Contacts of the helix formed by residues 198 - 212 (chain I) in PDB entry 1ZUM
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 198 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I PHE* 4.4 3.6 - - + -
39I THR* 3.6 9.2 - - - +
51I VAL* 4.0 26.2 - - + -
109I ASP* 3.4 7.9 - - - +
193I VAL* 3.8 20.5 - - + +
194I ALA 3.4 10.3 - - - +
195I GLU 3.4 16.8 - - - +
196I GLN 3.6 1.6 - - - -
197I THR* 1.3 90.5 - - - +
199I LEU* 1.3 64.1 + - + +
200I THR 3.7 0.7 - - - -
201I ALA* 3.6 5.4 + - - +
202I LEU* 3.1 30.0 + - + +
222I PRO* 4.3 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I VAL* 3.9 34.5 - - + -
19I CYS* 4.1 10.9 - - - +
20I ASN* 4.7 0.7 - - + -
39I THR* 3.9 14.6 - - + -
48I ILE* 3.9 11.4 - - + -
49I CYS* 3.8 20.6 - - - -
51I VAL* 4.0 18.4 - - + -
105I LEU* 4.0 23.2 - - + +
109I ASP* 3.4 28.4 + - + +
197I THR 3.5 0.2 - - - -
198I PRO* 1.3 75.0 - - + +
200I THR* 1.3 65.3 + - - +
202I LEU* 3.3 7.5 + - + +
203I TYR* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102I LEU* 4.0 10.6 - - + +
105I LEU* 3.7 23.1 - - + +
106I GLU* 2.8 55.9 + - + +
109I ASP* 4.8 3.2 + - + -
171I PRO* 3.7 10.7 - - - +
172I LEU* 3.4 22.3 + - + +
197I THR 4.7 1.2 + - - -
198I PRO 3.7 0.2 - - - -
199I LEU* 1.3 74.4 - - + +
201I ALA* 1.3 64.6 + - - +
203I TYR* 3.2 4.0 + - - +
204I VAL* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I ILE* 5.0 2.2 - - + -
171I PRO* 5.3 3.8 - - + +
172I LEU* 4.9 0.2 - - - -
175I GLN* 3.3 39.0 - - + +
193I VAL* 3.3 33.7 - - + -
197I THR 5.1 3.1 + - - +
198I PRO 3.6 6.4 + - - +
199I LEU 3.3 0.8 - - - -
200I THR* 1.3 81.5 + - - +
202I LEU* 1.3 63.3 + - - +
204I VAL 3.2 2.1 + - - -
205I ALA 3.0 16.6 + - - -
220I ILE* 3.6 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I CYS* 3.9 11.7 - - - +
20I ASN* 3.9 22.4 - - - -
21I GLN 3.7 25.6 - - - +
28I TRP* 3.1 34.0 - - + -
51I VAL* 4.3 7.0 - - + -
193I VAL* 4.8 1.8 - - + -
198I PRO* 3.1 21.3 + - + +
199I LEU* 3.3 9.3 + - + +
201I ALA* 1.3 76.9 - - - +
203I TYR* 1.3 61.8 + - - +
205I ALA* 3.2 8.8 + - - +
206I ASN 3.4 2.6 + - - -
220I ILE* 3.8 32.1 - - + +
222I PRO* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I PHE* 4.2 14.6 - + + -
19I CYS* 4.0 20.1 - - + +
97I ARG* 4.4 2.1 + - - -
98I ASP* 2.6 36.0 + - + -
101I TYR* 3.7 29.8 - + - -
102I LEU* 3.8 22.7 - - + -
105I LEU* 4.5 7.4 - - + -
199I LEU 3.1 12.4 + - - +
200I THR 3.2 7.8 + - - +
202I LEU* 1.3 73.4 - - - +
204I VAL* 1.3 66.8 + - - +
206I ASN* 3.0 30.0 + - + +
207I LEU* 3.2 28.1 + - + +
3127I EDO 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I LEU* 4.4 12.8 - - + -
95I ILE* 4.3 25.6 - - + -
102I LEU* 4.4 10.3 - - + -
172I LEU* 3.7 14.8 - - + -
175I GLN* 3.4 36.3 - - - +
179I LEU* 5.1 1.8 - - + -
200I THR 3.0 15.9 + - - +
201I ALA 3.2 3.1 + - - +
