Contacts of the strand formed by residues 119 - 126 (chain A) in PDB entry 2Q53
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 GLU 119 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 3.7 39.1 + - + +
112A VAL 3.1 12.3 - - - +
113A ALA* 3.7 6.7 - - + +
117A GLY 3.6 5.1 + - - +
118A LYS* 1.3 81.4 - - - +
120A ILE* 1.3 71.2 + - - +
121A THR* 5.8 0.9 - - - +
101B LYS* 4.7 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.8 28.3 - - + -
41A PHE* 4.3 11.0 - - + -
42A CYS* 3.3 34.3 - - - -
83A VAL* 4.6 5.2 - - + -
110A VAL 3.7 0.3 - - - +
111A LYS* 3.3 3.4 - - - -
112A VAL* 2.5 44.9 + - + +
113A ALA* 5.3 0.4 - - - -
114A THR* 3.7 17.7 - - + +
118A LYS* 3.8 17.5 - - + +
119A GLU* 1.3 83.2 - - - +
121A THR* 1.3 68.4 + - - +
122A CYS* 3.9 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.0 13.5 - - - +
109A GLU* 3.8 34.3 - - + +
110A VAL 3.3 5.6 - - - +
111A LYS* 4.1 20.4 - - + +
119A GLU* 5.7 1.0 + - - +
120A ILE* 1.3 80.4 - - - +
122A CYS* 1.3 66.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.6 10.5 - - - +
20A PHE* 3.4 29.4 - - + -
83A VAL* 3.7 36.8 - - - -
109A GLU* 3.3 10.0 - - - +
110A VAL* 2.7 38.4 + - + -
112A VAL* 4.0 9.9 - - - -
120A ILE* 3.9 9.6 - - - -
121A THR* 1.3 82.1 - - - +
123A ARG* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 4.1 25.8 - - + -
18A LEU 3.0 14.4 + - - +
19A TYR* 3.4 7.9 - - - -
20A PHE 2.9 23.0 + - - -
91A LEU* 4.4 25.2 + - - +
94A LEU* 4.9 1.1 - - - -
95A ASP* 2.8 36.3 + - - -
107A VAL* 3.4 23.5 - - + +
108A ILE 3.4 4.0 - - - +
109A GLU* 4.7 0.4 - - - +
122A CYS* 1.3 74.8 - - - +
124A SER* 1.3 66.7 + - - +
125A TYR* 3.5 11.9 + - + +
109B GLU* 2.8 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 4.5 0.7 - - - -
20A PHE* 2.6 25.0 + - - -
21A ALA* 4.7 0.2 - - - -
22A TYR* 3.6 19.8 - - - -
71A ILE* 5.7 0.2 - - - -
107A VAL* 3.8 2.3 - - - +
108A ILE* 2.9 43.7 + - - -
110A VAL* 4.1 15.9 - - - -
122A CYS 4.1 0.2 - - - -
123A ARG* 1.3 74.6 - - - +
125A TYR* 1.3 87.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.8 24.2 - + - -
22A TYR* 2.5 33.8 + - - -
94A LEU* 3.3 23.3 - - + +
95A ASP* 2.6 29.3 + - - -
98A GLU* 3.4 46.2 - - + +
100A VAL* 3.7 17.9 - - + -
105A TYR* 3.7 19.3 - - + -
106A VAL 3.4 16.6 - - - +
107A VAL* 4.0 7.0 - - + -
108A ILE* 3.4 3.9 - - - +
123A ARG* 3.5 11.7 + - + -
124A SER* 1.3 102.1 + - - +
126A LEU* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 4.0 0.9 - - - -
49A PHE* 4.0 15.5 - - + -
70A THR* 3.7 5.8 - - - +
71A ILE* 3.6 35.4 - - + +
105A TYR* 3.6 8.9 - - - -
106A VAL* 3.0 50.8 + - + +
108A ILE* 3.5 36.3 - - + -
125A TYR* 1.3 76.1 - - - +
127A MSE 1.3 69.9 + - - +
128A THR* 4.3 6.5 - - + -
106B VAL* 4.6 2.0 - - + -
126B LEU* 4.7 2.7 - - + -
128B THR* 4.1 22.4 - - + -
----------------------------------------------------------
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