Contacts of the helix formed by residues 101 - 105 (chain I) in PDB entry 3CII
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 ASN 101 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I LEU* 3.3 22.7 - - - +
100I GLN* 1.3 86.2 - - - +
102I THR* 1.3 64.3 + - - +
103I ASP* 3.4 29.2 + - - +
104I GLU* 3.8 4.8 + - - +
140I LEU* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 5.2 7.6 - - - +
99I LEU* 4.9 0.9 - - - +
101I ASN* 1.3 77.0 - - - +
103I ASP* 1.3 66.1 + - - +
104I GLU* 2.9 7.4 + - - +
105I LEU 3.9 12.6 + - - +
106I ASP* 4.5 2.1 - - - +
140I LEU* 3.6 20.9 + - + +
155I TYR* 4.0 23.9 + - - +
157I PRO 5.2 2.2 - - - +
158I ASN 5.1 3.4 - - - +
159I GLY* 4.5 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I TYR* 4.9 1.4 + - - -
69I ARG* 3.2 24.8 + - - +
101I ASN* 3.4 16.3 + - - +
102I THR* 1.3 84.1 - - - +
104I GLU* 1.3 58.3 - - - +
105I LEU 3.7 0.7 - - - -
106I ASP* 3.5 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I TYR* 3.7 25.8 - - - -
69I ARG* 5.0 7.0 - - - +
71I ASN* 4.5 2.5 + - - +
73I TYR* 3.2 26.3 + - + +
97I LEU* 3.3 25.9 - - - +
98I GLN 3.4 5.0 - - - +
99I LEU* 3.4 14.0 - - + +
100I GLN* 3.3 35.2 + - + +
101I ASN* 3.8 14.3 + - - +
102I THR 2.9 2.2 + - - -
103I ASP* 1.3 78.9 - - - +
105I LEU* 1.3 67.1 + - + +
106I ASP* 4.0 0.7 - - - -
107I PHE* 4.1 1.0 - - - -
175I LYS* 3.5 19.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I TYR* 4.5 17.9 - - + -
97I LEU* 3.7 31.0 - - + -
99I LEU* 4.5 5.2 - - + -
102I THR 3.9 6.3 + - - +
104I GLU* 1.3 90.4 - - + +
106I ASP* 1.3 72.8 + - - +
107I PHE* 3.8 11.4 - - + -
108I MET* 3.5 35.7 - - + -
155I TYR* 3.7 30.3 - - + -
157I PRO* 3.7 29.2 - - + +
173I ILE* 4.3 2.2 - - + -
----------------------------------------------------------
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