Contacts of the strand formed by residues 127 - 132 (chain C) 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 VAL 127 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 4.3 3.7 - - - +
94C VAL* 3.8 12.6 - - + -
113C ARG* 2.8 60.5 + - + +
116C ILE* 3.7 34.3 - - + -
117C ALA* 4.2 7.2 - - + +
122C CYS* 3.6 26.5 - - - -
123C HIS 4.0 3.4 - - - +
124C MET 2.9 10.5 + - - +
125C ASP 3.2 0.6 - - - -
126C ASP* 1.3 84.0 - - - +
128C ASN* 1.3 59.5 + - - +
129C VAL* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ARG* 5.5 0.4 - - - +
50B GLY* 3.3 31.3 - - - +
53B ALA* 3.2 16.1 - - + +
55B GLY* 2.9 48.7 + - - -
94C VAL 3.0 10.6 + - - +
95C ASP* 2.9 22.6 + - - +
96C VAL* 2.8 26.9 + - - +
113C ARG* 4.5 3.4 + - - +
127C VAL* 1.3 75.0 - - - +
129C VAL* 1.3 72.0 + - - +
130C LYS* 3.7 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY* 4.6 7.3 - - - -
56B ASP* 4.9 0.5 - - - +
40C ALA* 5.9 0.7 - - + -
96C VAL* 3.5 17.9 - - + +
98C ILE* 3.7 19.5 - - + -
109C ILE* 3.3 46.3 - - + +
112C MET* 4.0 12.1 - - + -
113C ARG* 4.0 20.0 - - + +
116C ILE* 3.9 27.6 - - + -
127C VAL* 4.3 3.3 - - + -
128C ASN* 1.3 86.2 + - - +
130C LYS* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B HIS 2.7 26.8 + - - +
6B GLY* 5.2 0.2 - - - -
46B ASP* 3.5 42.8 - - + +
55B GLY 3.8 7.4 - - - +
56B ASP* 3.4 22.0 - - + +
95C ASP* 2.8 31.7 + - - -
96C VAL 2.8 13.1 + - - +
97C THR* 2.8 30.3 + - + +
98C ILE* 2.8 36.0 + - - +
109C ILE* 4.8 4.3 - - - -
128C ASN* 3.7 7.4 - - - +
129C VAL* 1.3 77.0 - - - +
131C ALA* 1.3 56.7 + - - +
132C THR* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASP* 5.6 1.2 - - - +
56B ASP* 3.6 8.0 + - - +
98C ILE* 3.2 10.3 - - + +
105C MET* 3.6 35.2 - - + -
106C LEU 5.3 0.2 - - - +
109C ILE* 4.8 3.5 - - + +
130C LYS* 1.3 80.0 - - - +
132C THR* 1.3 63.7 + - - +
2901C 1AA 3.2 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.5 41.7 + - + +
8B ASP* 3.8 10.2 + - - -
46B ASP* 5.3 6.2 + - - -
57B ILE* 6.0 0.7 - - - +
97C THR* 4.1 15.3 - - + -
98C ILE 2.8 13.5 + - - +
99C ILE* 3.4 6.3 - - + -
100C ALA 2.8 29.8 + - - +
130C LYS* 6.1 0.4 - - - -
131C ALA* 1.3 75.8 - - - +
133C THR* 1.3 68.6 + - - +
2901C 1AA 3.0 20.7 + - - -
----------------------------------------------------------
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