Contacts of the strand formed by residues 148 - 153 (chain A) in PDB entry 2Z9K
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 VAL 148 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.8 29.2 - - + -
17A MET* 4.3 10.6 - - + +
30A LEU* 4.5 17.0 - - + -
113A SER 3.9 0.3 - - - +
114A VAL* 3.6 4.1 - - - +
115A LEU* 3.1 29.2 + - + -
146A GLY 3.3 16.6 - - - +
147A SER* 1.3 75.3 - - - +
149A GLY* 1.3 61.6 + - - +
150A PHE* 4.1 3.4 - - + -
159A PHE* 4.1 18.6 - - + -
161A TYR* 3.0 14.8 - - - +
162A MET* 3.6 20.2 - - + -
177A LEU* 5.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 3.6 17.0 - - - -
113A SER 3.1 10.8 - - - -
114A VAL* 4.2 1.8 - - - -
148A VAL* 1.3 76.5 - - - +
150A PHE* 1.3 64.3 + - - +
159A PHE* 3.7 2.9 - - - -
160A CYS* 3.0 26.9 + - - -
161A TYR* 2.7 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.9 24.3 - - + -
9A PRO 4.1 2.5 - - - -
10A SER* 4.2 20.2 - - - -
13A VAL* 3.7 37.5 - - + -
112A PHE* 3.4 5.4 - - - +
113A SER* 2.8 59.7 + - - -
114A VAL 4.7 0.2 - - - -
115A LEU* 4.2 17.7 - - + -
125A VAL* 4.8 1.3 - - + -
148A VAL* 4.1 6.1 - - + -
149A GLY* 1.3 78.4 - - - +
151A ASN* 1.3 69.7 + - - +
152A ILE* 4.0 20.4 - - + -
157A VAL* 4.2 5.4 - - + -
158A SER 3.3 12.6 - - - +
159A PHE* 4.2 13.9 - - + -
160A CYS* 4.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.2 27.1 - - + -
106A ILE* 4.0 17.0 - - - +
111A THR* 3.1 29.4 + - - +
112A PHE* 3.4 14.6 - - - +
150A PHE* 1.3 73.3 - - - +
152A ILE* 1.3 70.6 + - - +
153A ASP* 5.9 1.1 - - - +
157A VAL* 3.6 2.9 - - - +
158A SER* 2.8 40.4 + - - +
160A CYS* 4.1 4.6 - - - +
294A PHE* 5.8 4.7 - - + -
298A ARG* 4.6 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.5 34.7 - - + -
9A PRO* 3.4 31.0 - - + +
12A LYS* 5.0 13.5 - - + -
150A PHE* 4.0 15.7 - - + -
151A ASN* 1.3 82.9 - - - +
153A ASP* 1.3 71.4 + - - +
154A TYR 4.0 10.1 - - - +
155A ASP* 4.8 2.5 - - - -
156A CYS 3.5 13.7 - - - +
157A VAL* 4.4 15.9 - - + -
158A SER* 6.2 0.2 - - - -
294A PHE* 5.3 0.5 - - - -
298A ARG* 4.5 3.8 + - - -
305A PHE* 3.4 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS* 5.9 6.1 + - - +
151A ASN* 5.9 1.4 - - - +
152A ILE* 1.3 79.1 - - - +
154A TYR* 1.3 87.1 + - + +
155A ASP* 2.7 17.8 + - - +
156A CYS* 2.8 32.0 + - + +
158A SER* 5.4 6.3 + - - +
294A PHE* 3.8 28.1 - - - -
----------------------------------------------------------
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