Contacts of the helix formed by residues 133 - 147 (chain A) in PDB entry 1XYY
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 ALA 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 3.7 31.9 - - + -
127A ASP 5.7 1.3 - - - +
129A ASP 3.9 1.1 + - - +
130A PRO* 2.8 12.4 + - + +
132A ALA* 1.3 79.6 - - - +
134A ARG* 1.3 63.9 + - - +
135A ASP 3.4 2.2 - - - -
136A ASP* 2.9 34.5 + - + +
137A ILE* 3.1 13.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 3.4 26.1 + - + +
21A THR* 3.8 15.7 - - + +
130A PRO 3.5 3.5 + - - -
131A ARG 3.8 9.2 + - - +
132A ALA 3.5 3.8 + - - -
133A ALA* 1.3 75.9 - - - +
135A ASP* 1.3 74.8 + - - +
137A ILE* 3.2 4.9 + - - +
138A VAL* 3.0 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ALA 3.4 0.4 - - - -
134A ARG* 1.3 86.9 + - - +
136A ASP* 1.3 60.1 + - - +
138A VAL* 4.3 6.5 - - - -
139A GLY* 2.7 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 4.1 15.6 - - + +
133A ALA* 2.9 26.7 + - + +
135A ASP* 1.3 79.3 - - - +
137A ILE* 1.3 56.2 + - - +
139A GLY* 3.7 0.6 - - - -
140A TRP* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 4.3 10.5 - - + -
18A THR* 3.8 26.5 - - + +
21A THR* 3.6 22.0 - - + -
22A ILE* 3.6 27.6 - - + +
124A LEU* 3.8 9.6 - - + -
126A ILE* 3.7 25.6 - - + -
130A PRO 3.9 17.0 - - - +
133A ALA 3.1 15.3 + - - +
134A ARG* 3.7 6.5 - - - +
136A ASP* 1.3 71.4 - - - +
138A VAL* 1.3 68.8 + - - +
140A TRP* 3.0 5.0 + - - +
141A ALA* 2.8 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.8 13.5 - - + +
24A ARG* 6.5 1.1 - - + -
25A GLU* 4.0 27.8 - - + +
134A ARG* 3.0 48.9 + - - +
135A ASP* 3.9 5.8 - - - +
137A ILE* 1.3 80.3 - - - +
139A GLY* 1.3 65.7 + - - +
141A ALA* 3.2 3.3 + - - +
142A HIS* 3.0 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASP 2.7 22.7 + - - -
136A ASP 3.8 0.4 - - - -
138A VAL* 1.3 77.2 - - - +
140A TRP* 1.3 62.4 + - - +
142A HIS* 3.4 5.5 + - - +
143A ASP* 3.0 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.9 27.4 - - + -
54A LEU* 4.5 13.0 - - + -
89A ALA* 3.6 31.6 - - + -
90A CYS 3.4 29.4 - - - -
91A PHE* 4.2 7.6 - + + -
121A GLN* 3.9 16.8 + - + +
122A ASP 2.9 24.8 + - - -
123A GLY 4.8 0.4 - - - -
124A LEU* 3.6 41.6 - - + +
136A ASP 2.8 21.7 + - - +
137A ILE 3.0 3.1 + - - +
139A GLY* 1.3 73.8 - - - +
141A ALA* 1.3 63.1 + - - +
143A ASP* 3.5 6.8 + - - +
144A VAL* 2.7 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.0 25.6 - - + +
25A GLU* 3.5 20.0 - - + +
26A LEU* 4.0 13.6 - - + +
137A ILE 2.8 16.7 + - - +
138A VAL 3.8 5.2 - - - +
140A TRP* 1.3 72.0 - - - +
142A HIS* 1.3 61.4 + - - +
144A VAL* 3.0 11.5 - - - +
145A ARG* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 3.0 19.2 + - + +
138A VAL* 3.0 15.7 + - + +
139A GLY* 3.9 6.1 - - - +
140A TRP 3.3 0.2 - - - -
141A ALA* 1.3 76.9 - - - +
143A ASP* 1.3 68.9 + - - +
145A ARG* 3.3 25.8 + - - +
146A GLY* 2.7 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 3.1 29.1 + - - +
139A GLY* 3.0 21.6 + - - +
140A TRP* 3.9 4.4 - - - +
142A HIS* 1.3 91.3 + - - +
144A VAL* 1.3 59.9 + - - +
146A GLY* 3.2 4.3 + - - +
147A ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 5.5 1.1 - - + -
52A LEU* 3.9 25.8 - - + -
54A LEU* 4.3 15.3 - - + -
89A ALA* 4.6 3.6 - - + -
120A VAL* 4.2 16.3 - - + +
121A GLN* 4.4 17.0 - - + +
140A TRP* 2.7 42.7 + - + +
141A ALA* 3.0 22.4 - - + +
143A ASP* 1.3 71.4 - - - +
145A ARG* 1.3 66.9 + - + +
146A GLY 2.9 0.7 - - - -
147A ALA* 3.0 17.3 + - - +
148A ILE* 3.4 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 2.8 39.6 + - - -
26A LEU* 3.8 15.5 - - + -
29A ALA* 3.4 33.2 - - - +
31A TYR* 3.7 31.6 - - + -
52A LEU* 5.5 1.1 - - + -
141A ALA 2.8 13.1 + - - +
142A HIS* 3.6 26.0 + - - +
144A VAL* 1.3 75.8 - - - +
146A GLY* 1.3 60.3 + - - +
148A ILE* 2.7 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A HIS* 2.7 19.6 + - - -
143A ASP* 3.2 9.1 + - - -
144A VAL 2.9 0.4 - - - -
145A ARG* 1.3 79.4 - - - +
147A ALA* 1.3 56.1 + - - +
148A ILE 3.3 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 5.2 1.7 - - - -
118A GLU* 5.0 2.3 - - - +
120A VAL* 3.1 40.3 - - + +
121A GLN* 4.1 5.4 - - - +
143A ASP 2.9 13.3 + - - +
144A VAL* 3.0 8.3 + - - +
146A GLY* 1.3 73.6 - - - +
148A ILE* 1.3 65.1 + - - +
----------------------------------------------------------
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