Contacts of the strand formed by residues 34 - 40 (chain B) in PDB entry 5U03
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 VAL 34 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY* 3.7 15.7 - - - +
27B LEU* 3.5 29.4 - - + -
28B LYS* 3.5 14.8 - - - +
32B LEU 3.2 15.3 + - - +
33B HIS* 1.3 75.1 - - - +
35B THR* 1.3 72.2 + - - +
36B SER* 5.8 0.7 - - - -
78B LEU* 3.5 22.9 - - + -
80B ILE* 3.4 15.3 - - + +
133B VAL* 3.3 15.9 - - - +
142B VAL* 3.6 17.5 - - + +
144B VAL* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.3 4.5 - - + -
33B HIS 3.9 0.2 + - - -
34B VAL* 1.3 82.9 - - - +
36B SER* 1.4 69.8 + - - +
37B ILE* 5.9 0.4 - - + +
80B ILE* 4.8 4.0 - - - -
86B ASN* 4.0 7.3 + - - -
128B GLN 4.9 8.2 + - - +
131B ILE 4.2 2.3 + - - -
133B VAL* 3.3 29.4 - - - +
140B PRO* 3.5 32.8 - - + -
142B VAL 2.9 14.2 + - - +
143B CYS* 3.4 22.2 - - + -
144B VAL* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 5.8 0.4 - - - -
35B THR* 1.4 84.2 + - - +
37B ILE* 1.4 61.9 + - - +
71B LEU* 4.6 1.6 - - - +
74B TYR* 3.6 33.9 - - - +
80B ILE* 4.8 3.3 - - - +
82B LEU* 4.1 15.1 - - - +
86B ASN* 2.8 30.4 + - - +
143B CYS* 3.8 3.4 - - - -
144B VAL* 3.0 22.4 - - - -
----------------------------------------------------------
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 THR* 5.9 0.7 - - + +
36B SER* 1.4 81.5 - - - +
38B LYS* 1.3 58.8 + - - +
39B ILE* 3.9 23.1 - - + -
71B LEU* 5.5 0.2 - - - -
74B TYR* 6.0 1.1 - - - -
86B ASN* 3.7 12.3 - - - +
88B LEU* 4.6 15.5 - - + -
125B VAL* 4.0 25.8 - - + +
128B GLN* 3.6 33.7 - - + +
129B ALA 4.7 1.3 - - - +
143B CYS* 3.6 19.2 - - - -
144B VAL 3.0 6.1 + - - -
145B ILE* 3.2 20.6 - - + +
146B GLU* 2.7 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 1.3 72.1 - - - +
39B ILE* 1.3 62.8 + - - +
40B ASP* 2.7 35.9 + - - +
42B TYR* 5.7 0.4 - - - -
68B ASP* 3.4 32.8 + - + -
70B ASP* 3.6 19.7 + - + -
71B LEU* 3.8 28.8 - - + +
74B TYR* 5.2 0.4 - - + -
86B ASN 3.0 8.2 + - - +
87B ASN* 3.5 19.2 + - - +
88B LEU 3.2 23.4 + - - -
146B GLU* 3.5 34.3 - - + +
601B ATP 4.6 0.2 + - - -
602B UTP 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.9 17.5 - - + -
38B LYS* 1.3 75.8 - - - +
40B ASP* 1.4 66.4 + - - +
41B PRO* 3.5 2.2 - - + +
88B LEU* 3.9 17.3 - - + +
121B ILE* 5.4 2.9 - - + -
125B VAL* 5.6 4.3 - - + -
145B ILE* 3.6 24.0 - - + -
146B GLU 2.8 11.0 + - - +
147B LEU* 3.7 17.0 - - + -
148B GLY* 2.8 30.3 + - - -
159B PHE* 3.5 40.2 - - + -
163B PHE* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 2.7 31.8 + - - +
39B ILE* 1.4 76.0 - - - +
41B PRO* 1.3 68.1 - - - +
42B TYR* 2.9 32.6 + - + -
68B ASP* 4.7 2.8 - - - +
87B ASN* 3.0 29.8 + - - +
88B LEU 3.0 11.2 + - - +
89B THR* 3.3 23.5 - - + +
90B THR* 3.8 2.4 + - - +
602B UTP 2.8 19.0 + - - +
----------------------------------------------------------
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