Contacts of the strand formed by residues 168 - 173 (chain E) 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 CYS 168 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ALA* 3.5 39.5 - - + +
52E ALA* 3.8 7.9 - - - -
53E PHE* 3.5 27.3 - - + -
56E TRP* 4.2 3.4 - - - -
140E GLY 3.1 9.1 + - - +
141E VAL* 3.5 2.4 - - - -
142E VAL* 2.9 27.2 + - - +
167E ASN* 1.3 78.0 - - - +
169E PHE* 1.3 61.5 + - - +
197E VAL* 3.2 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ALA* 4.5 0.2 - - - +
142E VAL* 3.4 26.9 - - + -
143E ALA 4.5 0.2 - - - -
144E GLY* 3.6 33.4 - - - -
158E MET* 3.7 20.9 - - + -
159E PHE* 3.7 31.2 - - + -
162E ALA* 3.7 23.1 - - + -
163E ILE* 4.3 5.8 - - + -
168E CYS* 1.3 75.7 - - - +
170E VAL* 1.3 79.3 + - - +
171E LEU* 3.6 22.9 - - + -
197E VAL 2.8 12.0 + - - +
198E MET* 3.8 15.0 - - - -
199E ASN* 3.1 33.0 + - - -
471E TYR* 4.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E VAL* 5.3 1.1 - - + +
45E ALA* 3.9 42.6 - - + +
46E ILE* 4.2 5.4 - - + +
49E ALA* 4.1 9.2 - - + -
141E VAL* 4.2 11.7 - - + -
142E VAL 2.9 10.9 + - - +
143E ALA* 3.4 5.6 - - - +
144E GLY 3.1 21.3 + - - +
169E PHE* 1.3 81.7 - - - +
171E LEU* 1.3 62.4 - - - +
172E LYS 4.0 0.2 + - - -
199E ASN* 3.6 9.2 - - + +
201E VAL* 4.2 16.6 - - + -
211E LEU* 3.8 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E GLY* 3.4 16.4 - - - +
146E THR* 3.6 28.7 - - + +
155E PRO* 3.9 15.5 - - + -
158E MET* 5.0 0.2 - - - -
159E PHE* 4.5 2.5 - - + -
169E PHE* 3.6 19.7 - - + -
170E VAL* 1.3 74.9 - - - +
172E LYS* 1.3 61.1 + - - +
173E PRO* 3.7 8.5 - - + +
181E THR* 3.6 31.4 - - + +
185E ALA* 5.8 0.2 - - + -
198E MET* 3.9 19.3 - - + -
199E ASN 2.8 15.7 + - - +
200E VAL* 3.5 10.1 - - + -
201E VAL* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E GLY 2.8 12.1 + - - +
145E ILE* 3.5 8.3 - - + +
146E THR 3.5 16.4 + - - -
171E LEU* 1.3 75.2 - - - +
173E PRO* 1.4 87.0 + - - +
175E GLU* 3.2 1.0 + - - -
201E VAL* 3.3 16.2 - - + +
203E GLY 3.0 32.5 + - - +
204E ASP* 4.4 1.1 - - - +
207E ALA* 4.0 21.3 - - + -
208E VAL* 3.7 23.6 - - + -
211E LEU* 3.8 23.6 - - + -
501E NAD 2.6 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 173 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E THR* 3.2 19.1 - - - +
151E PRO* 6.3 0.2 - - + -
171E LEU* 3.7 12.8 - - + +
172E LYS* 1.4 107.3 + - - +
174E SER* 1.3 69.1 + - - +
175E GLU* 3.2 1.0 + - - -
178E PRO* 5.3 1.8 - - + -
181E THR* 3.7 38.4 - - + +
200E VAL* 4.1 13.9 - - + -
201E VAL 3.9 8.5 - - - +
202E ASN* 3.6 21.4 - - - +
203E GLY 4.4 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