Contacts of the helix formed by residues 89 - 94 (chain A) in PDB entry 2AN3
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 SER 89 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 4.5 4.2 + - - +
61A LEU* 4.3 7.0 - - - +
62A ALA* 3.6 36.5 + - - +
65A PHE* 4.0 13.8 - - - +
85A TYR 5.1 0.4 + - - -
86A GLN 5.4 0.6 + - - -
87A LEU 3.4 0.2 - - - -
88A LEU* 1.3 77.0 - - - +
90A ALA* 1.3 64.1 + - - +
92A SER* 3.4 18.2 + - - -
93A HIS* 3.6 10.2 + - - -
130A ALA* 4.5 7.1 - - - +
134A GLU* 2.6 26.2 + - - +
143A LYS* 4.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.2 36.3 - - + -
75A LEU* 3.9 18.8 - - + -
86A GLN 4.5 2.7 + - - +
87A LEU* 3.3 23.0 + - + +
89A SER* 1.3 76.7 - - - +
91A CYS* 1.3 54.6 + - - +
92A SER 3.1 2.9 - - - -
93A HIS* 2.8 34.3 + - - +
94A PHE* 3.7 7.0 + - - -
97A ILE* 5.6 0.2 - - + -
179A VAL* 5.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 2.9 14.0 + - - +
88A LEU 3.3 21.3 - - - -
90A ALA* 1.3 74.5 - - - +
92A SER* 1.3 60.1 + - - +
93A HIS 3.2 0.4 - - - -
94A PHE 3.3 2.6 - - - +
97A ILE* 3.6 17.0 - - + +
143A LYS* 4.2 12.8 - - - -
146A GLN* 3.9 17.4 - - + +
147A LEU* 3.8 40.2 - - + +
150A ARG* 3.0 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER 3.4 7.5 + - - -
90A ALA 2.8 3.4 + - - -
91A CYS* 1.3 79.0 - - - +
93A HIS* 1.3 80.9 + - - +
134A GLU* 5.1 2.4 + - - -
136A LYS* 4.2 12.0 + - - -
138A GLU* 6.1 0.7 - - - -
143A LYS* 5.3 5.8 + - - -
146A GLN* 3.5 26.8 + - - +
150A ARG* 3.6 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.4 38.9 + + + +
66A ALA* 5.3 1.5 - - - -
68A GLY* 5.1 6.3 - - - -
70A VAL 4.0 16.6 - - - +
71A SER* 4.4 8.3 - - - -
72A GLY 3.3 19.6 + - - +
89A SER 3.6 10.8 + - - -
90A ALA 2.8 4.2 + - - +
92A SER* 1.3 105.6 + - - +
94A PHE* 1.3 86.4 + - + +
136A LYS* 4.5 13.2 + - - -
150A ARG* 4.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.7 19.7 - + - -
70A VAL* 3.9 4.5 - - + -
71A SER* 3.4 24.9 - - - -
72A GLY* 3.3 29.8 - - - -
73A ARG 3.9 6.1 - - - +
74A THR 3.5 19.5 - - - -
75A LEU* 3.4 35.4 - - + +
90A ALA 3.7 6.3 + - - +
91A CYS 3.3 2.6 - - - +
93A HIS* 1.3 98.6 - - + +
95A GLU* 1.3 63.5 + - - +
96A ASP 3.4 0.2 - - - -
97A ILE* 3.7 13.4 - - + +
150A ARG* 2.9 22.8 - - - +
176A ASP* 4.0 2.5 - - + -
177A ALA* 3.6 25.6 - - + -
----------------------------------------------------------
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