Contacts of the helix formed by residues 123 - 135 (chain B) in PDB entry 4O8M
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 123 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS 3.4 7.3 + - - -
120B LEU* 2.7 27.8 + - - +
121B LEU 3.5 0.4 - - - -
122B HIS* 1.3 83.4 - - - +
124B ASP* 1.3 59.5 + - - +
125B TRP* 3.5 15.0 - - - +
126B PHE* 3.2 14.4 + - - +
127B LYS* 2.9 26.8 + - - +
324B LYS* 5.9 2.0 - - - -
328B PHE* 5.2 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B HIS 5.3 0.2 - - - +
123B SER* 1.3 70.9 - - - +
125B TRP* 1.3 67.2 + - - +
127B LYS* 3.5 22.1 - - - +
128B ASP* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASP* 3.9 7.2 + - - -
104B VAL* 3.6 26.0 - - + -
105B ILE* 4.1 14.6 - - + -
120B LEU* 3.7 35.7 - - + -
123B SER* 3.5 8.9 + - - +
124B ASP* 1.3 81.0 - - - +
126B PHE* 1.3 84.7 - + + +
128B ASP* 3.6 6.5 + - - +
129B LEU* 3.5 49.7 + - + +
317B LEU* 4.2 16.5 - - + +
320B ASN* 4.7 4.5 - - - +
321B VAL* 3.7 19.2 - - + +
324B LYS* 3.8 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 3.5 31.0 - + - -
102B LEU* 3.9 16.2 - - + -
105B ILE* 3.9 8.1 - - + -
120B LEU 3.5 21.5 - - - +
121B LEU* 3.4 38.1 - - + -
122B HIS* 5.4 0.2 - - - -
123B SER* 3.2 6.8 + - - +
125B TRP* 1.3 88.6 - + + +
127B LYS* 1.3 71.8 + - - +
129B LEU* 2.9 5.8 + - + +
130B SER* 2.9 30.4 + - - -
140B ILE* 3.8 21.1 - - + -
143B PRO* 3.6 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B HIS 4.6 11.1 + - - -
123B SER 2.9 12.5 + - - +
124B ASP* 3.2 28.0 + - - +
126B PHE* 1.3 81.3 - - - +
128B ASP* 1.3 59.9 + - - +
130B SER* 3.3 7.7 + - - -
131B ASP* 3.0 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 2.9 26.5 + - - +
125B TRP* 3.9 6.4 + - - +
127B LYS* 1.3 82.0 - - - +
129B LEU* 1.3 62.8 + - + +
131B ASP* 3.5 14.4 + - - +
132B LYS* 3.2 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.0 16.8 - - + +
101B ASP* 3.9 35.9 - - + +
102B LEU* 3.7 23.7 - - + +
125B TRP* 3.5 55.8 + - + +
126B PHE* 2.9 8.5 + - - +
128B ASP* 1.3 76.1 - - + +
130B SER* 1.3 65.6 + - - +
132B LYS* 3.2 23.2 + - + +
133B LEU* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 5.0 0.6 - - - +
126B PHE* 2.9 28.8 + - - -
127B LYS* 3.5 11.0 - - - -
129B LEU* 1.3 77.6 - - - +
131B ASP* 1.3 64.9 + - - +
133B LEU* 3.3 8.6 + - - +
134B ASP* 3.0 31.1 + - - +
139B HIS* 4.5 9.4 + - - -
140B ILE* 4.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LYS* 3.0 34.1 + - - +
128B ASP* 3.7 13.2 - - - +
129B LEU 3.3 0.2 - - - -
130B SER* 1.3 78.0 + - - +
132B LYS* 1.3 63.1 + - + +
134B ASP* 3.4 27.0 + - - +
135B GLN* 3.6 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.1 17.5 - - + +
128B ASP* 3.2 20.2 + - - +
129B LEU* 3.2 28.3 + - + +
131B ASP* 1.3 77.5 - - + +
133B LEU* 1.3 61.7 + - - +
135B GLN* 3.2 17.6 + - - +
136B HIS* 3.3 17.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.2 11.7 - - + -
98B ILE* 3.7 39.3 - - + -
99B VAL* 3.7 12.7 - - + +
102B LEU* 4.1 14.6 - - + -
129B LEU 3.0 13.0 + - - +
130B SER* 3.6 8.5 - - - +
132B LYS* 1.3 77.1 - - - +
134B ASP* 1.3 57.1 + - - +
136B HIS* 2.8 21.9 + - - +
137B ASP 3.3 5.2 + - - -
138B ILE* 3.1 37.5 + - + +
140B ILE* 3.7 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B SER* 3.0 21.6 + - - +
131B ASP* 3.5 19.8 - - - +
132B LYS 3.3 0.2 - - - -
133B LEU* 1.3 75.7 - - - +
135B GLN* 1.3 63.3 + - + +
136B HIS 3.1 0.2 - - - -
137B ASP* 2.9 17.2 + - - +
138B ILE 3.4 6.2 - - - +
139B HIS* 2.7 46.3 + - - -
243B THR* 3.2 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASP 3.7 15.0 + - - +
132B LYS* 3.2 11.2 + - - +
133B LEU 3.1 0.8 - - - -
134B ASP* 1.3 81.2 - - - +
136B HIS* 1.3 62.9 + - + +
137B ASP* 3.2 9.2 + - - +
----------------------------------------------------------
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