Contacts of the strand formed by residues 119 - 126 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LYS* 3.8 38.4 + - + +
112B VAL 3.3 8.3 - - - +
113B ALA* 4.7 2.4 - - - +
117B GLY 4.2 0.6 + - - -
118B LYS* 1.3 73.0 - - - +
120B ILE* 1.3 77.3 + - - +
121B THR* 4.0 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.5 25.1 - - + -
41B PHE* 4.1 21.8 - - + -
42B CYS* 4.8 2.7 - - - -
44B ALA* 5.6 0.2 - - + -
83B VAL* 4.3 9.2 - - + -
111B LYS* 3.5 1.3 - - - -
112B VAL* 2.8 43.3 + - + +
114B THR* 4.2 17.7 - - + -
118B LYS* 3.6 16.6 - - + +
119B GLU* 1.3 91.2 - - - +
121B THR* 1.3 58.0 + - - +
122B CYS* 3.1 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 4.0 16.2 - - - +
109B GLU* 3.8 35.4 - - + +
110B VAL 3.5 4.9 - - - +
111B LYS* 2.9 31.3 + - + +
119B GLU* 4.0 8.1 + - - +
120B ILE* 1.3 71.0 - - - +
122B CYS* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.3 20.2 - - + +
19B TYR 4.4 0.2 - - - -
20B PHE* 4.0 15.3 - - + +
83B VAL* 4.2 9.6 - - - -
109B GLU* 3.5 6.2 - - - +
110B VAL* 2.8 39.0 + - - +
112B VAL* 3.6 15.3 - - - -
120B ILE* 3.1 37.5 - - - -
121B THR* 1.3 77.8 - - - +
123B ARG* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 2.8 42.8 + - - -
17B PHE* 4.1 15.5 - - + -
18B LEU 2.8 13.5 + - - +
19B TYR* 3.3 5.7 - - + -
20B PHE 2.9 24.6 + - - -
91B LEU* 3.5 35.5 - - - +
94B LEU* 5.2 0.2 - - - -
95B ASP* 2.6 39.9 + - - -
107B VAL* 3.3 26.8 - - + +
108B ILE 3.5 4.7 - - - +
109B GLU* 4.8 0.9 - - - +
122B CYS* 1.3 72.9 - - - +
124B SER* 1.3 66.8 + - - +
125B TYR* 3.3 15.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 4.4 1.2 - - - -
20B PHE* 2.6 27.9 + - - -
22B TYR* 3.8 16.5 - - - -
71B ILE* 5.1 1.0 - - - +
107B VAL* 3.8 2.9 - - - +
108B ILE* 3.0 39.0 + - - +
110B VAL* 4.1 16.8 - - - -
123B ARG* 1.3 77.2 - - - +
125B TYR* 1.3 90.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.7 32.3 - + - -
22B TYR* 2.6 35.0 + - + -
94B LEU* 3.4 23.8 - - + +
95B ASP* 3.1 21.7 + - - -
98B GLU* 3.5 45.3 - - + +
100B VAL* 4.1 7.6 - - + -
105B TYR* 3.9 16.8 - - + -
106B VAL 3.4 12.1 - - - +
107B VAL* 3.6 28.7 - - + -
108B ILE* 3.6 5.6 - - - +
123B ARG* 3.3 13.0 + - - -
124B SER* 1.3 97.1 + - - +
126B LEU* 1.3 57.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 4.6 1.8 - - + -
126A LEU* 4.7 1.6 - - + -
128A THR* 3.8 31.0 - - + -
22B TYR* 3.6 6.5 - - - +
49B PHE* 4.1 10.1 - - + -
70B THR* 3.9 0.7 - - - +
71B ILE* 3.4 35.2 - - + +
105B TYR* 3.7 5.8 - - - -
106B VAL* 3.1 35.5 + - + +
108B ILE* 3.3 34.5 - - + -
125B TYR* 1.3 76.4 - - - +
127B MSE 1.3 75.6 + - - +
128B THR* 4.1 5.6 - - + -
----------------------------------------------------------
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