Contacts of the helix formed by residues 194 - 203 (chain D) in PDB entry 1VEW
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 TRP 194 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D THR* 3.0 29.4 + - - +
93D THR* 3.7 20.6 - - - +
94D LEU* 3.5 58.7 - - + +
98D LEU* 4.1 16.7 - - + +
102D ILE* 4.5 6.7 - - + -
112D PHE* 4.0 23.6 - + - -
113D LYS* 5.4 6.1 - - - -
131D LEU* 5.4 1.6 - - + -
164D MET* 4.1 21.3 - - + -
189D TRP* 4.3 25.6 + + - -
192D VAL* 3.2 24.6 + - + +
193D ASN* 1.3 70.9 - - - +
195D ASP* 1.3 61.1 + - - +
197D ALA* 3.6 8.4 - - + +
198D ALA* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D LYS* 4.4 12.7 + - - +
92D THR* 3.8 21.3 - - - +
93D THR 4.7 7.4 + - - +
95D GLN* 4.9 6.6 - - - +
193D ASN* 3.1 9.5 + - - +
194D TRP* 1.3 77.1 - - - +
196D GLU* 1.3 57.0 + - - +
198D ALA* 3.3 7.0 + - - +
199D ALA* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LYS* 3.5 50.1 + - + +
87D GLY* 4.6 4.3 - - - +
193D ASN* 3.1 18.7 + - + +
195D ASP* 1.3 74.7 - - - +
197D ALA* 1.3 60.6 + - - +
199D ALA* 3.3 11.4 + - - +
200D ARG* 3.0 51.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU* 3.8 17.0 - - + -
163D ILE* 3.5 32.0 - - + +
164D MET* 4.5 10.5 - - + -
192D VAL* 5.4 0.2 - - + -
193D ASN 3.2 15.1 + - - +
194D TRP* 3.6 17.3 - - + +
195D ASP 3.3 0.2 - - - -
196D GLU* 1.3 78.5 - - - +
198D ALA* 1.3 55.2 - - - +
200D ARG* 3.4 1.2 + - - +
201D PHE* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLN 5.3 5.6 - - - +
98D LEU* 3.8 19.7 - - + +
194D TRP 2.8 18.8 + - - +
195D ASP* 3.5 7.2 - - - +
197D ALA* 1.3 75.6 - - - +
199D ALA* 1.3 58.0 + - - +
201D PHE* 3.2 7.1 + - - +
202D ALA* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ASP 3.0 14.2 + - - +
196D GLU* 3.4 20.9 - - - +
198D ALA* 1.3 76.5 - - - +
200D ARG* 1.3 55.4 + - - +
202D ALA* 3.4 7.8 + - - +
203D ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D LEU* 3.7 30.2 - - - +
150D LEU* 5.9 2.4 - - - +
161D PHE* 3.4 40.7 - - + -
162D PRO* 2.8 34.3 + - - +
163D ILE* 3.3 24.1 + - + +
196D GLU* 3.0 40.5 + - - +
197D ALA 3.8 4.9 - - - +
199D ALA* 1.3 74.4 - - - +
201D PHE* 1.3 58.9 + - - +
203D ALA* 3.4 5.0 + - - +
204D LYS* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ASP* 3.7 30.3 - - + -
98D LEU* 3.8 32.5 - - + -
101D ALA* 3.6 25.1 - - + -
104D ARG* 5.5 3.6 - - - -
133D LEU* 4.5 17.7 - - + -
136D ASP 5.8 0.4 - - - -
138D LEU* 4.4 20.6 - - + -
163D ILE* 3.9 12.1 - - + +
197D ALA 3.0 14.4 + - - +
198D ALA* 3.2 9.6 + - - +
200D ARG* 1.3 77.3 - - - +
202D ALA* 1.3 57.4 + - + +
204D LYS* 2.7 55.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D ALA 2.9 16.6 + - - +
199D ALA* 3.6 8.7 - - - +
201D PHE* 1.3 82.0 - - + +
203D ALA* 1.3 60.7 + - - +
204D LYS* 4.3 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ALA 3.0 16.2 + - - +
200D ARG* 3.8 7.0 - - - +
201D PHE 3.3 0.2 - - - -
202D ALA* 1.3 77.1 - - - +
204D LYS* 1.3 63.2 + - - +
205D LYS* 3.1 25.8 + - - +
----------------------------------------------------------
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