Contacts of the strand formed by residues 31 - 46 (chain B) in PDB entry 1UXU
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 31 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG* 4.0 10.3 - - + +
23B PRO* 3.6 38.8 - - + +
24B VAL* 3.9 15.7 - - + -
30B VAL* 1.3 73.2 - - - +
32B ASN* 1.3 69.2 + - - +
33B VAL* 3.5 25.1 + - + -
62B TRP* 3.9 6.7 - - + -
63B HIS 3.8 16.8 - - - +
88B TRP* 3.9 21.3 - - + -
157B GLN 2.9 17.2 + - - +
158B VAL* 3.3 7.2 - - + +
159B ASP 3.0 21.4 + - - +
2214B NAG 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.9 6.2 + - - +
31B LEU* 1.3 75.8 - - - +
33B VAL* 1.3 61.1 + - - +
34B THR* 5.9 1.8 - - + -
61B ILE 3.9 0.6 - - - +
62B TRP* 3.3 24.4 - - - +
63B HIS 4.4 2.4 + - - -
159B ASP* 3.4 14.8 - - - +
161B PHE* 3.3 22.6 - - + -
2214B NAG 1.4 69.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.5 21.5 - - + -
32B ASN* 1.3 78.7 - - - +
34B THR* 1.3 77.7 + - - +
60B GLN* 4.1 9.4 - - + -
61B ILE 3.3 9.4 - - - +
62B TRP* 4.0 2.0 - - + -
90B PRO* 3.9 23.1 - - + -
92B ILE* 3.9 24.5 - - + -
158B VAL* 3.7 20.6 - - + -
159B ASP 2.9 9.0 + - - +
160B ILE* 3.3 4.5 - - - +
161B PHE* 2.8 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASN* 5.9 1.6 - - + -
33B VAL* 1.3 79.9 - - - +
35B LEU* 1.3 60.8 + - - +
59B ARG 3.6 0.6 - - - +
60B GLN* 3.3 6.8 - - - -
61B ILE* 2.9 60.5 + - + +
161B PHE* 3.3 22.0 - - + -
162B ASN 5.3 0.4 - - - +
163B ALA* 4.2 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 1.3 76.1 - - - +
36B GLN* 1.3 69.3 + - - +
37B ILE* 3.5 35.8 + - + -
58B ILE* 3.9 14.6 - - + -
59B ARG 3.4 3.1 - - - +
60B GLN* 4.7 5.8 - - + -
92B ILE* 3.9 15.0 - - + -
148B PHE* 3.8 16.6 - - + -
160B ILE* 3.6 30.7 - - + -
161B PHE 2.8 12.9 + - - +
162B ASN* 3.8 6.9 - - - +
163B ALA* 2.9 22.0 + - - -
164B LEU 4.5 0.5 + - - -
202B VAL* 3.6 17.3 - - + -
204B PHE* 4.6 5.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 1.3 78.5 - - - +
37B ILE* 1.3 63.5 + - - +
38B THR* 3.8 11.1 + - - +
57B TRP 3.6 1.2 - - - +
58B ILE* 3.5 5.0 - - - -
59B ARG* 2.8 59.3 + - + +
61B ILE* 6.1 0.4 - - + +
163B ALA* 4.1 14.0 - - + +
164B LEU* 3.7 34.1 - - + +
168B ASP* 3.1 25.9 + - - -
204B PHE* 5.3 0.2 - - - -
1216B EPE 3.9 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.5 15.2 - - + +
36B GLN* 1.3 73.2 - - - +
38B THR* 1.3 59.2 + - - +
39B LEU 4.1 0.2 + - - -
56B LEU* 4.1 22.0 - - + -
57B TRP 3.6 0.7 - - - +
58B ILE* 3.5 31.2 - - + -
146B LEU* 5.2 0.2 - - + -
148B PHE* 3.6 24.2 - - + -
166B SER 5.6 0.8 + - - -
167B GLY* 3.5 1.8 - - - -
168B ASP* 2.7 33.7 + - - +
183B MET* 3.9 25.8 - - + -
204B PHE* 3.4 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN* 3.8 6.9 + - - +
