Contacts of the strand formed by residues 106 - 117 (chain A) in PDB entry 2XB3
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 SER 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA* 4.2 1.7 - - - +
104A GLY 4.1 1.0 + - - -
105A ARG* 1.3 73.9 - - - +
107A SER* 1.3 65.2 + - - +
129A VAL* 3.5 5.5 - - - +
130A THR* 3.0 45.7 + - - +
132A PRO* 5.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.4 31.0 + - - +
99A ALA* 3.6 19.8 - - - +
106A SER* 1.3 79.1 + - - +
108A ALA* 1.3 64.0 + - - +
128A ALA 3.2 13.2 - - - -
129A VAL* 4.3 6.7 - - - +
130A THR 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.9 3.8 - - - -
107A SER* 1.3 78.1 - - - +
109A LEU* 1.3 63.0 + - - +
110A ILE* 3.5 4.8 + - + +
127A TYR* 3.1 5.2 - - - +
128A ALA* 2.8 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.9 33.2 - - + +
90A GLY* 4.1 14.8 - - - +
91A ASP* 3.9 30.1 - - - +
94A LEU* 3.7 17.3 - - + +
108A ALA* 1.3 72.2 - - - +
110A ILE* 1.3 62.7 + - - +
111A ALA* 3.8 17.0 - - - +
112A ALA* 4.7 3.8 - - + -
125A LEU* 4.5 8.1 - - + -
126A GLU 3.4 18.2 - - - +
127A TYR* 4.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 4.0 11.7 - - + +
109A LEU* 1.3 77.4 - - - +
111A ALA* 1.3 61.8 + - + +
126A GLU* 2.8 33.1 + - + +
127A TYR* 4.1 2.0 - - - -
128A ALA* 4.1 20.2 - - + +
142A HIS* 3.5 33.9 - - + +
163A GLU* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.8 6.2 - - - +
110A ILE* 1.3 84.1 - - + +
112A ALA* 1.3 61.8 + - - +
113A THR* 4.4 3.8 - - + -
124A ILE 4.4 1.1 - - - -
125A LEU* 3.4 2.1 - - - -
126A GLU* 2.8 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.6 12.7 - - - +
87A GLU* 3.5 37.4 - - + +
109A LEU* 4.7 7.9 - - + -
111A ALA* 1.3 75.6 - - - +
113A THR* 1.3 62.7 + - - +
124A ILE 3.4 6.5 - - - -
125A LEU* 3.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.8 12.6 - - - +
111A ALA* 5.9 3.1 - - + -
112A ALA* 1.3 76.3 - - - +
114A SER* 1.3 66.3 + - - +
115A GLN* 5.8 2.0 - - + -
123A TYR* 3.6 3.5 - - - -
124A ILE* 2.7 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 4.3 4.8 - - - +
113A THR* 1.3 83.5 + - - +
115A GLN* 1.3 69.6 + - - +
121A THR* 4.5 4.0 - - - -
122A TYR 3.4 11.4 - - - -
123A TYR* 3.9 20.6 - - - +
124A ILE* 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A THR* 5.8 2.2 - - + -
114A SER* 1.3 77.6 - - - +
116A LYS* 1.3 71.5 + - - +
117A ALA* 6.0 1.3 - - + -
121A THR* 3.4 4.9 - - - +
122A TYR* 3.0 37.0 + - + +
124A ILE* 3.6 30.7 - - + +
178A SER* 4.2 26.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 5.4 3.6 + - - -
115A GLN* 1.3 80.6 - - - +
117A ALA* 1.3 60.8 + - - +
118A ASP 4.4 7.0 - - - +
119A ASP 5.8 0.7 - - - -
120A LYS 3.2 12.1 - - - +
121A THR* 3.5 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLN* 4.4 1.5 - - + -
116A LYS* 1.3 75.4 - - - +
118A ASP* 1.3 70.7 + - - +
120A LYS* 3.1 24.4 + - - +
122A TYR* 4.0 17.8 + - + -
178A SER 6.1 1.6 - - - +
180A PHE 5.8 2.0 - - - +
181A THR* 6.0 1.6 - - - +
----------------------------------------------------------
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