Contacts of the helix formed by residues 131 - 141 (chain A) in PDB entry 5OA3
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 HIS 131 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13782 A 5.0 10.1 - - - -
127A PRO 4.1 8.7 - - - +
128A ARG 4.0 14.6 + - - -
129A ALA 4.1 10.7 + - - -
130A ASP* 1.3 74.3 - - - +
132A GLN* 1.3 88.7 + - + +
133A PRO 3.5 0.7 - - - -
134A LEU* 3.1 10.7 + - - +
135A THR* 2.9 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13782 A 3.4 44.9 + - - +
103A PHE* 3.6 15.0 - - + +
105A PRO* 3.7 24.3 - - + +
130A ASP* 5.2 1.6 - - + -
131A HIS* 1.3 95.3 + - + +
133A PRO* 1.3 71.2 - - + +
135A THR* 2.8 25.2 + - - +
136A GLU* 3.0 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.8 30.1 - - + -
103A PHE* 3.4 24.9 - - + -
108A PHE* 4.0 1.4 - - + -
122A LEU* 3.9 14.4 - - + +
124A VAL* 4.3 9.4 - - + -
130A ASP* 3.8 35.2 - - + +
131A HIS 3.6 1.6 - - - -
132A GLN* 1.3 95.2 - - + +
134A LEU* 1.3 59.6 + - + +
136A GLU* 3.0 6.6 + - - +
137A ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 4.7 1.1 - - + -
124A VAL* 4.4 16.4 - - + -
127A PRO* 4.0 24.7 - - + +
130A ASP 3.1 26.7 - - - +
131A HIS* 3.1 9.8 + - - +
133A PRO* 1.3 78.4 - - + +
135A THR* 1.3 57.2 + - + +
137A ALA* 2.7 29.5 + - - +
138A SER* 3.0 9.9 + - - -
144A THR* 3.3 33.4 - - + -
146A ALA* 5.6 1.8 - - + -
155A ARG 5.0 5.6 - - - +
156A TYR* 3.9 27.9 - - + +
157A VAL* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13782 A 5.6 0.7 + - - -
131A HIS* 2.9 24.3 + - + +
132A GLN* 2.8 29.9 + - - +
134A LEU* 1.3 76.5 - - + +
136A GLU* 1.3 63.1 + - - +
138A SER* 3.1 17.0 - - - -
139A TYR* 3.0 26.4 - - - -
156A TYR* 4.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13782 A 3.1 23.4 + - - +
103A PHE* 3.9 7.1 - - + -
106A GLY 3.2 20.6 + - - -
108A PHE* 3.5 28.0 - - + +
109A THR* 3.9 21.0 + - + +
132A GLN* 3.0 30.2 + - - +
133A PRO* 3.0 14.4 + - + +
135A THR* 1.3 83.6 + - - +
137A ALA* 1.3 54.4 + - - +
138A SER 3.0 1.8 - - - -
139A TYR* 2.6 34.5 + - - +
140A VAL* 3.0 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 4.5 0.4 - - - -
122A LEU* 4.2 7.0 - - + -
133A PRO 2.9 9.9 + - - +
134A LEU* 2.7 18.4 + - - +
136A GLU* 1.3 71.8 - - - +
138A SER* 1.3 61.1 + - - +
141A ASN* 3.2 20.3 + - - -
142A LEU* 3.4 45.9 + - + +
144A THR* 3.8 12.8 - - - +
156A TYR 5.4 0.7 - - - +
29V HIS 4.3 0.3 - - - +
30V ALA* 5.1 0.3 - - - -
60V ARG* 4.1 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11382 C 5.1 4.3 + - - -
134A LEU 3.0 4.9 + - - -
135A THR* 3.1 20.6 - - - -
137A ALA* 1.3 77.3 - - - +
139A TYR* 1.3 62.4 + - - +
156A TYR* 3.6 43.4 + - - -
29V HIS* 2.7 31.5 - - - +
30V ALA* 3.3 14.1 - - - +
60V ARG* 4.6 2.8 - - - +
61V ARG* 5.3 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11382 C 4.4 18.0 + - - -
13522 G 3.9 22.0 + - - +
13532 A 2.5 31.1 + - - -
13542 G 5.2 0.9 + - - -
109A THR* 3.6 21.8 - - + -
135A THR* 3.0 31.4 - - - -
136A GLU* 2.6 29.3 + - - +
138A SER* 1.3 84.5 - - - +
140A VAL* 1.3 57.8 + - - +
141A ASN 3.5 0.4 - - - -
87C PRO* 4.2 8.5 - - - +
29V HIS* 3.2 29.4 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.7 39.0 - - + +
109A THR* 4.0 12.8 - - + -
118A GLU* 4.4 22.2 - - + +
136A GLU 3.0 17.8 + - - +
137A ALA* 3.5 1.3 + - - +
139A TYR* 1.3 80.6 - - - +
141A ASN* 1.3 74.2 + - - +
142A LEU* 3.6 18.8 - - + +
87C PRO* 4.5 16.5 - - + +
89C LYS* 5.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG 4.7 0.9 - - - +
137A ALA 3.2 7.1 + - - -
140A VAL* 1.3 77.4 - - - +
142A LEU* 1.3 63.5 + - - +
143A PRO* 3.6 9.1 - - - +
84C PHE 4.7 4.0 + - - -
85C SER* 3.1 24.4 + - - +
86C LEU* 4.1 6.8 - - + +
87C PRO* 3.6 16.8 - - - +
28V ASP 3.8 0.8 + - - -
29V HIS* 2.8 29.6 + - - +
30V ALA 5.3 0.2 - - - -
31V SER* 2.5 45.5 + - - +
32V ILE* 4.5 3.2 - - - +
33V GLN 6.2 0.4 - - - +
----------------------------------------------------------
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