Contacts of the helix formed by residues 89 - 95 (chain A) in PDB entry 3F5T
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 89 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP 5.6 0.7 - - - +
88A MET* 1.3 77.2 - - - +
90A LEU* 1.3 67.3 + - - +
91A GLU* 3.7 9.6 + - - +
92A GLU* 2.9 40.3 + - - +
93A MET* 3.0 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 1.3 73.6 - - - +
91A GLU* 1.3 61.7 + - - +
93A MET* 3.2 26.2 + - + +
94A SER* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 3.1 10.3 + - - +
90A LEU* 1.3 78.5 - - - +
92A GLU* 1.3 66.6 + - - +
94A SER* 3.9 5.3 + - - -
95A ARG* 3.0 68.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP 3.6 6.1 - - - +
88A MET* 3.3 25.0 - - + -
89A THR* 2.9 37.2 + - - +
91A GLU* 1.3 87.2 - - - +
93A MET* 1.3 56.7 + - - +
95A ARG* 4.1 13.7 + - - +
126A LYS* 3.0 29.6 + - - +
143A ARG* 2.8 27.5 + - - -
145A PHE* 4.1 16.0 - - + -
151A ILE* 4.2 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 4.4 8.3 - - - +
88A MET* 3.7 23.3 - - + +
89A THR 3.0 4.8 + - - +
90A LEU* 3.7 36.1 - - + +
92A GLU* 1.3 79.9 - - - +
94A SER* 1.3 58.1 + - - +
128A ASN* 3.2 35.9 - - - +
140A ILE* 4.9 9.6 - - + -
141A LEU* 3.5 34.6 - - + +
143A ARG* 3.0 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 2.9 20.9 + - - +
91A GLU* 3.9 4.3 + - - -
93A MET* 1.3 76.1 - - - +
95A ARG* 1.3 69.0 + - - +
96A ASP* 3.5 5.4 + - - +
143A ARG* 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU* 3.0 49.2 + - - +
92A GLU* 4.2 16.0 + - - +
93A MET 3.5 0.8 - - - -
94A SER* 1.3 79.4 - - - +
96A ASP* 1.3 77.4 + - - +
97A TRP* 3.9 1.9 - - - -
143A ARG* 3.0 25.6 + - - +
145A PHE* 4.4 6.3 - - - -
149A GLY 2.8 29.5 + - - -
150A ALA* 4.8 0.8 - - - +
151A ILE* 3.8 26.0 - - + +
----------------------------------------------------------
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