Contacts of the strand formed by residues 89 - 96 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL 3.4 7.6 - - - -
85A PHE* 3.9 8.1 - - - -
88A ARG* 1.3 72.8 - - - +
90A THR* 1.3 64.1 + - - -
122A GLU* 2.8 32.7 + - - +
123A GLY* 4.1 1.1 - - - -
126A ARG* 2.8 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 6.1 0.7 - - - -
83A ILE* 3.5 1.7 - - - +
84A VAL* 2.9 44.3 + - - +
88A ARG* 4.5 9.7 + - - +
89A GLY* 1.3 77.1 + - - -
91A THR* 1.3 70.7 + - - +
92A LEU* 3.3 4.1 + - - +
126A ARG* 3.9 7.5 - - - +
222A ACT 5.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 3.8 1.8 - - - +
82A PHE 3.9 3.4 - - - +
83A ILE* 4.0 3.3 - - + +
90A THR* 1.3 78.4 - - - +
92A LEU* 1.3 61.3 + - - +
93A MET 3.5 28.0 - - - +
94A LYS* 3.7 22.0 + - + +
126A ARG* 3.3 31.7 + - - +
130A GLN* 3.7 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 2.8 30.3 + - + +
84A VAL* 4.2 14.8 - - + -
90A THR* 3.3 6.6 + - - -
91A THR* 1.3 73.2 - - - +
93A MET* 1.3 61.7 + - - +
105A GLY* 3.5 28.3 - - - +
108A GLU* 4.1 29.8 - - + +
109A LEU* 3.9 21.3 - - + +
112A VAL* 4.3 3.1 - - + -
222A ACT 3.8 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A MET* 3.2 42.8 - - + +
81A SER* 2.7 27.6 + - - -
82A PHE* 2.9 54.9 + - + +
91A THR* 3.5 3.1 - - - +
92A LEU* 1.3 81.9 - - + +
94A LYS* 1.3 62.7 + - - +
96A THR* 3.9 12.1 - - + -
101A GLN* 3.4 32.5 - - + +
102A ILE* 3.6 13.2 - - + -
105A GLY* 4.1 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A MET 3.7 1.7 - - - +
81A SER* 4.1 0.4 - - - -
91A THR* 3.8 21.5 - - + +
93A MET* 1.3 77.7 - - - +
95A LEU* 1.3 70.7 + - - +
96A THR* 3.2 15.9 + - - +
130A GLN* 3.7 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 3.4 37.0 - - + +
45A LEU 4.2 1.6 - - - +
46A TYR* 3.5 24.0 - - + +
79A ARG* 3.5 57.4 + - + +
80A MET* 3.3 13.0 - - - -
81A SER* 3.6 6.9 - - - +
94A LYS* 1.3 72.8 - - - +
96A THR* 1.3 60.3 + - - +
130A GLN* 2.9 20.1 + - + +
134A GLU* 3.7 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.2 9.8 - - - +
80A MET 2.9 27.9 + - - -
93A MET* 3.9 27.6 - - + -
94A LYS 3.5 12.3 - - - +
95A LEU* 1.3 77.5 - - - +
97A GLU* 1.3 58.2 + - - +
98A ASP* 3.0 24.6 + - - +
101A GLN* 4.1 14.9 - - + +
102A ILE* 3.8 14.4 - - + +
----------------------------------------------------------
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