37B ILE* 1.3 74.5 - - - +
39B LEU* 1.3 64.5 + - - +
40B SER* 3.5 3.9 + - - +
56B LEU* 3.3 6.2 - - - +
57B TRP* 2.8 54.4 + - + -
168B ASP* 3.2 33.6 + - - +
171B ASP* 3.9 35.2 - - + +
1216B EPE 3.8 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 4.1 1.8 + - - +
38B THR* 1.3 73.0 - - - +
40B SER* 1.3 59.7 + - - +
41B GLN 4.0 13.5 - - - +
42B ILE* 4.7 4.0 - - + +
54B ALA* 4.1 9.6 - - + -
55B TYR 3.8 7.4 - - - +
56B LEU* 3.6 23.8 - - + -
146B LEU* 5.9 0.2 - - + -
168B ASP 3.1 10.8 + - - +
169B LEU* 4.0 24.7 - - + -
171B ASP 4.1 1.6 - - - -
172B PHE* 3.5 52.2 + - + +
180B VAL* 4.3 2.9 - - + -
183B MET* 4.4 9.9 - - + -
206B LEU* 4.2 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 3.5 3.4 + - - +
39B LEU* 1.3 72.8 - - - +
41B GLN* 1.3 61.7 + - - +
55B TYR* 2.8 31.1 + - - -
56B LEU 4.2 1.0 - - - -
57B TRP* 3.3 32.1 + - - -
171B ASP* 3.9 11.4 - - - +
172B PHE* 3.7 1.9 - - - -
173B ILE* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.6 3.8 - - - +
40B SER* 1.3 84.1 - - - +
42B ILE* 1.3 76.3 + - - +
43B LYS* 3.4 24.8 + - - +
54B ALA* 3.6 4.5 - - - +
55B TYR* 2.8 59.0 + - + +
172B PHE* 4.0 8.6 - - - -
173B ILE* 3.9 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.7 8.3 - - + -
41B GLN* 1.3 81.9 + - - +
43B LYS* 1.3 61.3 + - - +
44B ASP* 4.0 14.1 - - - +
45B MET* 4.2 9.2 - - + +
52B LEU* 3.7 25.8 - - + -
53B THR 4.1 2.5 - - - -
54B ALA* 4.7 2.0 - - - +
172B PHE* 3.9 29.2 - - + -
173B ILE 5.0 0.6 + - - -
175B ASP* 3.7 39.6 - - + +
178B TRP* 4.4 8.7 - - + +
180B VAL* 4.2 3.6 - - + -
206B LEU* 5.1 2.0 - - + -
208B LEU* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN* 3.4 21.6 + - - +
42B ILE* 1.3 75.1 - - - +
44B ASP* 1.3 64.7 + - + +
53B THR* 2.8 27.9 + - + +
55B TYR* 3.2 51.3 + - + +
175B ASP* 5.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.4 6.3 - - - -
43B LYS* 1.3 83.9 - - + +
45B MET* 1.3 70.1 + - - +
46B ASP* 3.5 26.5 - - - +
51B ILE 3.7 1.0 - - - +
52B LEU* 3.5 4.5 - - - +
53B THR* 2.8 48.2 + - - +
175B ASP* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 4.2 10.4 - - + +
44B ASP* 1.3 76.7 + - - +
46B ASP* 1.3 87.3 + - - +
47B GLU* 3.3 9.4 + - + +
50B GLN* 4.2 3.6 - - - -
51B ILE 3.7 20.9 - - - +
52B LEU* 4.2 6.3 - - + -
130B CYS* 3.8 28.0 - - + -
142B GLN* 4.0 26.2 - - + +
144B CYS* 4.0 8.7 - - - -
178B TRP* 3.6 49.3 + - + +
208B LEU* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASP* 3.5 20.2 - - - +
45B MET* 1.3 72.7 - - - +
47B GLU* 1.3 50.8 + - - +
48B ARG* 2.8 23.8 + - - +
49B ASN* 2.8 32.6 + - - +
50B GLN* 2.7 30.3 + - - -
51B ILE* 2.9 31.1 + - + +
----------------------------------------------------------
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