Contacts of the helix formed by residues 119 - 130 (chain A) in PDB entry 1AAY
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 119 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR* 3.5 39.4 + - - -
118A ARG* 1.3 73.8 - - - +
120A ASP* 1.3 64.1 + - - +
122A LEU* 3.1 14.2 + - - +
123A THR* 3.1 17.2 + - - -
51C T 3.3 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ARG* 2.9 52.0 + - - +
119A SER* 1.3 80.7 + - - +
121A GLU* 1.3 58.8 + - - +
123A THR* 3.4 4.4 + - - -
124A ARG* 3.0 29.1 + - - +
9B C 4.4 4.9 + - - -
51C T 3.6 38.1 - - + +
52C A 3.8 24.4 + - + +
53C C 4.3 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 3.7 23.2 - - + -
117A SER* 3.0 20.1 + - - -
118A ARG* 2.9 42.2 + - + +
119A SER 3.2 0.4 - - - -
120A ASP* 1.3 80.4 - - - +
122A LEU* 1.3 57.4 + - - +
124A ARG* 3.6 15.9 + - - +
125A HIS* 3.1 28.8 + - - +
7B G 5.6 0.3 - - - +
8B G 3.5 35.5 + - - +
9B C 3.5 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR* 4.0 33.2 - - + -
106A ALA 3.8 14.4 - - - +
107A CYS* 3.8 28.5 - - + +
108A PRO* 4.4 4.3 - - + -
116A PHE* 3.9 21.3 - - + -
118A ARG 3.5 2.2 + - - -
119A SER* 3.1 10.6 + - - +
121A GLU* 1.3 77.1 - - - +
123A THR* 1.3 60.9 + - - +
125A HIS* 3.3 2.0 + - + +
126A ILE* 2.8 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 3.1 13.5 + - - -
120A ASP* 3.8 10.1 - - - -
121A GLU 3.4 0.2 - - - -
122A LEU* 1.3 78.6 - - - +
124A ARG* 1.3 61.8 + - - +
126A ILE* 3.5 19.3 + - + +
127A ARG* 3.8 22.3 + - - +
51C T 4.1 17.1 + - - +
52C A 4.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 6.2 1.2 - - - -
120A ASP 3.0 17.2 + - - +
121A GLU* 3.9 14.0 + - - +
122A LEU 3.3 0.2 - - - -
123A THR* 1.3 75.4 - - - +
125A HIS* 1.3 63.3 + - - +
127A ARG* 3.3 43.2 + - - +
128A ILE* 4.5 2.1 + - - +
145A SER* 6.0 0.3 - - - -
146A ARG* 3.6 47.1 - - + +
6B G 6.2 0.4 - - - +
7B G 3.4 18.6 - - - +
8B G 2.7 52.5 + - - -
9B C 3.5 16.2 - - - +
54C G 3.7 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A CYS* 3.5 12.0 - - + +
112A CYS* 3.6 1.7 - - - -
114A ARG* 3.5 22.4 - - + +
116A PHE* 3.4 27.0 - + + -
121A GLU 3.1 19.7 + - - +
122A LEU* 3.6 5.2 - - + +
124A ARG* 1.3 74.2 - - - +
126A ILE* 1.3 68.2 + - - +
127A ARG 3.0 2.5 - - - -
128A ILE* 3.0 48.5 + - + +
129A HIS* 3.2 0.6 + - - -
201A ZN 2.1 37.5 - - - -
7B G 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A CYS* 4.2 13.0 - - - -
108A PRO* 4.0 33.2 - - + -
109A VAL* 5.1 3.1 - - + -
122A LEU* 2.8 36.3 + - + +
123A THR* 3.5 12.6 - - + +
124A ARG 3.3 0.2 - - - -
125A HIS* 1.3 77.0 - - - +
127A ARG* 1.3 59.7 + - + +
129A HIS* 2.9 28.9 + - + +
130A THR* 3.1 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A THR* 3.8 15.4 + - - +
124A ARG* 3.3 47.6 + - - +
125A HIS 3.0 1.4 + - - -
126A ILE* 1.3 78.9 - - + +
128A ILE* 1.3 56.7 + - + +
130A THR* 3.5 8.3 - - - +
131A GLY* 2.9 27.4 + - - -
132A GLN* 3.6 34.0 + - + +
134A PRO* 3.9 21.1 - - - +
135A PHE* 5.6 3.7 - - - -
145A SER* 3.5 31.8 + - - -
146A ARG* 5.4 0.8 - - - +
52C A 4.6 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A CYS* 5.5 0.7 - - - -
124A ARG 5.1 1.8 - - - +
125A HIS* 3.0 43.6 + - + +
127A ARG* 1.3 78.2 - - + +
129A HIS* 1.3 83.2 + - + +
131A GLY* 4.1 4.9 + - - -
145A SER* 6.4 0.7 - - - -
6B G 3.4 52.0 - - - +
7B G 5.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A CYS* 3.4 11.8 - - - -
109A VAL* 3.6 27.8 - - + +
111A SER* 5.2 1.8 - - - -
112A CYS* 3.6 16.8 - - + -
125A HIS* 3.2 10.9 + + - -
126A ILE* 2.9 14.8 + - + +
128A ILE* 1.3 97.7 + - + +
130A THR* 1.3 65.5 + - + +
131A GLY 3.3 0.8 + - - -
201A ZN 1.9 36.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE* 3.1 26.2 + - + +
127A ARG* 3.5 12.0 - - - +
129A HIS* 1.3 77.6 - - + +
131A GLY* 1.3 61.5 + - - +
132A GLN* 3.1 23.6 + - - +
----------------------------------------------------------
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