Contacts of the strand formed by residues 32 - 38 (chain A) in PDB entry 1UA4
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 ASN 32 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN* 5.0 1.6 - - - +
31A THR* 1.3 77.2 - - - +
33A ILE* 1.3 67.8 + - - +
34A ASP* 2.8 24.1 - - - +
110A MET* 4.1 0.2 - - - -
111A GLY 2.7 32.5 + - - +
112A GLY* 3.2 24.7 - - - +
140A GLN* 3.0 24.7 + - - -
174A CYS* 3.4 12.3 - - - +
176A HIS* 3.3 35.2 + - - +
206A ASN* 3.7 14.9 - - - +
1457A GLC 3.8 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 1.3 74.1 - - - +
34A ASP* 1.3 63.5 + - - +
35A ALA 3.8 0.5 + - - -
108A LEU* 4.1 22.4 - - + -
109A ARG 3.7 4.0 - - - +
137A SER* 4.2 1.1 - - - +
139A LEU* 3.4 34.3 - - + -
140A GLN* 3.7 19.1 - - - +
143A LEU* 4.0 24.5 - - + -
173A ASN* 3.7 24.0 - - + +
174A CYS 2.9 11.9 + - - +
175A ILE* 3.4 25.0 - - + +
176A HIS 3.0 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 2.8 13.2 - - - +
33A ILE* 1.3 72.0 - - - +
35A ALA* 1.3 59.8 + - - +
36A ILE* 3.6 8.8 + - + +
107A GLU 3.5 1.7 - - - +
108A LEU* 3.3 5.4 - - - -
109A ARG* 2.8 44.5 + - + +
110A MET 4.3 5.0 - - - +
111A GLY* 3.6 9.4 - - - -
116A ILE* 4.6 0.9 - - - +
176A HIS* 3.5 6.2 - - - +
178A ILE* 3.6 15.3 - - + -
436A VAL* 3.6 16.5 - - - +
1457A GLC 2.6 46.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE 3.8 1.4 + - - -
34A ASP* 1.3 69.9 - - - +
36A ILE* 1.3 62.0 + - - +
37A LYS* 3.8 1.4 + - - +
105A TRP* 3.9 23.3 - - + +
107A GLU 3.6 5.6 - - - -
108A LEU* 3.8 17.5 - - + -
175A ILE* 4.0 16.2 - - + -
176A HIS 2.9 14.6 + - - +
177A TYR* 3.4 14.2 - - + +
178A ILE 2.8 24.5 + - - +
179A TYR* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 4.2 7.6 - - + +
35A ALA* 1.3 74.1 - - - +
37A LYS* 1.3 56.6 + - - +
38A TYR* 4.1 20.4 - - + +
105A TRP* 3.9 0.4 - - - -
106A ASN* 2.6 32.8 + - - +
107A GLU* 2.8 24.3 + - + +
109A ARG* 3.3 52.3 - - + +
178A ILE* 3.5 20.2 - - + +
180A GLU* 3.7 28.7 - - + -
434A SER* 5.1 0.4 - - - -
436A VAL* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA 3.8 1.7 + - - +
36A ILE* 1.3 74.1 - - - +
38A TYR* 1.3 73.1 + - - +
39A LEU* 3.4 9.2 + - + +
43A ASP* 5.0 1.8 + - - +
103A TRP* 2.9 66.8 + - + +
104A GLY 3.3 22.3 + - - +
105A TRP* 4.1 9.5 - - + +
106A ASN* 3.4 9.4 + - - +
178A ILE 2.8 13.4 + - - +
179A TYR* 3.7 22.4 - - + -
180A GLU* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 4.1 9.3 - - + +
37A LYS* 1.3 74.8 - - - +
39A LEU* 1.3 69.0 + - - +
40A ASP* 3.7 3.3 + - - +
106A ASN* 2.9 43.5 + - + +
107A GLU* 2.7 28.9 + - - -
109A ARG* 3.3 14.7 + - - -
180A GLU* 3.8 22.0 - - + -
433A LYS* 3.2 42.3 - - + +
434A SER* 3.7 11.1 - - - -
----------------------------------------------------------
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