Contacts of the strand formed by residues 43 - 50 (chain X) in PDB entry 1SHU
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 PHE 43 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40X ARG* 3.9 27.4 - - + -
41X ARG* 3.8 9.3 + - - -
42X ALA* 1.3 73.4 - - - +
44X ASP* 1.3 64.4 + - - +
45X LEU* 4.0 8.7 - - + +
77X GLU 3.1 8.5 + - - +
78X MET* 3.4 37.2 - - + +
79X ARG 3.0 24.3 + - - +
140X SER* 3.4 24.9 - - - +
142X ILE* 4.0 19.1 - - + -
213X ILE* 4.0 9.6 - - + -
216X GLN* 3.7 39.0 - - + -
217X SER* 3.4 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 44 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42X ALA* 6.0 0.7 - - - +
43X PHE* 1.3 75.2 - - - +
45X LEU* 1.3 61.8 + - - +
46X TYR* 3.8 16.2 + - + -
77X GLU 5.1 0.7 - - - +
79X ARG* 2.8 56.7 + - - +
95X LEU* 3.8 17.0 - - + +
134X ALA* 4.7 5.4 - - - +
139X THR* 4.7 6.9 - - - -
140X SER 2.9 13.4 + - - +
141X SER* 3.4 9.6 + - - +
142X ILE* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X PHE* 4.0 17.9 - - + -
44X ASP* 1.3 76.3 - - - +
46X TYR* 1.3 61.8 + - - +
47X PHE* 3.9 11.9 + - + -
69X LEU* 4.4 20.2 - - + +
73X PHE* 4.4 14.4 - - + -
78X MET* 4.1 19.1 - - + -
79X ARG 2.8 10.0 + - - +
80X LEU* 3.4 28.7 - - + -
81X SER 3.0 26.5 + - - +
95X LEU* 4.6 0.4 - - - +
142X ILE* 3.5 31.9 - - + +
144X ILE* 5.0 5.4 - - + -
213X ILE* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 46 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44X ASP* 3.8 24.0 + - + +
45X LEU* 1.3 71.1 - - - +
47X PHE* 1.3 62.3 + - - +
48X VAL* 3.7 2.7 + - + -
81X SER* 3.6 21.5 - - - -
83X ILE* 4.5 3.1 - - + -
95X LEU* 3.3 27.4 - - + +
127X ALA* 4.0 25.8 - - + -
130X GLN* 3.6 46.7 + - + +
131X ILE* 3.3 37.2 - - + +
134X ALA* 4.6 1.9 - - - +
141X SER* 4.1 4.1 + - - -
142X ILE 2.8 20.1 + - - +
143X ILE* 3.3 5.8 - - + +
144X ILE* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X LEU* 4.0 23.3 - - + -
46X TYR* 1.3 70.1 - - - +
48X VAL* 1.3 58.3 + - - +
49X LEU* 3.9 17.7 - - + -
65X PHE* 4.3 6.7 - + - -
66X VAL* 3.9 29.6 - - + -
69X LEU* 3.7 44.0 - - + -
70X ALA 4.9 2.7 - - - -
80X LEU* 4.3 12.3 - - + -
81X SER 2.9 20.0 + - - +
82X PHE* 3.7 26.9 - + + -
83X ILE* 2.8 34.8 + - - +
144X ILE* 3.5 21.8 - - + -
146X LEU* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X TYR 4.2 2.2 - - - +
47X PHE* 1.3 73.9 - - - +
49X LEU* 1.3 59.4 + - - +
50X ASP 4.0 0.2 + - - -
83X ILE* 3.7 10.3 - - + -
85X PHE* 3.8 22.0 - - + -
120X ILE* 4.7 1.3 - - + +
123X GLY* 3.7 36.6 - - - +
124X LEU* 3.9 11.9 - - + +
127X ALA* 4.1 13.9 - - + -
143X ILE* 3.9 24.0 - - + -
144X ILE 2.9 11.9 + - - +
145X ALA* 3.3 10.6 - - + +
146X LEU 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X PHE* 3.9 20.2 - - + +
48X VAL* 1.3 77.4 - - - +
50X ASP* 1.3 62.9 + - - +
51X LYS 3.4 0.3 + - - -
59X TRP* 4.2 18.6 - - + -
62X ILE* 4.0 5.6 - - + -
63X TYR* 6.3 0.4 - - - -
66X VAL* 3.8 27.4 - - + -
82X PHE* 4.9 2.2 - - + -
83X ILE 2.8 19.1 + - - +
84X VAL* 3.3 5.4 - - + +
85X PHE* 3.0 27.7 + - - -
109X LEU* 3.7 40.8 - - + -
146X LEU* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X LEU* 1.3 69.8 - - - +
51X LYS* 1.3 58.9 + - - +
52X SER* 2.6 39.0 + - - -
55X VAL* 3.2 24.2 - - + +
59X TRP* 3.3 13.2 - - - -
62X ILE* 3.6 4.7 - - + +
85X PHE* 3.4 24.3 - - + -
118X THR* 3.7 11.1 - - - +
146X LEU* 3.0 22.7 + - - +
147X THR* 2.7 27.1 + - - -
148X ASP* 3.8 8.1 + - - +
----------------------------------------------------------
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