Contacts of the strand formed by residues 158 - 164 (chain C) in PDB entry 3ZWG
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 LEU 158 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C SER* 3.5 44.0 - - - +
43C LYS* 4.7 9.6 - - + -
94C MET* 3.8 36.1 - - + -
96C ASP* 5.6 0.2 - - - +
100C LEU* 5.4 0.2 - - + -
121C VAL* 4.4 11.7 - - + -
153C GLY* 3.9 1.2 - - - -
154C LEU* 2.9 33.4 + - + -
155C GLY 2.8 15.9 + - - +
156C TYR* 3.7 14.1 - - + +
157C GLY* 1.3 81.0 - - - +
159C LYS* 1.3 61.3 + - - +
176C VAL* 4.3 9.2 - - + -
177C THR 3.5 7.4 - - - +
178C LYS* 4.6 2.9 - - + -
179C ALA* 3.6 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C SER* 5.2 15.9 - - - -
152C ARG 3.8 12.8 - - - +
153C GLY* 3.9 8.7 - - - +
154C LEU* 4.0 6.3 - - - +
158C LEU* 1.3 74.2 - - - +
160C SER* 1.3 60.2 + - - +
161C ARG* 6.1 5.2 - - + +
175C HIS 3.7 1.2 - - - +
176C VAL* 3.5 3.3 - - - +
177C THR* 2.9 50.8 + - - +
178C LYS 3.8 9.5 + - - -
179C ALA* 3.7 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TRP* 4.9 4.3 - - - -
119C VAL* 3.6 42.2 + - - +
143C PHE* 5.1 3.5 - - - -
150C HIS 3.6 1.5 - - - +
151C SER* 3.1 6.5 - - - -
152C ARG* 3.0 45.1 + - - +
154C LEU* 3.8 11.6 - - - +
159C LYS* 1.3 76.7 - - - +
161C ARG* 1.3 58.8 + - - +
162C GLY 4.3 0.2 - - - -
174C ILE* 4.8 2.2 - - - -
175C HIS 3.6 4.7 - - - -
176C VAL* 4.6 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TRP* 4.6 0.9 - - - -
149C TRP* 3.3 43.1 - - + -
150C HIS 3.6 4.5 - - - +
151C SER* 3.6 19.1 - - - +
159C LYS* 6.1 5.2 - - - +
160C SER* 1.3 74.0 - - - +
162C GLY* 1.3 58.6 + - - +
173C GLU 3.9 0.5 - - - +
174C ILE* 3.2 2.9 - - - +
175C HIS* 2.6 86.8 + - - +
177C THR* 5.8 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TRP* 3.4 24.8 - - - -
148C GLY 3.9 0.3 - - - +
149C TRP* 3.4 8.9 - - - -
150C HIS 3.0 33.9 + - - -
161C ARG* 1.3 77.3 - - - +
163C PHE* 1.3 59.7 + - - -
173C GLU 3.0 11.0 - - - -
174C ILE* 4.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TRP* 4.2 2.4 - - - -
147C ASN* 3.4 47.3 - - - -
148C GLY* 3.5 19.5 - - - -
149C TRP* 3.5 46.4 - + + -
162C GLY* 1.3 74.1 - - - -
164C MET* 1.3 75.9 + - - +
165C ASN* 4.4 4.3 - - + -
171C ILE* 3.6 7.3 - - + +
172C LEU* 3.4 8.2 - - - +
173C GLU* 2.8 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE* 3.8 18.8 - - + -
104C PHE* 4.8 2.0 - - + -
105C SER 4.2 1.6 - - - +
106C VAL* 3.8 29.2 - - + -
115C ASN* 4.1 13.0 - - - -
116C TRP 3.6 37.7 - - - +
117C TRP* 3.4 28.6 - - + +
145C GLY* 3.3 10.7 - - - -
146C ASP 3.5 0.7 + - - -
147C ASN* 3.1 22.9 + - - -
148C GLY 4.3 3.1 + - - -
163C PHE* 1.3 82.8 - - - +
165C ASN* 1.3 70.3 + - - +
170C ALA* 4.0 7.6 - - + -
171C ILE 3.3 12.6 - - - +
172C LEU* 4.0 6.5 - - + -
----------------------------------------------------------
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