Contacts of the helix formed by residues 178 - 191 (chain K) in PDB entry 4ZZ7
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 178 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K ILE* 4.1 14.3 - - + +
22K VAL* 4.3 6.5 - - + -
34K LEU* 3.7 25.6 - - + -
89K GLU* 3.4 9.2 - - - +
173K PRO* 5.1 3.7 - - + +
174K SER 3.8 9.0 - - - +
175K GLU 3.9 6.7 - - - +
176K ARG 3.8 4.3 - - - +
177K ASP* 1.3 89.2 - - - +
179K SER* 1.3 58.9 + - - +
180K SER 3.4 1.3 - - - -
181K THR* 3.8 10.2 - - - +
182K LEU* 3.0 30.1 + - - +
200K VAL* 6.2 0.2 - - - +
202K ASN* 3.4 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K ILE* 3.1 23.7 - - - +
32K LYS* 3.6 13.7 + - - -
85K LEU* 3.8 18.7 - - - +
88K GLU* 5.8 1.3 - - - -
89K GLU* 2.5 33.0 + - - -
178K PRO* 1.3 75.4 - - - +
180K SER* 1.3 66.7 + - - +
182K LEU* 3.6 5.0 + - - +
183K TYR* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82K ILE* 4.4 4.2 - - - +
85K LEU* 3.8 14.2 + - - +
86K ILE* 3.8 35.9 - - - +
89K GLU* 4.2 1.9 + - - -
151K PRO* 3.3 26.5 - - - +
152K VAL* 3.9 9.9 - - - -
177K ASP* 3.8 5.7 + - - +
179K SER* 1.3 77.4 - - - +
181K THR* 1.3 65.7 + - - +
183K TYR* 3.1 13.4 + - - +
184K ILE* 3.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K PRO* 2.2 47.8 + - - +
155K PRO* 4.2 3.9 - - + +
159K PHE* 6.0 0.2 - - - -
171K LEU* 3.7 20.7 - - + +
173K PRO* 3.5 38.2 - - + +
177K ASP 4.1 1.6 + - - -
178K PRO* 3.8 10.8 - - - -
179K SER 3.3 0.4 - - - -
180K SER* 1.3 79.3 + - - +
182K LEU* 1.3 63.6 + - - +
184K ILE* 3.1 22.5 - - + +
185K ALA* 3.5 7.6 + - - +
200K VAL* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K ILE* 3.8 27.1 - - + -
5K GLY 4.1 12.3 - - - +
6K HIS 4.5 0.9 - - - -
7K LEU* 3.8 37.5 - - + +
12K LEU* 4.3 17.9 - - + -
178K PRO 3.0 17.6 + - - +
179K SER* 4.0 4.7 - - - +
180K SER 3.3 0.2 - - - -
181K THR* 1.3 78.2 - - - +
183K TYR* 1.3 63.5 + - - +
185K ALA* 3.1 7.1 + - - +
186K GLN* 3.0 32.5 + - + +
200K VAL* 4.1 17.0 - - + +
202K ASN* 5.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 183 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K HIS* 3.2 37.9 + + + -
81K GLU* 3.8 21.5 + - + +
82K ILE* 3.8 28.7 - - + -
85K LEU* 3.7 21.5 - - + -
179K SER 3.2 16.2 + - - +
180K SER 3.1 6.2 + - - +
182K LEU* 1.3 76.6 - - - +
184K ILE* 1.3 67.7 + - - +
186K GLN* 3.1 29.0 + - - +
187K LEU* 3.3 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K PHE* 3.3 25.4 - - + -
75K LEU* 4.0 23.8 - - + -
82K ILE* 4.0 26.9 - - + -
152K VAL* 4.3 23.1 - - + +
155K PRO* 4.7 3.6 - - + -
156K LEU* 4.2 29.2 - - + -
159K PHE* 4.2 13.5 - - + -
180K SER 3.2 8.7 + - - +
181K THR* 3.1 24.5 - - + +
183K TYR* 1.3 76.8 - - - +
185K ALA* 1.3 66.6 + - - +
187K LEU* 3.4 15.0 + - - +
188K LEU 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K LEU* 3.7 11.6 - - + +
159K PHE* 5.2 4.0 - - + -
171K LEU* 6.0 0.4 - - + -
181K THR 3.7 6.5 - - - +
182K LEU 3.1 11.3 + - - +
184K ILE* 1.3 84.3 - - + +
186K GLN* 1.3 56.1 + - - +
188K LEU* 3.1 30.8 + - - +
189K GLN* 3.4 9.0 - - - +
198K MET* 4.7 12.0 - - + +
200K VAL* 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 186 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K LEU* 4.4 14.0 - - + +
12K LEU* 3.2 41.4 - - + +
182K LEU* 3.0 27.9 + - + +
183K TYR* 3.1 23.7 + - + +
185K ALA* 1.3 73.6 - - - +
187K LEU* 1.3 63.7 + - - +
188K LEU 3.1 2.2 + - - -
189K GLN* 3.6 20.6 + - - +
190K GLU* 4.0 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K PHE* 4.1 6.1 - - + -
74K LEU* 3.4 30.6 - - + +
75K LEU* 3.8 27.4 - - + -
78K HIS* 3.4 35.9 - - + +
82K ILE* 4.4 9.9 - - + -
183K TYR* 3.3 20.1 + - + +
184K ILE* 3.5 13.9 - - - +
185K ALA 3.3 0.2 - - - -
186K GLN* 1.3 77.6 - - + +
188K LEU* 1.3 64.5 + - - +
190K GLU* 3.0 28.5 + - - +
191K ALA 3.1 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K VAL* 4.4 13.7 - - + -
68K MET* 4.7 7.4 - - - -
71K PHE* 3.6 39.7 - - + -
159K PHE* 3.7 26.9 - - + -
163K ILE* 4.0 4.5 - - + -
184K ILE 3.6 4.4 + - - +
185K ALA* 3.1 16.5 + - - +
186K GLN 3.1 0.6 - - - -
187K LEU* 1.3 78.1 - - - +
189K GLN* 1.3 62.0 + - - +
191K ALA* 3.4 9.3 + - + +
193K LEU* 3.2 51.7 + - + +
198K MET* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K LEU* 3.7 15.3 - - - +
10K GLY* 4.0 25.2 - - - +
185K ALA 3.4 15.6 - - - +
186K GLN* 3.6 10.0 + - - +
187K LEU 3.2 0.6 - - - -
188K LEU* 1.3 78.4 - - - +
190K GLU* 1.3 58.9 + - - +
192K GLY* 3.0 20.6 + - - -
193K LEU* 3.7 19.9 + - - +
194K PRO 4.0 17.4 + - - -
195K ASP* 3.7 21.4 + - - +
198K MET* 4.1 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K ARG* 5.5 1.4 - - - -
74K LEU* 3.9 28.5 - - + +
78K HIS* 4.8 5.8 + - - -
186K GLN 4.0 2.9 + - - +
187K LEU* 3.0 24.9 + - - +
189K GLN* 1.3 71.7 - - - +
191K ALA* 1.3 57.4 + - - +
192K GLY* 3.1 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K VAL* 3.5 28.7 - - + +
70K ARG* 3.0 36.8 + - - +
71K PHE* 3.7 13.7 - - + +
74K LEU* 3.7 20.8 - - + +
187K LEU 3.1 6.0 + - - +
188K LEU* 3.5 12.6 - - - +
189K GLN 3.2 1.0 - - - -
190K GLU* 1.3 75.3 - - - +
192K GLY* 1.3 58.7 + - - +
193K LEU 3.5 0.2 - - - -
----------------------------------------------------------
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