Contacts of the helix formed by residues 189 - 198 (chain E) in PDB entry 6C1V
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 SER 189 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E PHE* 4.5 0.9 - - - +
188E ARG* 1.3 83.6 + - - +
190E LYS* 1.3 64.4 + - - +
191E PRO* 3.5 8.1 - - - +
192E GLN* 3.3 16.2 + - - +
193E LEU* 3.2 17.5 + - - +
208E PHE* 3.3 19.7 - - - -
4H T 5.7 0.2 - - - -
5H A 3.8 24.0 - - - -
6H C 2.6 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 190 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E SER* 1.3 74.6 - - - +
191E PRO* 1.3 66.3 - - + +
193E LEU* 3.2 6.5 + - + +
194E ALA* 2.9 27.7 + - + +
203E LEU* 3.1 38.9 + - + +
204E SER 3.6 12.1 + - - -
205E SER 4.7 0.4 - - - -
206E PHE* 2.7 32.2 + - + +
208E PHE* 3.7 25.6 - - + -
5H A 3.4 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E SER* 3.5 9.9 - - - +
190E LYS* 1.3 95.4 - - + +
192E GLN* 1.3 54.4 + - - +
194E ALA* 3.8 7.9 - - + +
195E ARG* 3.0 47.0 + - - +
5H A 3.3 39.3 - - - +
6H C 4.8 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E LYS* 4.7 11.2 - - - +
186E LYS 3.5 18.8 + - - -
187E PHE* 3.7 15.3 - - + +
188E ARG* 3.1 33.4 + - - +
189E SER* 3.3 21.9 + - - +
190E LYS 3.3 0.4 - - - -
191E PRO* 1.3 76.2 - - - +
193E LEU* 1.3 62.8 + - - +
195E ARG* 3.4 29.1 + - - +
196E TYR* 3.3 22.3 + - - +
304E UNX 4.1 8.1 - - - -
6H C 4.3 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E LEU* 4.7 9.4 - - + -
159E TRP* 3.5 38.4 - - + -
179E TYR* 4.6 9.4 - - + -
187E PHE* 4.1 19.7 - - + -
189E SER 3.2 9.7 + - - +
190E LYS* 3.2 10.9 + - - +
192E GLN* 1.3 80.4 - - - +
194E ALA* 1.3 54.3 + - - +
196E TYR* 3.3 2.6 + - - +
197E LEU* 3.0 46.3 + - + +
203E LEU* 4.1 11.9 - - + -
206E PHE* 4.0 26.9 - - + -
208E PHE* 4.3 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E LYS* 2.9 17.5 + - + +
191E PRO* 3.8 8.3 - - + +
192E GLN 3.3 0.2 - - - -
193E LEU* 1.3 73.2 - - - +
195E ARG* 1.3 59.3 + - - +
197E LEU* 4.8 0.9 - - - -
198E GLY* 2.8 35.2 + - - +
203E LEU* 4.1 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 195 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E PRO* 3.0 38.9 + - - +
192E GLN* 3.4 32.1 + - - +
194E ALA* 1.3 74.6 - - - +
196E TYR* 1.3 60.7 + - - +
198E GLY* 4.6 2.3 + - - -
304E UNX 3.5 23.4 - - - -
6H C 3.7 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 196 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E TRP* 4.1 24.2 - + - -
181E SER* 4.4 5.3 + - - -
183E SER* 4.4 4.9 - - - -
185E LYS* 4.5 20.1 - - + +
187E PHE* 3.8 37.5 - + + -
192E GLN 3.3 3.9 + - - +
193E LEU 3.3 4.7 + - - +
194E ALA 3.2 0.6 - - - -
195E ARG* 1.3 81.5 - - - +
197E LEU* 1.3 68.8 + - + +
301E UNX 2.9 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E LEU* 4.5 15.5 - - + -
156E PRO* 5.0 3.8 - - + -
159E TRP* 3.9 32.5 - - + +
193E LEU* 3.0 42.5 + - + +
194E ALA* 4.3 2.5 - - - +
196E TYR* 1.3 85.8 - - + +
198E GLY* 1.3 64.3 + - - +
199E ASN* 3.5 0.7 + - - +
200E THR* 2.7 41.8 + - - +
201E VAL* 4.5 20.4 - - + +
203E LEU* 4.5 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 198 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E ALA* 2.8 24.0 + - - -
195E ARG 4.5 2.4 - - - -
196E TYR 3.6 1.0 - - - -
197E LEU* 1.3 74.2 - - - +
199E ASN* 1.3 63.4 + - - -
200E THR 3.1 1.4 + - - -
201E VAL 3.1 18.0 + - - +
----------------------------------------------------------
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