Contacts of the strand formed by residues 90 - 99 (chain B) in PDB entry 2AMT
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 THR 90 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TRP* 3.7 7.6 - - + -
85B GLN* 5.4 3.6 - - - +
88B GLY 4.4 3.6 + - - -
89B TYR* 1.3 75.3 - - - +
91B LEU* 1.3 73.7 + - - +
154B LEU* 3.4 11.4 - - - +
155B ILE* 2.5 53.8 + - + +
156B LYS* 5.1 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.7 30.5 - - + -
81B TRP* 3.5 22.3 - - + -
90B THR* 1.3 80.8 - - - +
92B GLY* 1.3 70.7 + - - +
93B ASN 4.2 0.4 - - - +
94B VAL* 3.7 18.4 - - + -
120B LEU* 4.0 16.2 - - + +
122B CYS* 3.4 41.3 - - + -
126B ASP* 4.1 19.9 - - + +
127B VAL* 5.1 0.2 - - + -
153B LEU 4.3 2.7 - - - +
154B LEU* 4.1 5.2 - - + -
155B ILE* 4.0 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 5.4 2.9 - - - -
2A ARG* 4.8 2.0 + - - -
1B MET* 4.6 4.7 - - - -
90B THR 3.6 2.8 + - - -
91B LEU* 1.3 77.9 - - - +
93B ASN* 1.3 63.4 + - - +
126B ASP* 3.6 19.1 - - - +
153B LEU* 2.8 24.2 + - - -
154B LEU* 4.0 1.0 - - - +
155B ILE* 3.9 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.4 0.2 - - - +
2A ARG* 3.4 41.1 - - + +
3A ILE* 2.8 48.2 + - - +
50A GLY 4.5 2.0 + - - -
51A ALA* 4.0 6.3 + - - +
91B LEU* 4.4 2.7 - - - -
92B GLY* 1.3 76.8 - - - +
94B VAL* 1.3 73.6 + - - +
126B ASP 3.4 13.5 - - - +
152B ALA* 3.5 1.6 - - - -
153B LEU* 2.8 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 5.8 0.2 - - - -
44B LEU* 3.6 34.1 - - + -
48B LEU* 4.1 2.5 - - + -
91B LEU* 3.7 23.3 - - + -
93B ASN* 1.3 85.9 + - - +
95B ASP* 1.3 62.9 + - - +
96B VAL* 4.8 4.7 - - + -
116B ILE* 4.5 5.2 - - + -
120B LEU* 4.2 4.3 - - + -
126B ASP 2.8 17.3 + - - +
127B VAL* 3.8 28.0 - - + -
128B ASN* 3.0 25.0 + - - +
151B VAL 3.4 4.7 - - - +
152B ALA* 3.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE 4.0 11.2 - - - +
4A GLY* 3.3 2.9 - - - -
5A HIS* 2.6 29.4 + - - +
50A GLY* 3.4 15.6 - - - +
94B VAL* 1.3 75.6 - - - +
96B VAL* 1.3 63.0 + - - +
128B ASN* 2.7 29.8 + - - +
130B LYS* 2.8 24.2 + - - -
149B GLU 4.1 0.3 - - - +
150B ALA* 3.4 2.9 - - - -
151B VAL* 3.0 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA* 4.2 18.4 - - + +
44B LEU* 4.3 26.9 - - + -
94B VAL* 4.8 4.0 - - + -
95B ASP* 1.3 79.8 + - - +
97B THR* 1.3 61.0 + - - +
98B ILE* 4.6 1.1 - - + -
116B ILE* 4.9 3.6 - - + -
128B ASN 2.7 17.5 + - - +
129B VAL* 3.5 21.4 - - + -
130B LYS* 2.8 36.6 + - - -
148B CYS* 3.4 26.2 - - - -
149B GLU 3.5 3.6 - - - +
150B ALA* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A HIS* 3.3 21.9 + - - +
7A PHE* 4.1 19.3 - - + +
96B VAL* 1.3 71.3 - - - +
98B ILE* 1.3 62.0 + - - +
99B ILE* 3.5 6.6 + - + +
130B LYS* 2.8 40.3 + - + +
132B THR* 4.0 26.0 - - + -
148B CYS* 3.3 4.5 - - - -
149B GLU* 2.6 43.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 3.7 26.2 - - + -
40B ALA* 4.3 13.0 - - + -
96B VAL* 4.6 0.7 - - + -
97B THR* 1.3 71.8 - - - +
99B ILE* 1.3 61.9 + - - +
100B ALA* 3.8 4.0 + - + -
105B MET* 3.9 40.2 - - + -
109B ILE* 4.8 0.9 - - + -
112B MET* 3.8 13.9 - - + -
129B VAL* 3.7 28.0 - - + -
130B LYS 2.7 14.7 + - - +
131B ALA* 3.2 4.4 - - + +
132B THR* 2.8 28.2 + - - +
146B ILE* 4.0 15.7 - - + -
147B ALA 3.9 2.9 - - - +
148B CYS* 4.2 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.7 30.1 - - + -
7903A GPP 3.8 19.1 - - + -
97B THR* 3.8 9.0 - - + +
98B ILE* 1.3 74.3 - - - +
100B ALA* 1.3 62.3 + - - +
132B THR* 3.4 13.2 - - + +
133B THR 4.8 0.4 - - - -
134B THR* 3.6 30.7 - - + -
140B THR* 3.8 13.2 - - + +
146B ILE* 3.6 2.0 - - - +
147B ALA* 2.7 50.0 + - + +
149B GLU* 3.7 31.0 - - + +
----------------------------------------------------------
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