Contacts of the helix formed by residues 138 - 148 (chain C) in PDB entry 5I94
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 LEU 138 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C SER* 1.3 82.3 - - - +
139C GLU* 1.3 92.2 + - - +
140C ASP 3.2 1.9 + - - -
141C LEU* 3.1 21.2 + - - +
142C LEU* 3.7 9.5 + - - +
207C ILE* 4.2 20.4 - - + +
211C THR* 4.9 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C SER* 3.1 4.6 + - - -
138C LEU* 1.3 107.7 - - - +
140C ASP* 1.3 64.5 + - - +
142C LEU* 3.7 5.9 - - - +
143C PHE* 3.3 17.5 + - - +
199C PHE* 3.8 10.9 - - - -
200C LYS* 3.6 51.5 + - + +
203C VAL* 4.2 9.9 - - + -
204C GLN* 4.6 12.0 + - - +
207C ILE* 3.5 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PRO* 5.0 11.5 - - + -
137C SER* 2.7 28.1 + - - +
138C LEU 3.2 0.6 - - - -
139C GLU* 1.3 86.6 - - - +
141C LEU* 1.3 63.8 + - - +
142C LEU 3.2 1.1 - - - -
143C PHE* 3.3 7.5 + - - +
144C TYR* 3.3 32.7 + - + -
196C LYS* 3.1 38.2 + - - +
200C LYS* 3.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PRO* 4.5 5.1 - - + -
137C SER* 3.2 20.2 - - - +
138C LEU* 3.1 37.2 - - - +
140C ASP* 1.3 76.4 - - - +
142C LEU* 1.3 52.3 + - - +
144C TYR* 3.2 9.0 + - - +
145C THR* 2.7 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU 3.7 7.7 + - - +
139C GLU 3.7 8.7 - - - +
140C ASP 3.2 0.4 - - - -
141C LEU* 1.3 80.6 - - - +
143C PHE* 1.3 60.0 + - - +
145C THR* 3.0 19.2 + - - +
146C ILE* 3.2 35.6 - - + +
158C PHE* 5.2 1.3 - - + -
199C PHE* 3.5 20.9 - - + -
203C VAL* 3.7 17.7 - - + -
207C ILE* 3.5 26.5 - - + -
210C LEU* 4.4 14.6 - - + +
211C THR* 5.0 7.6 - - + +
214C PHE* 4.1 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C GLU 3.3 8.2 + - - +
140C ASP* 3.6 10.3 - - - +
141C LEU 3.2 0.8 - - - -
142C LEU* 1.3 79.9 - - - +
144C TYR* 1.3 84.8 + + - +
146C ILE 3.3 1.0 + - - -
147C ALA* 2.9 41.7 + - + +
150C GLN 5.6 0.4 - - - -
151C GLU 4.5 14.4 - - - -
152C LYS* 4.5 2.2 - - + -
153C ILE* 3.5 36.9 - - + +
194C LEU 3.9 10.1 - - - -
195C ASP 3.9 1.6 - - - -
196C LYS* 3.4 54.3 - - + +
199C PHE* 3.7 27.3 - + + -
200C LYS* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C PRO* 6.0 6.3 - - + -
140C ASP* 3.3 20.8 + - + -
141C LEU* 3.2 8.9 + - - +
143C PHE* 1.3 98.5 - + - +
145C THR* 1.3 61.1 + - + +
147C ALA* 4.4 4.7 - - + -
148C GLU* 2.9 28.8 + - - -
149C GLY* 3.9 10.6 + - - +
196C LYS* 3.7 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 2.7 25.1 + - + +
142C LEU* 3.0 21.7 + - - +
144C TYR* 1.3 75.3 - - + +
146C ILE* 1.3 62.5 + - - +
148C GLU* 4.1 11.6 - - - +
214C PHE* 6.0 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU* 3.2 39.0 - - + +
143C PHE 3.3 0.8 + - - -
145C THR* 1.3 81.8 + - - +
147C ALA* 1.3 66.1 + - - +
148C GLU* 3.1 14.3 + - - +
153C ILE* 3.9 25.1 - - + +
157C LYS* 5.1 8.4 - - + +
158C PHE* 3.6 38.8 - - + +
161C ALA* 5.1 8.1 - - + -
199C PHE* 3.9 9.0 - - + -
214C PHE* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C PHE* 2.9 33.5 + - + +
144C TYR* 4.4 3.1 - - + +
146C ILE* 1.3 77.4 - - - +
148C GLU* 1.3 59.5 + - - +
149C GLY* 4.2 6.1 - - - +
150C GLN* 2.8 42.4 + - - +
152C LYS 4.1 10.1 - - - +
153C ILE* 3.8 22.8 - - + +
154C PRO* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C TYR 2.9 14.2 + - - -
145C THR 4.1 11.3 - - - +
146C ILE 3.1 14.1 - - - +
147C ALA* 1.3 78.3 - - - +
149C GLY* 1.3 59.1 + - - +
150C GLN* 3.1 9.7 + - + +
----------------------------------------------------------
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