Contacts of the helix formed by residues 108 - 115 (chain D) in PDB entry 3G3B
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 TRP 108 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU* 3.6 21.0 - - + +
28D TRP* 4.4 8.5 - + - -
31D ALA* 5.2 2.7 - - + -
35D GLU* 3.5 35.0 - - + +
56D LEU* 2.7 39.1 + - + +
58D ILE* 3.7 23.1 - - + +
95D ALA* 4.0 21.1 - - + -
98D ILE* 4.0 21.8 - - + -
99D VAL* 3.4 27.1 - - + -
105D MET* 3.1 34.9 + - + +
106D ASN 3.9 1.5 - - - +
107D ALA* 1.3 74.8 - - + +
109D VAL* 1.3 60.3 + - - +
110D ALA 3.4 1.1 - - - -
111D TRP* 3.4 18.8 - - + +
112D ARG* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ASN 6.2 0.2 - - - -
140C LEU 4.1 9.6 - - - +
141C ASP* 3.6 39.0 - - + +
35D GLU* 4.9 0.6 + - - -
107D ALA 3.3 6.7 + - - +
108D TRP* 1.3 68.0 - - - +
110D ALA* 1.3 54.3 + - - +
112D ARG* 2.9 25.1 + - - +
113D ASN* 2.7 52.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PHE* 3.7 28.7 - - + +
35D GLU* 3.7 18.0 + - - +
108D TRP 3.4 0.4 - - - -
109D VAL* 1.3 76.4 - - - +
111D TRP* 1.3 55.7 + - - +
113D ASN* 3.1 5.9 + - - -
114D ARG* 2.7 45.4 + - - +
115D CYS* 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TYR* 3.9 19.1 - + - -
27D ASN* 3.0 54.6 + - - +
31D ALA* 3.8 15.1 - - + +
34D PHE* 5.4 0.6 - - - +
35D GLU* 4.6 0.8 + - - -
105D MET* 3.2 46.6 - - + +
106D ASN* 3.5 25.1 - - - -
108D TRP* 3.3 22.5 + - + +
109D VAL 3.2 0.2 - - - -
110D ALA* 1.3 76.4 - - - +
112D ARG* 1.3 78.6 + - + +
115D CYS* 2.9 51.5 + - + +
116D LYS* 2.9 45.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ASP* 2.7 41.8 + - - -
143C ASP* 3.6 19.8 + - - +
146C ARG* 3.7 18.8 - - - +
106D ASN* 2.5 63.7 + - - +
108D TRP 2.9 11.0 + - - +
109D VAL* 2.9 31.6 + - - +
111D TRP* 1.3 86.1 - - + +
113D ASN* 1.3 69.8 + - - +
116D LYS* 3.6 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D VAL* 2.7 36.5 + - - +
110D ALA* 3.9 3.8 - - - +
112D ARG* 1.3 86.5 + - - +
114D ARG* 1.3 67.4 + - + +
115D CYS 3.8 0.4 - - - -
116D LYS 5.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D CYS* 4.5 2.6 - - - -
34D PHE* 3.2 55.0 - - + -
110D ALA* 2.7 26.0 + - - +
113D ASN* 1.3 87.3 - - + +
115D CYS* 1.3 58.8 + - - +
116D LYS 5.1 0.4 - - - -
118D THR* 3.7 16.6 + - - +
123D TRP* 5.9 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D CYS* 2.0 62.8 - - + -
34D PHE* 3.8 11.9 - - - -
111D TRP* 2.9 37.0 + - + +
114D ARG* 1.3 79.2 - - - +
116D LYS* 1.3 67.5 + - - +
118D THR* 2.6 25.5 + - - -
120D VAL* 3.1 14.9 - - + +
----------------------------------------------------------
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