Contacts of the helix formed by residues 139 - 147 (chain H) in PDB entry 5EIG
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 LYS 139 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H ASP* 3.3 37.8 + - - +
137H CYS 3.3 2.1 - - - -
138H SER* 1.3 83.8 + - - +
140H ILE* 1.3 64.9 + - - +
141H LYS 3.4 2.9 - - - +
142H LEU* 3.2 30.1 + - + +
143H LEU* 3.8 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H CYS 4.1 16.4 - - - +
138H SER 4.1 9.2 - - - +
139H LYS* 1.3 68.7 - - - +
141H LYS* 1.3 64.9 + - + +
142H LEU 3.2 0.6 + - - -
143H LEU* 3.5 16.3 + - + +
144H GLU* 3.7 22.5 + - - +
168H ASP* 5.9 6.1 - - + +
171H GLY* 5.6 1.6 - - - -
172H CYS* 5.4 7.6 - - + +
175H ILE* 3.5 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H LYS* 3.3 1.6 + - + +
140H ILE* 1.3 82.2 - - + +
142H LEU* 1.3 65.5 + - + +
143H LEU 3.3 0.2 - - - -
144H GLU* 3.8 9.5 + - - +
145H ALA* 3.4 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H VAL* 3.5 16.9 - - + +
136H ASP* 3.9 31.9 - - + +
139H LYS* 3.2 28.8 + - + +
141H LYS* 1.3 80.2 - - + +
143H LEU* 1.3 62.3 + - - +
145H ALA* 3.7 7.1 + - + +
146H ALA* 3.4 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H ILE* 4.0 22.7 - - + -
135H VAL* 4.0 6.9 - - + +
137H CYS* 3.7 34.3 - - + +
139H LYS 3.8 4.9 + - - +
140H ILE* 3.5 13.6 + - + +
141H LYS 3.3 0.4 - - - -
142H LEU* 1.3 79.4 - - - +
144H GLU* 1.3 59.0 + - - +
146H ALA* 3.2 4.7 + - - +
147H ILE* 3.0 40.3 + - + +
154H VAL* 4.4 9.0 - - + -
172H CYS* 3.6 29.8 - - + -
175H ILE* 4.0 25.8 - - + -
176H VAL* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H ILE* 3.7 20.7 + - - +
141H LYS* 4.3 9.4 - - - +
142H LEU 3.4 0.2 - - - -
143H LEU* 1.3 72.4 - - - +
145H ALA* 1.3 64.7 + - - +
146H ALA 3.1 1.8 - - - -
147H ILE* 3.3 24.2 + - - +
175H ILE* 3.6 33.7 - - + +
178H LYS* 4.4 15.6 + - - +
179H HIS* 5.0 17.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H LYS 3.4 17.5 + - - +
142H LEU* 4.0 9.4 - - + +
143H LEU 3.3 0.6 - - - -
144H GLU* 1.3 79.5 - - - +
146H ALA* 1.3 59.7 + - - +
147H ILE 4.3 3.1 - - - +
148H THR* 5.1 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H GLN* 3.4 21.4 + - - +
108H ILE* 3.7 12.5 - - + +
133H SER* 4.6 5.4 - - - +
135H VAL* 3.6 26.0 - - + -
142H LEU 3.4 15.7 + - - +
143H LEU 3.2 5.9 + - - +
144H GLU 3.1 0.2 - - - -
145H ALA* 1.3 80.7 - - - +
147H ILE* 1.3 63.8 + - - +
148H THR* 3.4 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H ILE* 3.6 14.1 - - + -
143H LEU* 3.0 37.1 + - + +
144H GLU* 3.3 16.8 + - - +
145H ALA 4.3 2.3 - - - +
146H ALA* 1.3 78.1 - - - +
148H THR* 1.3 71.3 + - - +
151H THR* 3.6 4.5 - - - +
154H VAL* 5.2 1.1 - - + -
175H ILE* 4.3 17.0 - - + -
176H VAL* 4.4 19.5 - - + -
179H HIS* 3.1 34.7 + - + +
182H ILE* 3.8 23.8 - - + -
----------------------------------------------------------
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