Contacts of the helix formed by residues 135 - 145 (chain A) in PDB entry 4O8H
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 GLY 135 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG 3.5 17.9 - - - -
20A VAL* 4.0 2.5 - - - +
132A VAL* 4.2 3.6 - - - -
134A GLU* 1.3 79.1 + - - +
136A MET* 1.3 67.6 + - - +
137A ASP* 3.1 16.9 + - - -
138A VAL* 2.9 16.4 + - - +
139A VAL* 3.1 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 4.1 13.9 - - + -
96A GLY* 3.9 24.2 - - - +
115A CYS 3.9 17.5 - - - +
116A THR* 4.4 7.4 - - + -
132A VAL* 3.9 13.6 - - + +
134A GLU* 3.6 2.2 - - - +
135A GLY* 1.3 76.4 - - - +
137A ASP* 1.3 55.8 + - - +
139A VAL* 3.1 35.6 + - + +
140A LYS* 2.8 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 4.9 3.5 - - - +
135A GLY* 3.4 17.2 + - - -
136A MET* 1.3 78.7 - - - +
138A VAL* 1.3 74.7 + - - +
140A LYS* 3.4 7.9 + - - +
141A LYS* 3.0 27.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
10A VAL* 4.4 5.2 - - + -
17A LEU* 3.5 39.7 - - + +
18A GLY* 3.9 7.9 - - - +
19A ARG 3.8 24.2 - - - +
20A VAL* 3.7 20.0 - - + -
135A GLY 2.9 8.3 + - - +
137A ASP* 1.3 87.0 - - - +
139A VAL* 1.3 65.5 + - - +
141A LYS* 3.1 8.8 + - - +
142A ILE* 2.9 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.0 20.4 - - + -
62A CYS* 3.9 9.3 - - - -
114A ILE* 4.0 31.6 - - + -
116A THR* 3.9 16.6 - - + -
132A VAL* 4.4 1.6 - - + -
135A GLY 3.1 12.2 + - - +
136A MET* 3.1 38.1 + - + +
138A VAL* 1.3 77.0 - - - +
140A LYS* 1.3 56.9 + - - +
142A ILE* 3.2 11.7 + - + +
143A GLU* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A THR* 4.6 11.5 + - + -
136A MET* 2.8 46.0 + - + +
137A ASP* 3.8 6.7 - - - +
138A VAL 3.3 0.2 - - - -
139A VAL* 1.3 69.6 - - - +
141A LYS* 1.3 66.1 + - - +
143A GLU* 2.8 32.8 + - - +
144A SER* 3.0 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.2 28.9 - - + +
137A ASP* 3.0 20.4 + - + +
138A VAL* 3.1 9.2 + - - +
140A LYS* 1.3 75.8 - - - +
142A ILE* 1.3 62.6 + - - +
144A SER* 2.7 25.7 + - - +
145A PHE* 3.2 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.0 21.1 - - + -
17A LEU* 4.0 15.5 - - + -
20A VAL* 5.1 3.6 - - + -
53A PHE* 4.1 30.3 - - + -
56A VAL* 3.4 21.8 - - + +
62A CYS* 3.7 23.3 - - + -
138A VAL* 2.9 28.5 + - + +
139A VAL* 3.5 13.9 - - + +
141A LYS* 1.3 75.4 - - - +
143A GLU* 1.3 64.4 + - - +
145A PHE* 2.9 25.7 + - - +
156A ILE* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 3.6 11.5 - - - +
57A ILE 4.5 3.1 - - - +
58A PRO* 3.5 29.2 - - + +
59A SER* 2.8 21.9 + - - -
62A CYS* 3.7 8.2 - - - -
116A THR* 2.8 34.8 + - + +
139A VAL 2.8 17.0 + - - +
140A LYS* 2.8 41.5 + - - +
141A LYS 3.2 0.2 - - - -
142A ILE* 1.3 76.8 - - - +
144A SER* 1.3 58.6 + - - +
145A PHE 3.1 0.2 - - - -
146A GLY* 3.0 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 5.3 3.9 - - - +
140A LYS 3.0 13.5 + - - -
141A LYS* 2.7 24.4 + - - +
143A GLU* 1.3 75.7 - - - +
145A PHE* 1.3 75.8 + - - +
146A GLY 3.3 5.0 + - - +
153A SER* 4.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 3.9 11.4 - - + -
17A LEU* 4.4 4.5 - - + -
56A VAL* 4.7 0.7 - - - -
141A LYS* 3.2 50.0 - - + -
142A ILE* 2.9 11.3 + - - +
144A SER* 1.3 91.3 - - - +
146A GLY* 1.3 60.1 + - - +
152A THR* 3.2 6.8 - - - -
153A SER* 2.8 42.0 + - - +
154A LYS* 3.5 48.5 - - + +
156A ILE* 3.6 31.9 - - + -
----------------------------------------------------------
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