Contacts of the helix formed by residues 179 - 193 (chain C) in PDB entry 5ID3
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 GLU 179 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C SER 2.7 16.1 + - - +
178C ARG* 1.4 100.3 + - - +
180C LYS* 1.4 64.2 + - - +
181C LYS* 3.3 9.6 - - + +
182C LEU* 3.4 32.5 + - + +
183C LEU* 3.8 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C SER* 4.0 36.8 + - - +
179C GLU* 1.4 69.0 - - - +
181C LYS* 1.4 78.5 + - + +
183C LEU* 3.2 26.8 + - + +
184C LEU* 3.4 12.6 + - + +
312C ARG* 3.8 12.9 - - - +
311D LYS* 3.8 20.1 - - - +
314D ARG* 3.6 26.2 - - - +
315D ASP* 5.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C GLU* 4.9 6.1 - - + +
180C LYS* 1.4 91.6 - - - +
182C LEU* 1.4 61.8 + - - +
184C LEU* 3.6 4.0 + - - +
185C GLN* 3.3 21.4 + - - +
307D ARG* 5.1 2.3 + - - -
308D ASN* 5.7 5.6 + - - +
311D LYS* 4.0 29.6 + - + +
312D ARG* 5.3 12.4 + - + +
315D ASP* 3.2 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C VAL* 5.9 7.2 - - + -
178C ARG 5.6 2.0 - - - +
179C GLU* 3.4 26.2 + - + +
180C LYS 3.3 0.4 - - - -
181C LYS* 1.4 79.2 - - - +
183C LEU* 1.4 59.2 - - + +
185C GLN* 3.3 14.5 + - + +
186C LEU* 2.9 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C VAL* 3.7 35.2 - - + +
172C ASP* 6.0 0.9 - - - +
175C LYS* 4.1 31.6 - - + +
178C ARG 5.2 5.2 - - - +
179C GLU 4.1 12.6 - - - +
180C LYS* 3.2 17.9 + - + +
182C LEU* 1.4 77.1 - - + +
184C LEU* 1.4 65.2 + - + +
186C LEU* 3.2 14.5 + - + +
187C GLU* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LYS* 3.4 10.3 + - + +
181C LYS 4.1 4.9 - - - +
182C LEU 3.5 0.2 - - - -
183C LEU* 1.4 82.0 - - + +
185C GLN* 1.4 58.4 + - - +
187C GLU* 3.2 30.7 + - - +
188C ASN* 2.8 27.0 + - - +
305C GLU* 4.2 4.7 - - + +
308C ASN* 6.3 0.2 - - + -
309C GLN* 3.6 31.9 - - + +
307D ARG* 3.6 31.9 - - - +
311D LYS* 3.6 32.8 - - + +
314D ARG* 5.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C LYS 3.3 14.8 + - - +
182C LEU* 3.3 18.4 + - + +
184C LEU* 1.4 75.0 - - - +
186C LEU* 1.4 62.4 + - - +
188C ASN* 3.4 24.5 + - - +
189C ALA* 3.4 18.5 + - - +
304D ASP* 5.2 5.1 + - - +
307D ARG* 4.6 4.4 - - - +
308D ASN* 3.7 29.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C VAL* 4.2 29.2 - - + -
182C LEU* 2.9 18.7 + - + +
183C LEU* 3.2 17.2 + - + +
185C GLN* 1.4 76.4 - - - +
187C GLU* 1.4 60.9 + - - +
189C ALA* 3.2 22.6 + - + +
190C GLU* 3.3 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C LEU 3.0 13.0 + - - +
184C LEU* 3.2 27.5 + - - +
186C LEU* 1.4 74.4 - - - +
188C ASN* 1.4 62.5 + - - +
190C GLU* 3.3 12.2 + - + +
191C THR* 3.2 23.9 + - - +
305C GLU* 3.2 38.8 - - - +
308C ASN* 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C LEU 2.8 13.9 + - - +
185C GLN* 3.5 24.9 + - - +
187C GLU* 1.4 75.8 - - - +
189C ALA* 1.4 60.2 + - - +
191C THR* 3.3 11.2 + - - -
192C LEU* 3.3 22.6 + - + +
302C GLU* 2.7 35.0 + - - +
305C GLU* 2.8 23.9 - - - +
304D ASP* 4.4 4.6 + - - -
307D ARG* 3.4 30.9 - - - +
308D ASN 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C GLN 3.4 8.4 + - - +
186C LEU* 3.2 22.0 + - + +
188C ASN* 1.4 77.5 - - - +
190C GLU* 1.4 63.8 + - + +
192C LEU* 3.5 10.6 + - - +
193C LEU* 3.3 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C LEU* 3.3 30.0 + - + +
187C GLU* 3.6 10.8 - - + +
188C ASN 3.3 0.2 - - - -
189C ALA* 1.4 78.2 - - - +
191C THR* 1.4 61.9 + - - +
193C LEU* 3.1 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C GLU* 3.2 9.6 + - - +
188C ASN* 3.3 9.9 + - - -
190C GLU* 1.4 76.1 - - - +
192C LEU* 1.4 61.4 + - + +
193C LEU* 3.6 1.2 + - - +
298C ARG* 3.0 68.6 - - + +
299C LEU* 4.5 3.0 + - - -
301C THR* 4.2 12.0 - - + +
302C GLU* 4.2 14.4 - - + +
305C GLU* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ASN* 3.3 17.9 + - + +
189C ALA* 3.8 11.4 - - - +
190C GLU 3.4 0.4 - - - -
191C THR* 1.4 80.4 - - - +
193C LEU* 1.4 72.9 + - - +
194C ALA* 3.0 10.6 + - + +
197C HIS* 3.8 8.8 + - - -
298C ARG* 5.2 0.3 - - - -
299C LEU* 4.5 22.2 - - + -
302C GLU* 3.6 20.9 - - - +
301D THR* 5.0 17.7 - - + -
304D ASP* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ALA 3.3 9.7 + - - -
190C GLU* 3.1 21.3 - - - +
191C THR* 3.4 6.5 - - - +
192C LEU* 1.4 77.7 - - - +
194C ALA* 1.4 62.9 + - - +
195C PRO* 3.6 6.1 - - - -
196C LEU* 3.8 26.3 + - + +
197C HIS* 3.2 45.2 + - + +
285C ARG* 4.9 9.0 - - - +
288C LYS* 3.9 20.6 - - + -
298C ARG* 3.8 20.6 - - - +
----------------------------------------------------------
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