Contacts of the strand formed by residues 138 - 149 (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 138 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J ALA* 3.6 24.2 - - + -
97J ILE 3.6 16.4 - - - +
99J LYS* 3.5 16.8 + - - -
128J LYS* 4.0 29.8 - - + -
131J PHE* 3.9 20.6 - - + -
136J TRP 3.4 3.4 + - - +
137J GLU* 1.3 71.8 - - - +
139J ASP* 1.3 62.6 + - - +
140J ARG* 3.6 19.7 - - - +
141J ILE* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J ILE* 2.8 29.4 + - - +
98J PRO 3.5 17.0 - - - +
99J LYS* 3.7 18.4 - - + +
101J LYS* 3.8 6.7 + - - -
137J GLU 3.8 2.4 + - - -
138J LEU* 1.3 74.7 - - - +
140J ARG* 1.3 96.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J ILE* 5.0 6.1 - - - +
97J ILE* 2.9 54.4 + - + +
101J LYS* 5.0 2.8 - - - +
138J LEU* 3.6 6.5 - - - +
139J ASP* 1.3 115.0 + - - +
141J ILE* 1.3 70.8 - - - +
142J GLU* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J SER* 3.8 19.7 - - - -
95J VAL 3.3 9.6 - - - +
96J ALA* 4.1 5.6 - - - -
124J ARG* 2.9 74.5 + - + +
127J ALA* 4.3 2.5 - - + -
128J LYS* 4.1 20.0 - - - +
138J LEU* 3.8 28.9 - - + -
140J ARG* 1.3 83.3 - - - +
142J GLU* 1.3 75.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU* 4.0 12.6 - - + +
61J ILE* 3.3 38.4 - - + -
94J SER* 3.2 2.6 - - - -
95J VAL* 2.7 36.6 + - + +
97J ILE* 3.9 9.2 - - + -
124J ARG* 4.3 0.2 - - - +
140J ARG* 2.9 30.0 + - - +
141J ILE* 1.3 77.7 - - - +
143J SER* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU* 3.8 8.4 - - - +
93J ILE 3.1 14.8 - - - -
94J SER* 4.1 2.7 - - - -
120J GLU* 2.7 30.3 + - - +
123J VAL* 4.7 0.7 - - - -
124J ARG* 2.9 40.4 + - - +
142J GLU* 1.3 76.3 + - - +
144J ILE* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU* 3.8 28.9 - - + +
21I VAL* 3.8 40.4 - - - +
22I ALA* 3.9 12.8 - - + +
92J ALA* 3.4 1.9 - - - +
93J ILE* 2.9 46.5 + - + +
120J GLU* 4.1 5.6 - - - +
143J SER* 1.3 77.6 - - - +
145J ALA* 1.3 70.2 + - - +
158J ALA* 4.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I ALA* 4.4 4.6 - - - +
91J ALA 3.3 13.2 - - - +
92J ALA* 3.7 11.2 - - + -
116J LYS* 3.2 49.7 + - + +
119J ALA* 4.9 0.4 - - + -
120J GLU* 3.8 14.3 + - + +
144J ILE* 1.3 85.4 - - - +
146J VAL* 1.3 64.5 + - - +
158J ALA* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 146 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I ALA* 3.9 10.8 - - + -
23I GLY* 3.6 26.2 - - - +
24I SER* 4.3 7.4 - - - +
40I ASN* 5.7 0.2 - - - +
90J SER* 3.2 6.3 - - - -
91J ALA* 3.0 35.3 + - + +
116J LYS* 4.2 7.6 - - - +
145J ALA* 1.3 76.8 - - - +
147J GLU* 1.3 71.4 + - - +
156J ALA* 4.4 3.3 - - + +
157J PHE 3.3 33.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I SER* 4.2 3.9 + - - -
88J THR* 4.2 13.8 - - + +
89J ILE 3.3 5.4 - - - +
90J SER* 3.2 16.2 - - - +
115J SER* 3.7 11.6 - - - -
116J LYS* 3.0 36.0 + - + +
146J VAL* 1.3 83.8 - - - +
148J HIS* 1.3 62.4 + - - +
149J THR* 6.0 1.6 - - - +
156J ALA* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 148 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I SER* 3.0 32.5 + - - -
25I SER* 3.9 20.4 - - - -
26I GLU* 2.8 33.1 + - + -
87J GLU 3.6 0.7 - - - +
88J THR* 3.3 3.1 - - - -
89J ILE* 2.7 48.8 + - + +
147J GLU* 1.3 76.8 - - - +
149J THR* 1.3 78.2 + - - +
150J VAL* 3.7 8.7 - - + -
151J GLU* 5.5 2.7 - - - -
154J GLY* 3.9 15.4 - - - -
155J CYS 4.3 5.4 - - - +
156J ALA* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I GLU* 4.1 0.2 - - - +
86J GLY* 3.9 26.0 - - - +
87J GLU 3.5 2.7 - - - -
88J THR* 3.7 16.3 + - - +
147J GLU* 6.0 1.9 - - - +
148J HIS* 1.3 84.2 + - - +
150J VAL* 1.3 67.9 + - - +
151J GLU* 3.4 10.0 + - - +
----------------------------------------------------------
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