2.4 - - - +
120W GLY* 3.1 3.5 - - - -
121W PHE* 3.0 53.6 + - + +
123W VAL* 4.0 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W ILE* 4.7 0.2 - - - +
40W PRO* 3.5 2.9 - - - +
41W CYS* 2.9 45.4 + - + +
43W GLU* 3.8 25.6 - - - +
106W ARG* 4.0 18.4 - - + +
107W LEU* 1.3 84.2 - - - +
109W ALA* 1.3 62.7 + - - +
110W PHE* 3.8 28.3 - - + -
117W GLN* 3.3 32.5 - - - +
119W MET* 3.4 9.1 - - - +
120W GLY* 4.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W ILE* 3.9 25.8 - - + -
38W TRP* 4.0 10.3 - - + -
39W ILE 3.1 10.8 - - - +
108W VAL* 1.3 77.7 - - - +
110W PHE* 1.3 58.3 + - - +
117W GLN* 3.4 5.2 - - - +
118W ILE* 2.8 32.7 + - + -
119W MET* 3.2 28.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H ASN* 4.9 5.4 - - - -
187H ARG* 3.8 43.3 - - - -
74R LEU* 3.9 27.6 - - + +
38W TRP* 3.5 5.7 - - - +
39W ILE* 2.8 56.7 + - + +
41W CYS* 3.6 29.8 - - + -
43W GLU* 4.7 2.0 - - - -
75W MET* 5.7 0.2 - - + -
79W PRO* 4.4 8.7 - - + -
108W VAL* 3.8 13.7 - - + -
109W ALA* 1.3 73.0 - - - +
111W ASP* 1.3 62.9 - - - +
112W ASN 4.0 0.2 - - - -
116W VAL* 3.7 3.8 - - - +
117W GLN* 3.8 34.5 - - + -
118W ILE* 4.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R LEU 4.5 0.5 - - - +
38W TRP* 3.2 29.3 + - + -
110W PHE* 1.3 75.6 - - - +
112W ASN* 1.3 59.2 + - - +
113W GLN* 2.8 38.4 + - - +
114W LYS* 2.9 26.2 + - + +
115W GLN* 2.9 26.5 + - - -
116W VAL 2.9 15.6 + - - +
118W ILE* 3.9 20.8 - - + +
----------------------------------------------------------
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