Contacts of the strand formed by residues 172 - 183 (chain C) in PDB entry 4ZIN
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 HIS 172 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER* 4.6 18.0 + - - -
204A HIS* 3.2 40.7 + - - -
205A ASN* 4.0 10.4 + - + +
210A ILE* 6.2 2.5 - - + +
100C GLU* 4.0 6.9 - - - +
144C GLU* 6.1 1.6 - - + -
164C ARG* 3.6 36.1 + - + +
165C LEU 3.1 12.6 - - - +
166C LYS* 5.1 1.1 - - + -
167C LEU* 3.5 14.0 - - - +
171C GLY* 1.3 81.2 - - - +
173C TYR* 1.3 61.0 + - - +
174C ASP* 2.7 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C PHE* 3.2 38.7 - + + +
100C GLU* 3.5 24.7 - - + -
101C ASP* 2.5 43.5 + - - -
129C PHE* 3.6 13.2 - - - -
134C PRO* 3.7 23.8 - - + -
135C VAL* 3.6 19.8 - - + +
140C THR* 4.4 2.0 - - + -
163C GLN 4.2 0.2 - - - +
165C LEU* 2.8 51.7 + - + +
167C LEU* 4.1 17.7 - - + -
172C HIS* 1.3 74.8 - - - +
174C ASP* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A HIS 4.6 2.9 - - - +
99C PHE* 3.6 6.8 - - - +
100C GLU* 2.7 46.5 + - + +
163C GLN 3.3 6.3 - - - +
164C ARG* 3.4 23.2 - - - +
172C HIS* 2.7 37.5 + - - -
173C TYR* 1.3 80.1 + - - +
175C ALA* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C MET* 4.9 0.2 - - + -
98C ASN 3.2 16.6 - - - +
99C PHE* 3.8 26.7 - - + -
100C GLU 4.7 0.2 - - - +
143C 4OO 4.2 11.0 - - - +
162C LYS* 3.7 4.7 - - - +
163C GLN* 2.9 33.4 + - + +
174C ASP* 1.3 76.5 - - - +
176C GLU* 1.3 63.9 + - - +
177C VAL* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C VAL 3.8 1.2 - - - +
97C MET* 3.5 1.9 - - - -
98C ASN* 2.9 48.9 + - + +
161C ILE 3.6 5.4 - - - +
162C LYS* 3.9 29.1 + - + +
175C ALA* 1.3 75.9 - - - +
177C VAL* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ARG* 3.8 27.6 - - + +
96C VAL 3.4 8.3 - - - +
97C MET* 3.8 26.0 - - + -
159C GLY 3.9 0.2 - - - +
160C GLU* 3.3 5.9 - - - +
161C ILE* 2.8 56.0 + - + +
163C GLN* 3.7 27.4 - - + +
175C ALA* 4.3 5.2 - - + -
176C GLU* 1.3 78.9 - - - +
178C LYS* 1.3 64.6 + - - +
179C THR* 4.0 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLU 4.0 0.3 - - - +
95C ARG* 3.4 1.7 - - - +
96C VAL* 3.0 39.7 + - + +
151C TYR* 3.4 26.3 + - - -
153C GLU* 4.9 2.6 + - - -
158C LYS* 4.3 27.7 - - - +
159C GLY 3.4 9.4 - - - +
160C GLU* 4.0 14.9 + - + +
177C VAL* 1.3 75.1 - - - +
179C THR* 1.3 71.8 + - - +
180C THR* 5.2 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C TRP* 4.0 11.4 - - + -
94C GLU 3.3 11.7 - - - +
95C ARG* 2.8 34.8 + - + +
148C GLU* 4.2 2.8 + - - -
157C LEU 3.8 0.2 - - - +
158C LYS* 3.3 6.9 - - - +
159C GLY 2.9 33.3 + - - +
161C ILE* 5.6 0.3 - - - +
177C VAL* 4.0 5.5 - - - +
178C LYS* 1.3 79.3 - - - +
180C THR* 1.3 68.7 + - - +
181C TYR* 3.4 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LYS 3.9 0.2 - - - +
93C TRP* 3.1 6.1 - - - +
94C GLU* 2.9 47.0 + - + +
156C ALA* 3.9 24.7 - - + -
157C LEU 3.6 2.7 - - - -
158C LYS* 3.3 25.8 + - - +
178C LYS* 5.2 4.0 - - - +
179C THR* 1.3 73.9 - - - +
181C TYR* 1.3 63.0 + - - +
182C LYS* 4.1 5.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LYS* 3.0 38.8 - - + -
82C TYR* 3.6 7.8 - - - -
83C LEU* 3.8 34.3 - - + -
91C PHE* 4.6 1.1 - + + -
92C LYS 3.6 5.4 - - - +
93C TRP* 3.6 23.8 - + + -
95C ARG* 3.2 14.9 + - - -
148C GLU* 2.6 26.7 + - - -
150C MET* 4.0 18.4 - - + -
156C ALA* 3.8 1.0 - - - +
157C LEU* 2.8 49.1 + - + +
159C GLY 4.0 0.7 - - - -
179C THR* 3.4 29.1 - - + -
180C THR* 1.3 73.4 - - - +
182C LYS* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C TYR* 3.7 4.0 + - - -
91C PHE* 3.2 4.1 - - - +
92C LYS* 3.0 38.0 + - + +
154C ASP 5.2 4.0 - - - +
155C GLY* 3.7 27.5 + - - +
156C ALA* 3.9 12.6 - - + -
180C THR* 4.1 6.0 - - + +
181C TYR* 1.3 75.1 - - - +
183C ALA* 1.3 77.0 + - - +
184C LYS* 3.7 1.1 + - - +
185C LYS 6.1 0.2 - - - -
186C PRO* 5.9 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C TYR* 2.9 30.7 + - + +
86C SER* 3.7 21.5 - - - -
90C GLY 3.8 4.9 - - - -
91C PHE* 3.9 4.5 - - - -
182C LYS* 1.3 93.3 + - - +
184C LYS* 1.3 66.7 + - - +
185C LYS 3.3 21.0 + - - +
186C PRO* 5.3 0.2 - - + -
187C VAL* 3.9 8.1 - - + +
----------------------------------------------------------
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