Contacts of the helix formed by residues 101 - 109 (chain A) in PDB entry 3E2A
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 CYS 101 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A CYS* 3.9 5.2 - - - -
44A ASP* 3.2 4.3 - - - -
67A ALA* 4.4 6.3 - - - -
68A ASN* 5.0 2.2 - - - -
98A HIS* 3.6 21.5 - - + +
99A THR 3.2 1.4 - - - -
100A ASN* 1.3 72.6 - - - +
102A GLY* 1.3 65.2 + - - +
103A GLY* 3.4 9.2 - - - -
104A ILE* 3.5 31.8 - - + +
105A HIS* 3.0 26.8 + - - -
147A THR* 4.5 5.4 + - + +
230A ZN 2.3 38.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 3.3 19.2 + - - +
100A ASN 3.3 6.6 + - - -
101A CYS* 1.3 71.4 - - - +
103A GLY* 1.3 51.1 + - - +
105A HIS* 3.3 8.4 + - - +
106A ALA* 2.5 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 3.1 12.9 + - - -
66A VAL* 3.8 27.8 - - - -
67A ALA* 4.5 4.7 - - - -
101A CYS* 3.3 5.4 - - - -
102A GLY* 1.3 74.1 - - - +
104A ILE* 1.3 53.1 + - - +
106A ALA* 3.2 8.1 + - - +
107A ALA* 2.7 33.8 + - - +
120A LEU* 3.8 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA* 4.6 8.1 - - + -
68A ASN* 6.1 0.2 - - - +
101A CYS* 3.3 26.9 + - + +
103A GLY* 1.3 71.5 - - - +
105A HIS* 1.3 68.2 + - - +
107A ALA* 3.1 6.9 + - - +
108A MET* 3.0 33.8 + - - +
123A ILE* 4.2 14.4 - - + -
143A ALA* 3.9 13.0 - - + +
146A LEU* 3.9 20.9 - - + +
147A THR* 3.7 30.7 - - + +
150A ASN* 3.9 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASN* 4.3 22.6 + - + +
101A CYS 3.0 26.0 + - - +
102A GLY* 3.6 7.6 - - - +
104A ILE* 1.3 77.3 - - + +
106A ALA* 1.3 61.9 - - - +
108A MET* 3.2 8.2 + - - +
109A ALA* 3.2 23.0 + - - +
143A ALA* 3.4 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 6.2 0.2 - - + -
102A GLY 2.5 22.5 + - - +
103A GLY* 3.3 8.5 - - - +
105A HIS* 1.3 75.1 - - - +
107A ALA* 1.3 61.4 + - - +
108A MET 3.4 0.2 + - - -
109A ALA* 3.5 18.2 + - - +
111A LYS 5.5 0.7 - - - +
113A LEU* 4.2 23.4 - - + +
116A ILE* 6.0 0.2 - - + -
117A ASN* 4.7 3.8 - - - +
120A LEU* 3.6 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY 2.7 17.0 + - - +
104A ILE 3.1 9.4 + - - +
106A ALA* 1.3 73.5 - - - +
108A MET* 1.3 57.4 + - + +
109A ALA 3.9 0.5 - - - +
117A ASN* 5.8 0.4 - - - -
120A LEU* 3.8 22.8 - - + +
123A ILE* 3.6 38.1 - - + -
124A ARG* 2.9 34.6 + - + +
127A TRP* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 3.0 17.6 + - - +
105A HIS* 3.2 6.9 + - - +
107A ALA* 1.3 73.6 - - - +
109A ALA* 1.3 68.7 + - - +
110A ASP* 3.8 1.6 + - - +
124A ARG* 3.6 6.8 + - - -
127A TRP* 3.5 48.9 - - + +
134A LEU* 5.7 0.9 - - + -
142A ARG* 3.9 27.8 - - + +
143A ALA* 3.6 32.1 - - - +
146A LEU* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A HIS 3.2 12.9 + - - +
106A ALA* 3.8 15.6 - - - +
107A ALA 3.5 3.2 - - - +
108A MET* 1.3 82.3 - - - +
110A ASP* 1.3 64.3 + - - +
111A LYS* 4.3 15.7 - - + +
113A LEU* 5.8 2.7 - - + -
124A ARG* 3.3 13.5 + - - -
----------------------------------------------------------
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