Contacts of the strand formed by residues 106 - 112 (chain J) in PDB entry 1N13
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 106 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G ASP* 4.1 7.6 - - - +
53J PYR 3.6 14.8 - - - +
54J ILE* 4.0 6.7 - - + -
94J SER 3.7 0.9 - - - +
95J VAL* 3.3 2.0 - - - +
96J ALA* 2.8 36.9 + - + +
104J CYS* 6.4 0.2 - - - -
105J GLY* 1.3 73.5 - - - -
107J ILE* 1.3 64.0 + - - +
108J MET* 3.7 28.2 + - + -
127J ALA* 3.9 12.2 - - - +
130J GLY* 3.4 35.7 - - - -
131J PHE* 3.8 15.8 - - + -
134J ARG* 3.8 31.9 - - - +
136J TRP* 6.4 0.2 - - + -
7013J AG2 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I VAL* 4.5 4.7 - - + -
51I ILE* 4.9 2.9 - - + -
53J PYR 2.8 39.1 + - + +
54J ILE 4.0 23.8 - - - +
55J MET* 4.1 7.4 - - - +
76J ALA* 3.7 19.1 - - + -
93J ILE* 4.2 8.1 - - + -
94J SER 3.2 10.1 - - - +
95J VAL* 4.1 16.4 - - + -
106J LEU* 1.3 75.6 - - - +
108J MET* 1.3 66.4 + - - +
109J GLU* 4.4 0.4 - - - -
160J ALA* 3.7 32.1 - - + -
162J LEU* 4.4 16.6 - - + -
7013J AG2 3.0 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 3.7 29.2 - - - +
32G ASN* 3.8 17.9 - - - +
35G ASP* 3.8 19.7 - - + +
93J ILE* 3.4 8.2 - - - +
94J SER* 2.9 44.3 + - - +
106J LEU* 3.7 27.9 + - + -
107J ILE* 1.3 74.8 - - - +
109J GLU* 1.3 62.4 + - - +
123J VAL* 3.3 12.2 - - + +
126J MET* 3.8 15.5 - - + +
127J ALA* 3.7 24.9 - - + +
7013J AG2 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 3.4 21.8 - - + +
7003H MRD 4.6 11.7 + - + +
50I ARG* 4.7 8.1 + - - +
51I ILE 4.8 7.3 - - - +
52I SER* 5.8 0.2 - - - -
53J PYR 4.4 1.7 - - - +
76J ALA* 4.6 5.6 - - - +
77J TYR 3.6 24.2 + - - +
78J GLY* 3.9 13.9 - - - +
92J ALA 3.4 4.9 - - - +
93J ILE* 3.5 19.1 - - + -
107J ILE 3.9 2.1 - - - +
108J MET* 1.3 77.4 - - - +
110J TYR* 1.3 63.2 + - - +
111J GLU* 5.1 2.7 - - - +
123J VAL* 3.7 1.6 - - - -
126J MET* 3.6 8.0 - - - +
7013J AG2 2.8 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J GLY* 4.6 2.6 - - - -
91J ALA* 3.3 3.6 - - - +
92J ALA* 2.8 32.2 + - + +
109J GLU* 1.3 76.4 - - - +
111J GLU* 1.3 99.8 + - - +
112J GLY* 4.6 3.5 - - - -
114J CYS* 4.0 24.0 - - - +
118J GLU* 4.7 7.0 + - - -
119J ALA* 3.8 25.6 - - + +
122J THR* 3.9 29.4 + - + +
123J VAL* 3.8 20.2 - - + +
126J MET* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I ARG* 5.2 3.5 + - - -
78J GLY* 3.7 9.0 - - - -
79J TYR* 3.2 47.3 + - - +
80J ILE* 4.0 8.5 - - + -
90J SER 3.2 13.0 - - - +
91J ALA* 4.4 0.7 - - - -
109J GLU* 5.1 3.5 - - - +
110J TYR* 1.3 103.3 + - - +
112J GLY* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 112 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J ILE* 3.6 17.1 - - - +
89J ILE* 3.6 1.0 - - - -
90J SER* 2.9 32.7 + - - +
110J TYR* 4.3 7.4 - - - -
111J GLU* 1.3 76.8 - - - +
113J LYS* 1.3 62.1 + - - -
114J CYS* 3.0 12.5 + - - -
----------------------------------------------------------
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