Contacts of the helix formed by residues 195 - 205 (chain C) in PDB entry 5C16
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 195 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 1.3 91.1 - - - +
196C ILE* 1.3 61.8 + - - -
197C PHE* 3.0 3.4 - - - -
198C GLU* 3.1 14.4 + - - -
199C ASN* 3.0 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ALA* 6.2 1.3 - - + -
110C VAL* 4.0 31.6 - - + -
113C VAL* 5.3 3.4 - - + -
127C LEU* 3.9 27.8 - - + -
129C VAL* 5.6 3.8 - - + -
172C ILE* 4.4 7.0 - - + -
184C LEU* 4.2 15.9 - - + -
186C TYR* 3.3 41.6 + - + +
194C LEU* 3.6 8.5 - - + +
195C GLY* 1.3 73.4 - - - +
197C PHE* 1.3 60.5 + - - +
199C ASN* 3.7 6.0 - - - +
200C LEU* 2.9 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C VAL* 3.5 35.6 - - + +
158C GLU* 4.5 1.3 - - - -
159C LYS* 4.5 15.9 - - + -
172C ILE* 3.6 31.2 - - + -
186C TYR* 4.4 5.5 + - - +
195C GLY* 3.0 0.6 - - - -
196C ILE* 1.3 80.5 - - - +
198C GLU* 1.3 89.7 + - + +
200C LEU* 4.2 1.6 - - - +
201C ASN* 3.1 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU 3.7 11.2 - - - +
195C GLY* 3.1 19.9 + - - +
197C PHE* 1.3 101.1 - - + +
199C ASN* 1.3 57.7 + - - +
201C ASN* 3.8 3.7 - - - +
202C LYS* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LYS* 4.0 13.5 + - - +
108C ALA* 4.2 13.1 - - + +
129C VAL* 4.4 13.9 - - + -
194C LEU* 3.3 33.3 + - - +
195C GLY 3.0 22.2 + - - -
196C ILE* 3.7 9.6 - - - +
197C PHE 3.2 0.4 - - - -
198C GLU* 1.3 74.2 - - - +
200C LEU* 1.3 66.0 + - - +
202C LYS* 3.0 6.5 + - - +
203C HIS* 2.9 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LEU* 5.3 0.9 - - + -
129C VAL* 3.7 30.7 - - + -
134C LEU* 4.0 23.1 - - + -
151C LEU* 4.4 15.0 - - + -
154C ILE* 5.0 3.1 - - + -
157C VAL* 4.4 13.2 - - + -
172C ILE* 4.4 12.3 - - + -
174C ILE* 3.6 28.3 - - + -
184C LEU* 4.6 3.8 - - + -
196C ILE* 2.9 34.8 + - + +
197C PHE 4.2 2.7 - - - +
199C ASN* 1.3 72.1 - - - +
201C ASN* 1.3 57.7 + - - +
203C HIS* 5.4 0.7 - - - -
204C ALA* 2.8 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C VAL* 4.7 13.6 + - + +
197C PHE* 3.1 38.6 + - + +
198C GLU* 3.9 5.2 - - - +
200C LEU* 1.3 79.2 - - - +
202C LYS* 1.3 62.1 + - - +
205C PHE* 3.3 39.3 + - - -
209C ASN* 3.3 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C GLU 2.9 20.8 + - - +
199C ASN* 3.0 8.0 + - - +
201C ASN* 1.3 79.0 - - - +
203C HIS* 1.3 88.6 + - + +
205C PHE 3.6 1.7 - - - -
206C PRO* 3.5 20.4 - - - +
209C ASN* 3.7 27.9 + - + +
211C GLN* 5.5 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LYS* 3.6 47.8 + - + +
129C VAL* 4.5 3.2 - - + +
130C THR 4.2 4.9 - - - +
131C ASP* 4.4 20.4 - - + +
151C LEU* 3.4 30.0 - - + +
199C ASN* 2.9 37.0 + - - +
202C LYS* 1.3 107.4 + - + +
204C ALA* 1.3 62.7 + - - +
205C PHE 3.3 0.7 - - - -
206C PRO* 3.6 15.4 - - + +
211C GLN* 5.8 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LEU* 3.8 34.4 - - + +
152C GLY* 5.2 2.9 - - - -
154C ILE* 4.2 16.3 - - + +
157C VAL* 5.2 0.2 - - + -
200C LEU 2.8 24.2 + - - +
203C HIS* 1.3 72.3 - - - +
205C PHE* 1.3 87.6 + - + +
206C PRO* 3.3 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 3.5 26.0 - - + -
155C SER* 3.6 27.8 - - - -
156C ARG* 4.1 6.5 - - - -
157C VAL* 4.4 9.0 - - + -
201C ASN* 3.3 47.5 + - - +
202C LYS 3.6 1.1 - - - -
203C HIS 3.3 0.2 - - - -
204C ALA* 1.3 98.7 - - + +
206C PRO* 1.3 57.0 - - - +
207C LEU 3.2 2.5 - - - -
208C SER* 2.8 27.2 + - - +
209C ASN* 2.7 30.2 + - - +
----------------------------------------------------------
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