Contacts of the strand formed by residues 127 - 133 (chain A) in PDB entry 2QNJ
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 127 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 3.8 25.4 - - + -
87A ILE 3.9 9.4 - - - +
88A ASP* 4.7 5.6 + - - +
89A LYS* 3.8 3.8 - - - +
122A ILE 4.0 1.0 - - - +
123A GLU* 3.6 2.8 - - - -
124A THR* 2.7 48.7 + - - +
126A LYS* 1.3 88.2 + - - +
128A LEU* 1.3 63.4 + - - +
129A TYR* 3.7 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS 3.2 3.3 - - - +
86A ILE* 3.4 1.9 - - - -
87A ILE* 2.7 50.2 + - + +
89A LYS* 3.9 11.0 - - + +
100A LEU* 3.9 30.5 - - + -
101A PHE* 4.8 8.5 - - + -
104A VAL* 4.3 9.6 - - + -
121A VAL* 4.0 12.6 - - + -
122A ILE 3.7 5.8 - - - +
123A GLU* 3.3 40.8 - - + +
127A THR* 1.3 75.2 - - - +
129A TYR* 1.3 62.9 + - - +
130A LEU* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.7 44.6 - - + +
58A LEU* 5.5 3.1 - - + -
84A ILE* 3.8 15.9 - - + -
85A LYS 3.2 4.3 - - - -
86A ILE* 3.8 34.5 - - + +
121A VAL* 3.7 4.2 - - - +
122A ILE* 2.9 53.2 + - + +
124A THR* 4.8 7.5 - - + +
127A THR* 3.7 32.5 - - + +
128A LEU* 1.3 76.7 - - - +
130A LEU* 1.3 66.3 + - - +
131A ILE* 3.7 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA 3.6 1.4 - - - +
84A ILE* 3.4 2.4 - - - -
85A LYS* 2.8 49.5 + - + +
87A ILE* 4.1 18.2 - - + -
100A LEU* 5.2 3.8 - - + -
103A GLU* 6.2 0.9 - - + -
104A VAL* 3.6 35.9 - - + -
107A MET* 4.7 8.7 - - - -
118A LEU* 3.9 8.1 - - + -
120A GLU 3.9 2.2 - - - -
121A VAL* 4.2 20.4 - - + -
128A LEU* 3.9 17.9 - - + -
129A TYR* 1.3 78.6 - - - +
131A ILE* 1.3 62.5 + - - +
132A MET* 3.7 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 3.5 40.2 - - + +
82A VAL* 3.8 20.9 - - + -
83A ALA 3.7 3.8 - - - -
84A ILE* 3.5 22.7 - - + +
118A LEU* 3.4 4.2 - - - +
119A PHE* 2.7 39.6 + - + +
120A GLU* 3.1 27.7 + - + +
122A ILE* 3.9 26.2 - - + -
129A TYR* 3.7 21.5 - - + +
130A LEU* 1.3 71.6 - - - +
132A MET* 1.3 55.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 6.3 2.2 - - - -
82A VAL* 3.7 5.5 - - - +
83A ALA* 2.7 48.9 + - + +
85A LYS* 4.6 19.5 - - + +
107A MET* 3.4 29.8 - - + -
116A VAL* 5.0 11.0 - - + -
117A LYS 3.1 17.3 - - - +
118A LEU* 4.3 2.2 - - + -
119A PHE* 3.4 7.9 - - - -
130A LEU* 3.7 39.3 - - + +
131A ILE* 1.3 72.9 - - - +
133A GLU* 1.3 66.1 + - - +
134A TYR 3.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU 5.6 0.4 - - - -
82A VAL* 5.4 0.2 - - - +
83A ALA* 3.8 4.0 - - - +
112A HIS 5.2 0.3 - - - +
115A ILE 3.4 6.1 - - - +
116A VAL* 3.3 20.8 - - + +
117A LYS* 2.9 41.6 + - + +
119A PHE* 3.2 18.4 - - + -
132A MET* 1.3 85.0 - - - +
134A TYR* 1.3 66.3 + - - +
135A ALA* 3.8 1.6 + - - +
193A LYS* 2.9 39.2 + - + +
366A ARG* 3.1 31.2 + - - +
----------------------------------------------------------
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