Contacts of the strand formed by residues 145 - 152 (chain A) in PDB entry 5XPT
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 THR 145 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 4.1 7.6 - - - -
37A TYR* 5.1 2.6 + - - -
87A ILE* 3.4 7.4 - - - +
88A LEU* 2.8 58.7 + - + +
89A ASP 5.0 2.0 - - - +
92A HIS* 4.7 15.7 - - + +
143A GLY 3.8 1.9 + - - +
144A CYS* 1.3 74.7 - - - +
146A PHE* 1.3 74.0 + - - +
340B ALA* 4.4 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.2 11.9 - - + -
31A LEU* 3.5 35.9 - - + -
36A VAL* 4.2 2.7 - - + -
37A TYR* 3.5 35.0 - + - -
60A LEU* 3.8 11.4 - - + -
63A TYR* 4.0 24.9 - + - -
64A ILE* 4.2 6.3 - - + -
85A VAL* 4.3 12.8 - - + -
86A VAL 3.1 13.2 - - - +
87A ILE* 4.7 4.5 - - + -
88A LEU* 4.6 1.7 - - - +
145A THR* 1.3 86.6 + - - +
147A THR* 1.3 75.5 + - - +
148A VAL* 4.1 17.0 - - + -
340B ALA* 3.5 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 4.0 9.8 + - - -
85A VAL* 3.6 4.3 - - - -
86A VAL* 2.8 42.5 + - + +
88A LEU* 4.3 17.5 - - + -
146A PHE* 1.3 82.8 - - - +
148A VAL* 1.3 71.5 + - - +
149A LEU* 3.6 22.2 - - + -
178A ASP* 5.2 4.3 - - - +
335B LYS* 4.2 13.1 - - + +
336B PRO* 3.9 17.7 + - - +
338B LYS 5.6 0.2 + - - -
340B ALA 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 5.0 8.1 - - + -
63A TYR* 4.7 3.7 + - + -
64A ILE* 6.5 0.2 - - + -
67A THR* 4.0 32.3 - - + +
68A LEU* 5.9 1.6 - - + -
71A VAL* 5.7 0.2 - - + -
83A VAL* 3.9 25.6 - - + -
84A VAL 3.3 9.4 - - - +
85A VAL* 4.7 12.1 - - + -
146A PHE* 4.1 19.5 - - + -
147A THR* 1.3 83.4 + - - +
149A LEU* 1.3 66.1 + - - +
150A VAL* 4.4 7.2 - - + -
171A TRP* 4.1 1.4 - - - -
334B TRP 3.7 0.7 - - - +
335B LYS* 3.5 6.8 - - - +
336B PRO* 3.2 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS 3.8 0.9 - - - +
83A VAL* 3.5 2.8 - - - -
84A VAL* 2.8 49.4 + - + +
86A VAL* 4.1 16.6 - - + -
97A LYS* 5.9 1.3 - - - +
147A THR* 3.6 24.7 - - + -
148A VAL* 1.3 80.8 - - - +
150A VAL* 1.3 61.8 + - - +
151A HIS* 4.1 7.2 - - + -
174A ALA* 4.0 18.8 - - + -
178A ASP* 4.4 8.5 - - + +
179A VAL* 3.6 31.6 - - + -
333B PRO* 4.3 12.6 - - + -
334B TRP 3.2 4.9 - - - +
335B LYS* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.9 18.4 - - + -
74A LEU* 4.6 10.3 - - + -
80A VAL* 4.2 18.6 - - + -
82A LYS 3.5 7.4 - - - +
83A VAL* 4.7 6.3 - - + -
148A VAL* 4.4 8.5 - - + -
149A LEU* 1.3 77.8 - - - +
151A HIS* 1.3 70.5 + - - +
152A THR* 4.4 9.4 - - - +
163A ILE* 4.6 6.5 - - + -
171A TRP* 3.6 31.6 - - + -
333B PRO* 3.4 1.6 - - - +
334B TRP* 2.8 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.7 4.7 - - - +
81A GLU* 2.8 48.5 + - - +
82A LYS* 2.9 45.2 + - + +
84A VAL* 3.8 23.4 - - + +
149A LEU* 4.3 9.8 + - + -
150A VAL* 1.3 74.3 - - - +
152A THR* 1.3 55.9 - - - +
179A VAL* 5.8 5.0 - - + +
331B SER* 3.6 9.0 - - - +
333B PRO* 3.6 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.0 20.4 - - + +
79A ASP* 3.4 17.7 + - + +
81A GLU* 4.6 7.9 - - - +
150A VAL* 3.8 4.3 + - - +
151A HIS* 1.3 74.8 - - - +
153A ARG* 1.3 77.9 + - - +
154A GLU 3.8 0.2 + - - -
155A ALA 4.9 4.0 - - - +
331B SER* 3.0 36.7 + - - +
334B TRP* 4.2 19.9 + - - +
----------------------------------------------------------
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