Contacts of the strand formed by residues 168 - 172 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ALA* 3.3 40.8 - - + +
52G ALA 3.9 5.8 - - - -
53G PHE* 3.6 24.2 - - + -
56G TRP* 4.4 4.3 - - - -
140G GLY 2.9 9.8 + - - +
141G VAL* 3.4 3.4 - - + -
142G VAL* 2.8 29.6 + - - +
167G ASN* 1.3 79.2 - - - +
169G PHE* 1.3 62.2 + - - +
197G VAL* 3.4 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ALA* 4.6 0.2 - - - +
142G VAL* 3.4 27.4 - - + -
143G ALA 4.3 0.2 - - - -
144G GLY* 3.7 18.2 - - - -
158G MET* 3.6 25.8 - - + -
159G PHE* 3.6 29.6 - - + -
162G ALA* 3.8 22.9 - - + -
163G ILE* 4.2 8.7 - - + -
168G CYS* 1.3 75.7 - - - +
170G VAL* 1.3 86.7 - - - +
171G LEU* 3.7 21.1 - - + -
197G VAL 2.7 14.5 + - - +
198G MET* 3.8 16.8 - - - -
199G ASN* 3.0 33.5 + - - -
471G TYR* 4.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G VAL* 5.2 0.4 - - + -
45G ALA* 4.1 36.6 - - + +
46G ILE* 4.2 11.2 - - + +
49G ALA* 4.3 0.7 - - + -
141G VAL* 4.3 13.2 - - + -
142G VAL 2.9 9.6 + - - +
143G ALA* 3.3 3.9 - - - +
144G GLY 2.9 24.6 + - - +
169G PHE* 1.3 81.7 - - - +
171G LEU* 1.3 62.2 - - - +
199G ASN* 3.4 14.8 - - + +
201G VAL* 4.1 18.8 - - + -
211G LEU* 3.7 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G GLY* 3.4 16.8 - - - +
146G THR* 3.6 29.2 - - + +
155G PRO* 4.0 17.5 - - + -
158G MET* 5.0 0.7 - - - -
159G PHE* 4.5 2.0 - - + -
169G PHE* 3.7 18.1 - - + -
170G VAL* 1.3 75.5 - - - +
172G LYS* 1.3 63.4 + - - +
173G PRO* 3.7 8.4 - - + +
181G THR* 3.6 29.8 - - + +
198G MET* 4.0 19.7 - - + -
199G ASN 2.8 14.9 + - - +
200G VAL* 3.5 9.3 - - + -
201G VAL* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G GLY 2.6 14.4 + - - +
145G ILE* 3.5 10.4 - - + +
146G THR 3.4 19.6 + - - -
170G VAL 4.1 0.2 + - - -
171G LEU* 1.3 74.6 - - - +
173G PRO* 1.4 86.0 + - - +
174G SER* 4.5 1.0 - - - +
175G GLU* 3.3 23.0 + - - -
201G VAL* 3.2 17.3 - - + +
203G GLY 3.3 19.4 + - - +
204G ASP* 4.1 9.5 + - - +
207G ALA* 3.9 17.5 - - + -
208G VAL* 3.4 30.8 - - + +
211G LEU* 4.0 17.3 - - + -
----------------------------------------------------------
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