Contacts of the strand formed by residues 147 - 153 (chain A) in PDB entry 4P7A
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 GLY 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 4.5 2.2 - - - -
63A ASP* 3.6 11.0 - - - -
65A GLY 3.2 22.0 + - - -
67A GLY 4.4 0.4 - - - -
116A THR 3.9 0.7 - - - +
117A THR* 3.2 4.3 + - - -
118A LYS 2.9 36.7 + - - -
145A ASN 3.2 5.4 + - - +
146A GLN* 1.3 74.4 - - - +
148A THR* 1.3 64.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE 3.5 2.6 - - - +
62A GLN* 3.4 5.1 - - - +
63A ASP* 2.7 52.3 + - - +
67A GLY* 3.3 13.7 + - - -
68A ILE* 4.0 3.3 + - + -
115A ILE* 4.1 9.9 - - + -
116A THR 3.4 8.1 - - - +
117A THR* 2.7 20.9 + - - +
147A GLY* 1.3 73.6 - - - -
149A GLN* 1.3 60.6 + - - +
150A ILE* 3.7 28.9 - - + +
402A ADP 3.6 20.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 3.6 39.5 + - + +
61A ILE 3.2 9.6 - - - +
62A GLN* 3.3 29.3 - - - +
114A THR* 3.8 1.3 - - - +
115A ILE* 3.5 3.1 - - - +
116A THR* 2.7 61.7 + - + +
127A ARG* 4.8 7.7 - - - +
148A THR* 1.3 72.1 - - - +
150A ILE* 1.3 62.3 + - - +
151A THR* 3.7 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET* 4.1 33.5 - - + +
39A CYS* 6.5 0.9 - - - -
59A ILE 3.8 0.9 - - - +
60A GLN* 3.3 3.6 - - - +
61A ILE* 2.9 35.9 + - + +
68A ILE* 5.1 1.1 - - + -
104A LEU* 4.7 13.0 - - + -
113A VAL* 4.2 18.2 - - + -
114A THR 3.5 8.3 - - - +
115A ILE* 3.9 21.5 - - + -
148A THR* 3.7 25.6 - - + -
149A GLN* 1.3 74.9 - - - +
151A THR* 1.3 65.9 + - - +
152A VAL* 4.4 3.1 - - + -
402A ADP 4.6 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 3.5 22.7 - - + -
59A ILE 3.3 3.4 - - - -
60A GLN* 3.1 24.1 + - - +
112A HIS 3.5 0.9 - - - +
113A VAL* 3.4 5.2 - - - +
114A THR* 2.9 45.7 + - - +
149A GLN* 3.7 11.4 + - - -
150A ILE* 1.3 77.5 - - - +
152A VAL* 1.3 64.2 + - - +
153A GLU* 3.8 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 5.4 1.6 - - + -
35A MET* 3.7 33.7 - - + -
55A GLY 4.9 1.6 - - - +
58A LEU* 3.5 2.4 + - - -
59A ILE* 2.7 55.4 + - + +
107A ILE* 3.8 21.8 - - + -
111A ALA* 3.5 27.4 - - + -
112A HIS 3.6 3.1 - - - -
113A VAL* 4.5 3.6 - - + -
150A ILE* 4.4 6.5 - - + -
151A THR* 1.3 75.3 - - - +
153A GLU* 1.3 60.7 + - - +
154A ASP 4.3 0.2 + - - -
155A LEU* 4.5 10.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 3.3 19.8 + - - +
58A LEU* 4.1 14.8 - - + +
111A ALA* 3.5 2.6 - - - +
112A HIS* 2.9 44.9 + - + +
114A THR* 4.8 6.4 + - - -
151A THR* 3.8 24.5 - - + +
152A VAL* 1.3 78.3 - - - +
154A ASP* 1.3 83.5 + - - +
155A LEU 3.4 2.7 - - - -
----------------------------------------------------------
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