203I TYR* 1.3 73.4 - - - +
205I ALA* 1.3 60.3 + - - +
207I LEU* 3.0 9.5 + - - +
208I ILE* 2.8 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I PHE* 3.3 42.6 - - + -
28I TRP* 3.8 5.4 - - + -
201I ALA 3.0 5.8 + - - +
202I LEU 3.2 12.8 - - - +
203I TYR 3.1 0.2 - - - -
204I VAL* 1.3 77.5 - - - +
206I ASN* 1.3 61.8 + - - +
208I ILE* 3.0 24.2 + - + +
209I LYS 3.0 10.6 + - - -
220I ILE* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I PHE* 5.8 1.8 - - - +
19I CYS* 3.8 20.7 - - - -
23I PHE* 4.8 0.4 - - - -
28I TRP* 3.1 27.1 + - - -
202I LEU 3.4 1.8 + - - -
203I TYR* 3.0 24.2 + - + +
205I ALA* 1.3 78.9 - - - +
207I LEU* 1.3 60.1 + - + +
209I LYS* 3.3 16.7 + - - +
210I GLU* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I LEU* 3.8 13.0 - - + +
94I LEU* 3.5 14.6 - - + +
95I ILE* 3.9 38.6 - - + +
97I ARG* 3.6 16.8 - - - +
98I ASP* 3.6 17.7 - - - +
102I LEU* 4.5 5.4 - - + -
203I TYR* 3.7 35.0 - - + +
204I VAL* 3.0 10.8 + - - +
206I ASN* 1.3 79.2 - - + +
208I ILE* 1.3 54.6 + - - +
210I GLU* 3.7 11.2 - - - +
211I ALA* 2.7 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I PHE* 4.9 6.3 - - + -
26I ASN* 5.0 3.1 - - - +
91I LEU* 3.7 24.9 - - + -
175I GLN* 4.9 2.2 - - - +
179I LEU* 3.7 29.8 - - + -
183I LEU* 5.8 0.7 - - + -
204I VAL* 2.8 26.0 + - + +
205I ALA* 3.3 14.8 - - - +
207I LEU* 1.3 74.1 - - - +
209I LYS* 1.3 64.9 + - - +
211I ALA 3.3 7.6 + - - -
212I GLY 3.4 0.5 + - - -
213I PHE* 3.4 46.1 + - + -
218I VAL* 3.9 33.9 - - + +
220I ILE* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 209 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I PHE* 4.2 13.4 - - + -
26I ASN* 3.4 49.5 + - + +
27I GLU* 5.3 3.0 - - - +
28I TRP* 5.8 6.1 - - - +
205I ALA 3.0 10.2 + - - +
206I ASN* 3.4 18.3 + - - +
208I ILE* 1.3 77.7 - - - +
210I GLU* 1.3 63.0 + - - +
212I GLY* 3.1 14.6 + - - -
213I PHE 4.4 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I ARG* 4.4 12.2 + - - +
94I LEU* 3.8 13.3 - - + +
97I ARG* 2.9 44.2 + - - -
206I ASN 3.0 14.2 + - - +
207I LEU* 3.2 16.6 + - - +
209I LYS* 1.3 78.7 - - - +
211I ALA* 1.3 62.5 + - - +
212I GLY* 3.2 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I LEU* 3.4 17.7 - - - +
90I ARG* 3.8 31.6 + - + +
91I LEU* 4.0 16.4 - - + +
94I LEU* 3.7 4.7 - - + +
207I LEU 2.7 21.1 + - - +
208I ILE 3.6 6.7 - - - +
209I LYS 3.2 0.2 - - - -
210I GLU* 1.3 74.5 - - - +
212I GLY* 1.3 57.3 + - - +
213I PHE* 3.7 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I MET* 5.4 0.9 - - - +
87I LEU* 4.1 12.4 - - - +
209I LYS 3.1 12.5 + - - -
210I GLU 3.2 1.9 - - - -
211I ALA* 1.3 79.8 - - - +
213I PHE* 1.3 66.8 + - - +
214I PRO* 3.4 7.6 - - - +
----------------------------------------------------------
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