Contacts of the helix formed by residues 154 - 164 (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 PRO 154 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ALA* 6.5 0.2 - - - -
150C GLN* 6.5 0.7 - - + -
152C LYS 4.1 5.2 - - - +
153C ILE* 1.3 94.5 - - + +
155C VAL* 1.3 65.0 + - - +
156C HIS* 3.2 32.5 - - + +
157C LYS* 3.0 31.7 + - + +
158C PHE 3.4 1.6 + - - -
192C VAL 4.0 7.2 - - - +
193C MET* 4.2 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ILE 3.5 0.8 + - - -
154C PRO* 1.3 70.8 - - - +
156C HIS* 1.3 66.3 + - - +
158C PHE* 3.2 12.9 + - + +
159C ILE* 3.2 25.3 + - + +
181C LEU* 4.5 12.8 - - + -
185C LEU* 3.7 34.5 - - + -
192C VAL* 3.3 21.3 + - + +
194C LEU* 3.7 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C PRO* 3.2 31.8 - - + +
155C VAL* 1.3 84.2 - - + +
157C LYS* 1.3 81.8 + - + +
159C ILE* 4.0 5.6 - - - +
160C THR* 3.0 29.1 + - - +
192C VAL* 5.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ILE* 5.1 9.9 - - + +
153C ILE* 4.8 3.6 - - + -
154C PRO* 3.0 32.2 + - + +
156C HIS* 1.3 92.9 - - + +
158C PHE* 1.3 57.7 + - - +
160C THR* 3.5 19.6 + - - +
161C ALA* 3.1 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU* 5.2 1.6 - - + -
146C ILE* 3.6 31.0 - - + -
153C ILE* 4.4 12.1 - - + +
154C PRO 3.4 6.5 + - - +
155C VAL* 3.2 10.8 + - + +
157C LYS* 1.3 78.4 - - - +
159C ILE* 1.3 77.4 + - + +
161C ALA* 3.5 4.7 + - - +
162C LEU* 3.0 31.2 + - + +
177C CYS* 4.5 3.1 - - - -
178C MET* 4.2 8.5 - - + -
181C LEU* 3.8 27.6 - - + -
194C LEU* 4.9 5.6 - - + -
199C PHE* 3.9 22.0 - + - -
203C VAL* 4.1 17.9 - - + -
210C LEU* 4.5 17.9 - - + -
214C PHE* 4.3 14.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 3.2 26.8 + - + +
156C HIS* 3.5 5.6 + - - +
157C LYS 3.4 0.2 - - - -
158C PHE* 1.3 95.1 - - + +
160C THR* 1.3 65.7 + - - +
162C LEU* 3.7 7.4 - - + +
163C LYS* 3.0 52.1 + - + +
169C THR* 4.3 10.8 - - - +
178C MET* 4.0 23.8 - - + -
181C LEU* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C HIS 3.0 19.9 + - - -
157C LYS* 3.7 20.6 - - - +
159C ILE* 1.3 74.1 - - - +
161C ALA* 1.3 67.8 + - - +
162C LEU 3.2 0.2 + - - -
163C LYS* 3.2 11.6 + - - +
164C SER* 3.2 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ILE* 5.1 8.3 - - + -
157C LYS* 3.1 19.3 + - - +
158C PHE* 3.7 6.1 - - - +
159C ILE 3.4 0.2 - - - -
160C THR* 1.3 80.0 - - - +
162C LEU* 1.3 60.3 + - - +
164C SER* 2.8 22.2 + - - -
165C THR* 3.5 11.3 - - - +
214C PHE* 3.4 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PHE* 3.0 23.9 + - + +
159C ILE* 3.7 13.0 - - + +
160C THR 3.1 0.2 - - - -
161C ALA* 1.3 75.4 - - - +
163C LYS* 1.3 62.3 + - + +
165C THR* 2.6 34.3 + - - +
166C GLY 3.8 0.9 + - - -
167C LEU* 4.0 26.5 - - + +
168C ARG 4.9 5.6 - - - +
169C THR* 5.0 5.8 - - - +
174C LEU* 4.1 19.1 - - + -
178C MET* 4.1 22.4 - - + -
210C LEU* 3.6 27.1 - - + -
213C ALA* 5.1 0.7 - - + -
214C PHE* 3.7 17.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ILE* 3.0 43.8 + - + +
160C THR* 3.2 8.7 + - - +
162C LEU* 1.3 76.9 - - + +
164C SER* 1.3 57.6 + - - +
166C GLY* 3.1 18.6 + - - -
167C LEU 3.6 15.0 - - - +
168C ARG* 5.7 0.7 - - - -
169C THR* 4.8 19.3 - - - +
224C MET* 3.7 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C THR* 3.2 13.5 + - - -
161C ALA* 2.8 22.0 + - - -
162C LEU 3.1 0.2 - - - -
163C LYS* 1.3 73.1 - - - +
165C THR* 1.3 59.2 + - - +
166C GLY 3.1 5.7 + - - -
223C PHE* 4.4 6.2 + - - +
224C MET* 3.6 39.6 + - - +
----------------------------------------------------------
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