Contacts of the strand formed by residues 23 - 31 (chain B) in PDB entry 1SZU
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 HIS 23 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.3 21.1 + - + +
81A LEU* 3.6 12.6 - - + -
21B GLN* 3.0 23.9 + - - -
22B ILE* 1.3 96.8 - - + +
24B PRO* 1.3 58.1 - - + +
25B ILE* 2.8 24.3 + - + +
377B VAL* 3.8 22.0 - - + -
381B ARG* 3.5 16.1 - - + +
386B ILE* 3.8 20.6 - - + -
387B LEU 2.8 37.7 + - - -
1022B EDO 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASN* 3.9 13.0 - - - +
8B MET* 3.4 51.6 - - + +
21B GLN* 4.1 2.6 - - + +
22B ILE 4.1 4.3 - - - +
23B HIS* 1.3 79.1 - - + +
25B ILE* 1.3 60.9 + - + +
381B ARG* 3.7 22.9 - - - +
1002B SO4 4.4 11.2 - - - +
1022B EDO 3.8 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.7 16.6 - - + -
82A ALA* 3.0 25.8 + - - +
4B ASN* 3.8 9.4 - - - +
8B MET* 4.9 0.2 - - - -
21B GLN* 5.0 0.2 - - - +
23B HIS* 2.8 20.0 + - + +
24B PRO* 1.3 83.5 - - + +
26B PHE* 1.3 67.9 + - - +
27B ALA* 3.9 2.2 + - - +
35B VAL* 6.4 0.7 - - + -
37B ASP* 3.6 26.0 - - + -
43B TYR* 3.3 44.0 - - + +
381B ARG* 3.4 34.1 - - + +
386B ILE* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 4.6 2.0 - + - -
82A ALA* 3.2 25.1 - - + +
83A TYR* 3.5 33.9 - - - -
84A GLU* 3.8 2.7 - - + -
87A LEU* 4.0 18.8 - - + -
4B ASN* 3.0 19.4 + - - +
7B LEU* 3.4 69.3 - - + -
8B MET* 3.6 19.5 - - + -
11B ARG* 4.3 11.7 - - + -
25B ILE* 1.3 75.7 - - - +
27B ALA* 1.3 62.3 + - - +
37B ASP* 3.2 4.5 - - - +
38B VAL* 2.9 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.8 15.2 - - + +
76A THR* 4.1 12.1 - - + -
81A LEU* 4.4 8.1 - - + -
82A ALA 2.8 14.8 + - - +
83A TYR* 3.7 19.6 - - + +
84A GLU* 4.8 0.9 + - - +
1030A EDO 4.1 4.9 + - - -
25B ILE* 3.9 4.5 + - + +
26B PHE* 1.3 73.1 - - - +
28B ASP* 1.3 60.1 + - - +
35B VAL* 3.6 27.4 - - + -
36B TRP 3.6 5.2 - - - -
37B ASP* 4.0 2.9 - - - +
38B VAL* 4.7 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 3.4 16.4 + - - +
73A LEU* 3.7 1.8 - - - -
84A GLU* 5.2 2.8 - - - +
1030A EDO 2.7 39.3 + - - -
26B PHE 3.6 0.6 + - - -
27B ALA* 1.3 75.3 - - - +
29B ARG* 1.3 85.6 + - - +
36B TRP 2.7 15.3 + - - +
37B ASP 3.8 16.6 - - - +
38B VAL* 4.1 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS 5.1 1.3 - - - +
72A LYS* 3.2 24.9 - - + +
73A LEU* 3.9 3.8 - - - -
28B ASP* 1.3 107.4 + - - +
30B ALA* 1.3 65.3 - - - +
35B VAL* 3.6 2.8 - - - +
36B TRP* 2.8 74.9 + - + +
37B ASP 4.4 4.6 + - - -
40B GLY* 4.6 10.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS 5.2 0.7 - - - +
72A LYS 2.7 18.3 + - - +
73A LEU* 4.2 9.0 - - + -
29B ARG* 1.3 78.4 - - - +
31B GLU* 1.3 63.3 - - - +
34B ARG 3.1 15.3 - - - +
35B VAL* 3.9 9.6 - - + -
36B TRP* 4.2 4.9 - - - -
57B HIS* 3.4 33.8 - - + +
58B LEU* 3.7 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 1.3 76.4 - - - +
32B ASN* 1.3 67.2 + - + +
33B CYS 2.9 1.0 + - - -
34B ARG* 2.8 47.1 + - - +
36B TRP* 4.0 21.1 - - + -
57B HIS 3.9 5.6 - - - +
58B LEU* 5.3 2.9 - - + +
----------------------------------------------------------
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