Contacts of the strand formed by residues 89 - 96 (chain F) in PDB entry 3N2N
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 GLY 89 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F VAL 3.5 7.9 - - - -
85F PHE* 3.9 7.4 - - - -
88F ARG* 1.3 73.2 + - - +
90F THR* 1.3 63.5 + - - -
122F GLU* 2.8 35.2 + - - +
123F GLY* 4.1 0.7 - - - -
126F ARG* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F LYS* 6.1 0.5 - - - -
83F ILE* 3.5 1.8 - - - -
84F VAL* 2.9 45.1 + - - +
88F ARG* 4.5 8.7 + - - +
89F GLY* 1.3 78.6 + - - +
91F THR* 1.3 72.5 + - - +
92F LEU* 3.3 4.9 + - - +
126F ARG* 3.9 9.0 - - - +
224F ACT 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F SER* 3.9 1.6 - - - +
82F PHE 3.9 3.8 - - - +
83F ILE* 4.1 3.5 - - + +
90F THR* 1.3 79.3 - - - +
92F LEU* 1.3 60.7 + - - +
93F MET 3.5 28.9 - - - +
94F LYS* 3.7 21.5 - - + +
126F ARG* 3.4 31.2 + - - +
130F GLN* 3.7 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F PHE* 2.8 27.8 + - + +
84F VAL* 4.2 16.4 - - + -
90F THR* 3.3 5.6 + - - -
91F THR* 1.3 73.0 - - - +
93F MET* 1.3 61.2 + - + +
105F GLY* 3.6 29.6 - - - +
108F GLU* 3.8 31.2 - - + +
109F LEU* 3.9 22.0 - - + +
112F VAL* 4.4 0.9 - - + -
224F ACT 3.8 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F MET* 3.2 38.8 - - + +
81F SER* 2.7 27.0 + - - -
82F PHE* 2.9 60.8 + - + +
91F THR* 3.6 3.6 - - - -
92F LEU* 1.3 83.0 - - + +
94F LYS* 1.3 64.4 + - - +
96F THR* 3.9 11.7 - - + -
101F GLN* 3.4 31.2 - - + +
102F ILE* 3.7 13.5 - - + -
105F GLY* 4.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F MET 3.7 0.9 - - - +
91F THR* 3.8 21.5 - - + +
92F LEU 4.4 0.2 - - - -
93F MET* 1.3 77.0 - - - +
95F LEU* 1.3 70.4 + - - +
96F THR* 3.2 17.2 + - - +
130F GLN* 3.6 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ASP* 3.5 34.3 - - + +
45F LEU 4.2 1.8 - - - +
46F TYR* 3.5 28.9 - - + +
79F ARG* 3.5 53.4 + - + +
80F MET* 3.4 12.6 - - - -
81F SER* 3.6 7.4 - - - +
94F LYS* 1.3 74.7 - - - +
96F THR* 1.3 60.8 + - - +
130F GLN* 2.9 19.6 + - + +
134F GLU* 3.6 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ARG* 3.2 10.1 - - - +
80F MET 3.0 29.7 + - - +
93F MET* 3.9 21.5 - - + -
94F LYS 3.4 13.2 - - - +
95F LEU* 1.3 76.5 - - - +
97F GLU* 1.3 59.6 + - - +
98F ASP* 2.9 25.2 + - - +
101F GLN* 4.0 17.7 - - + +
102F ILE* 3.9 12.4 - - + +
----------------------------------------------------------
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