Contacts of the strand formed by residues 121 - 126 (chain A) in PDB entry 1XR9
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 LYS 121 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA* 3.1 3.2 - - - -
118A TYR* 2.9 31.0 + - - +
119A ASP* 4.2 2.9 - - + +
120A GLY* 1.3 84.2 - - - +
122A ASP* 1.3 70.5 + - - +
123A TYR* 4.1 0.5 - - - +
1B ILE* 3.7 35.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLN* 4.3 8.8 - - - +
116A SER 3.9 4.2 - - - +
117A ALA* 4.2 2.0 - - - +
120A GLY 4.2 1.0 + - - -
121A LYS* 1.3 77.1 - - - +
123A TYR* 1.3 60.8 + - - +
124A ILE 5.5 0.2 - - - +
136A ALA* 3.2 22.2 - - + +
137A ASP* 5.3 1.9 - - - +
60B TRP* 2.7 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.2 24.1 - - + +
84A TYR* 3.2 14.2 - - - -
85A TYR* 3.3 27.1 - + - -
95A LEU* 5.4 1.3 - - + -
116A SER* 2.9 17.3 + - - +
117A ALA* 3.9 12.1 - - - -
118A TYR* 4.0 14.4 - - + +
121A LYS 4.1 0.4 - - - +
122A ASP* 1.3 75.8 - - - +
124A ILE* 1.3 68.5 + - + +
136A ALA* 2.9 28.4 + - - -
137A ASP* 4.6 0.9 - - - -
139A ALA 3.1 14.4 + - - -
140A ALA* 3.0 31.9 - - + +
143A THR* 2.8 34.7 + - + -
9C TYR* 3.7 23.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLN* 3.6 0.9 - - - +
116A SER* 2.8 35.1 + - - +
122A ASP* 5.5 0.6 - - - +
123A TYR* 1.3 97.6 - - + +
125A ALA* 1.3 65.3 + - - +
133A TRP* 4.1 18.2 - - + -
134A THR 3.4 15.3 - - - +
135A ALA* 4.3 3.4 - - - -
140A ALA* 4.0 5.6 - - + +
143A THR* 4.0 3.4 - - + -
144A GLN* 3.8 38.8 - - + +
147A TRP* 3.4 43.1 - - + -
9C TYR* 4.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP 3.5 8.7 - - - +
115A GLN* 4.1 16.8 - - + +
124A ILE* 1.3 75.6 - - - +
126A LEU* 1.3 67.2 + - - +
127A ASN* 3.5 1.1 + - - +
133A TRP* 3.3 9.0 - - - -
134A THR* 2.8 41.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
111A ARG* 4.4 8.3 + - - -
113A HIS* 5.6 0.3 - - - -
114A ASP* 2.8 34.3 + - + +
115A GLN* 5.5 1.4 - - - +
125A ALA* 1.3 76.1 - - - +
127A ASN* 1.3 72.0 + - - +
130A LEU* 3.8 42.6 - - + -
132A SER 3.5 15.7 - - - +
133A TRP* 3.4 35.5 - - + -
153A ALA* 4.0 9.0 - - + -
156A TRP* 3.7 27.4 - - + -
160A LEU* 3.8 9.9 - - + -
----------------------------------------------------------
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