Contacts of the strand formed by residues 142 - 149 (chain F) in PDB entry 6NQN
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 SER 142 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LYS* 3.5 15.0 - - - +
190D PHE* 4.2 3.6 - - - -
219D LEU* 5.8 2.4 + - - +
63F KZ4 2.9 46.5 + - - +
140F GLU 3.6 2.0 + - - -
141F PRO* 1.3 77.0 - - - +
143F THR* 1.3 69.8 + - - +
144F GLU* 4.1 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D THR* 3.7 42.0 - - - +
145D LYS* 3.3 12.6 + - - +
190D PHE* 4.8 2.6 - - - -
216D HIS* 4.7 8.5 - - - -
142F SER* 1.3 78.0 + - - +
144F GLU* 1.3 64.1 + - - +
145F LYS* 2.7 37.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F KZ4 5.4 15.9 - - + -
66F ARG* 3.2 37.8 + - - -
142F SER* 4.1 3.0 + - - +
143F THR* 1.3 79.1 - - - +
145F LYS* 1.3 71.4 + - - +
146F LEU* 3.6 36.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D PRO 5.4 7.4 - - - +
142D SER* 5.7 2.7 - - - -
143D THR 3.7 28.8 + - - +
145D LYS* 4.2 8.5 - - - +
157D VAL* 4.8 4.1 - - - +
158D ASN* 3.3 36.1 + - + +
159D THR* 5.4 2.9 - - - -
170D ARG* 6.5 1.1 - - - -
143F THR* 2.7 33.5 + - + +
144F GLU* 1.3 84.0 - - - +
146F LEU* 1.3 63.3 + - - +
147F TYR* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ARG* 4.9 4.9 - - + -
71F TYR* 4.2 11.9 - - - +
79F PHE* 4.0 32.1 - - + -
144F GLU* 3.6 47.8 - - + +
145F LYS* 1.3 75.9 - - - +
147F TYR* 1.3 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D HIS* 4.2 35.0 - - + +
170D ARG* 3.9 35.6 + - + +
145F LYS* 4.0 19.1 - - + -
146F LEU* 1.3 78.5 - - - +
148F VAL* 1.3 74.5 + - - +
149F ARG* 3.8 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D GLY* 4.7 15.4 - - - -
168D HIS* 4.9 3.7 + - - -
78F TYR* 6.5 0.7 - - + -
147F TYR* 1.3 84.5 - - - +
149F ARG* 1.3 68.3 + - - +
150F ASP 4.6 0.7 - - - +
151F GLY* 4.1 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLU* 2.7 36.9 + - - -
168D HIS* 2.8 32.3 + - - +
170D ARG* 4.5 3.2 - - - +
147F TYR* 3.8 30.4 + - + +
148F VAL* 1.3 76.7 + - - +
150F ASP* 1.3 89.4 + - - +
151F GLY 3.2 6.8 + - - -
----------------------------------------------------------
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