Contacts of the strand formed by residues 90 - 99 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TRP* 3.9 10.3 - - - -
85A GLN* 5.1 7.9 - - - +
88A GLY 4.0 3.7 + - - +
89A TYR* 1.3 77.1 - - - +
91A LEU* 1.3 60.9 + - - +
154A LEU* 3.4 8.3 - - - +
155A ILE* 2.8 51.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.6 30.5 - - + -
81A TRP* 3.6 18.8 - - + -
90A THR* 1.3 75.9 - - - +
92A GLY* 1.3 64.3 + - - +
93A ASN* 4.1 7.4 - - - +
94A VAL* 3.7 18.8 - - + -
120A LEU* 3.9 17.7 - - + +
122A CYS* 3.5 40.2 - - + -
126A ASP* 4.6 15.0 - - + +
153A LEU 4.3 3.6 - - - +
154A LEU* 4.0 8.1 - - + -
155A ILE* 3.8 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.6 8.5 - - - -
90A THR 3.8 1.4 + - - -
91A LEU* 1.3 74.9 - - - +
93A ASN* 1.3 64.4 + - - +
126A ASP* 3.6 21.5 - - - +
153A LEU 2.8 20.0 + - - -
155A ILE* 3.8 19.8 - - - +
1C MET 5.4 2.9 - - - -
2C ARG* 4.5 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.9 5.6 - - - +
92A GLY* 1.3 79.1 - - - +
94A VAL* 1.3 72.0 + - - +
126A ASP* 3.4 14.6 - - - +
152A ALA* 3.7 0.3 - - - -
153A LEU* 2.9 33.3 + - - +
1C MET 4.3 0.2 - - - +
2C ARG* 3.3 42.6 - - + +
3C ILE* 2.8 53.4 + - - +
50C GLY 4.5 1.4 + - - -
51C ALA* 4.0 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.8 33.2 - - + -
48A LEU* 4.1 3.6 - - + -
91A LEU* 3.7 22.7 - - + -
93A ASN* 1.3 87.1 + - - +
95A ASP* 1.3 61.5 + - - +
96A VAL* 5.1 1.6 - - + -
116A ILE* 4.6 1.3 - - + -
120A LEU* 4.4 8.5 - - + -
126A ASP 2.9 17.0 + - - +
127A VAL* 4.1 25.4 - - + -
128A ASN* 3.0 27.8 + - - +
151A VAL 3.4 4.3 - - - +
152A ALA* 3.8 16.6 - - + -
2C ARG* 5.6 0.3 + - - -
3C ILE* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 1.3 74.4 - - - +
96A VAL* 1.3 65.3 + - - +
97A THR 4.2 0.7 + - - -
128A ASN* 2.8 28.3 + - - -
130A LYS* 2.8 24.8 + - - -
150A ALA* 3.3 2.4 - - - -
151A VAL* 2.9 51.5 + - + +
3C ILE* 4.0 10.7 - - - +
4C GLY* 3.5 0.2 - - - -
5C HIS* 2.7 28.4 + - - +
50C GLY* 3.4 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 4.4 11.7 - - + +
44A LEU* 4.0 33.2 - - + -
94A VAL* 5.1 2.7 - - + -
95A ASP* 1.3 78.7 + - - +
97A THR* 1.3 60.1 + - - +
98A ILE* 4.3 5.8 - - + -
116A ILE* 5.0 3.8 - - + -
128A ASN 2.8 17.1 + - - +
129A VAL* 3.4 24.6 - - + -
130A LYS* 2.7 36.8 + - - +
148A CYS* 3.5 26.5 - - - -
149A GLU 3.6 3.1 - - - +
150A ALA* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP 4.2 0.4 + - - -
96A VAL* 1.3 70.1 - - - +
98A ILE* 1.3 62.1 + - - +
99A ILE* 3.5 4.8 + - + +
130A LYS* 2.7 36.6 + - + +
132A THR* 4.0 27.4 - - + +
148A CYS* 3.5 1.6 - - - -
149A GLU* 2.7 42.5 + - - +
5C HIS* 3.1 25.3 + - - +
7C PHE* 4.0 21.1 - - + +
46C ASP* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.8 18.4 - - + -
39A VAL* 5.7 0.4 - - + -
40A ALA* 4.6 1.6 - - + -
96A VAL* 4.3 3.1 - - + -
97A THR* 1.3 71.3 - - - +
99A ILE* 1.3 61.1 + - - +
100A ALA* 3.7 3.9 + - + -
105A MET* 4.1 31.4 - - + -
109A ILE* 4.7 0.7 - - + -
112A MET* 3.8 22.7 - - + -
129A VAL* 3.7 28.5 - - + -
130A LYS 2.7 17.2 + - - +
131A ALA* 3.2 5.3 - - + +
132A THR* 2.9 27.9 + - - +
146A ILE* 3.9 23.1 - - + -
147A ALA 4.0 2.5 - - - +
148A CYS* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 4.8 1.1 - - + -
97A THR* 3.8 10.1 - - + +
98A ILE* 1.3 72.4 - - - +
100A ALA* 1.3 62.8 + - - +
132A THR* 3.5 11.7 - - + +
134A THR* 3.6 31.4 - - + -
140A THR* 3.4 15.1 - - + +
146A ILE* 3.5 0.3 - - - +
147A ALA* 2.8 54.6 + - + +
148A CYS 4.7 0.2 - - - +
149A GLU* 3.7 30.3 - - + +
7903A GPP 4.2 13.0 - - + -
7C PHE* 3.8 30.5 - - + -
----------------------------------------------------------
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