Contacts of the helix formed by residues 88 - 99 (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 ILE 88 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D PHE* 3.7 32.5 - - + -
8D LEU* 4.0 7.6 - - + -
11D ALA* 3.8 24.2 - - + +
12D MET* 3.7 29.4 - - + +
15D HIS* 4.0 14.4 - - + +
40D THR* 4.3 9.4 - - + -
55D ILE* 4.1 22.9 - - + -
85D SER 5.1 0.9 - - - +
87D ASP* 1.3 71.6 + - - +
89D THR* 1.3 52.0 + - - +
90D ALA 3.3 2.7 - - - -
91D SER* 3.1 9.4 + - - -
92D VAL* 2.8 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D HIS* 3.0 33.1 - - + +
87D ASP* 2.6 27.7 + - - -
88D ILE* 1.3 76.0 - - - +
90D ALA* 1.3 57.4 + - - +
92D VAL* 3.2 4.7 + - - +
93D ASN* 2.9 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ILE* 4.4 14.5 - - + +
82D ALA* 3.7 32.3 - - + +
83D LEU* 3.9 13.8 - - + +
87D ASP 4.5 2.7 + - - +
88D ILE 3.3 0.2 - - - -
89D THR* 1.3 79.4 - - - +
91D SER* 1.3 59.0 + - - +
93D ASN* 3.5 8.1 + - - +
94D CYS* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D TYR 4.6 2.3 + - - -
54D GLY* 4.6 1.6 - - - -
55D ILE* 4.0 31.4 + - - +
56D LEU* 4.5 7.7 + - - +
58D ILE* 4.7 8.4 - - - +
82D ALA 5.0 0.6 + - - -
83D LEU* 3.7 37.7 + - - +
87D ASP 5.5 0.2 + - - -
88D ILE* 3.1 12.1 + - - -
90D ALA* 1.3 75.8 - - - +
92D VAL* 1.3 58.3 + - - +
94D CYS* 3.6 2.6 + - - +
95D ALA* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D MET* 5.2 0.4 - - + -
15D HIS* 3.5 40.2 - - + +
17D LEU* 3.9 25.2 - - + +
55D ILE* 5.6 3.1 - - + -
56D LEU* 5.7 1.1 - - + -
88D ILE* 2.8 45.7 + - + +
89D THR 3.5 7.9 - - - +
91D SER* 1.3 71.2 - - - +
93D ASN* 1.3 61.1 + - - +
95D ALA* 3.1 7.7 + - - +
96D LYS* 2.8 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D CYS* 5.7 0.7 - - - -
89D THR* 2.9 43.2 + - - +
90D ALA* 3.8 6.9 - - - +
92D VAL* 1.3 75.5 - - - +
94D CYS* 1.3 62.1 + - - +
96D LYS* 3.5 19.7 + - - +
97D LYS* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ILE* 3.8 16.8 - - + -
63D TRP* 3.8 19.5 - - - -
76D CYS* 2.1 53.4 - - + -
78D ILE* 4.3 6.7 - - + -
83D LEU* 4.6 8.7 - - + -
90D ALA 3.0 18.8 + - - +
91D SER* 4.1 3.4 - - - +
93D ASN* 1.3 77.2 - - - +
95D ALA* 1.3 58.0 + - - +
97D LYS* 3.2 2.8 + - - +
98D ILE* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 5.1 1.8 - - + -
28D TRP* 4.2 13.5 - - + -
56D LEU* 3.7 24.5 - - + -
58D ILE* 5.2 1.7 - - + +
91D SER 3.0 19.3 + - - +
92D VAL* 3.1 6.7 + - - +
94D CYS* 1.3 75.8 - - - +
96D LYS* 1.3 52.3 + - - +
98D ILE* 3.3 6.3 + - - +
99D VAL* 2.8 40.2 + - - +
108D TRP* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 4.1 13.1 + - - -
15D HIS 2.8 29.7 + - - -
16D GLY 4.0 12.6 + - - -
17D LEU* 3.9 18.6 - - + +
20D TYR* 2.7 51.1 + - + +
21D ARG* 4.0 2.3 + - - -
92D VAL* 2.8 30.6 + - + +
93D ASN* 3.5 20.2 + - - +
95D ALA* 1.3 73.2 - - - +
97D LYS* 1.3 54.9 + - - +
99D VAL 2.8 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ARG* 5.9 0.2 + - - -
63D TRP* 4.0 13.1 - - + -
75D LEU* 3.6 41.5 - - - +
76D CYS* 4.0 20.9 - - + -
93D ASN 3.2 11.0 + - - +
94D CYS 3.2 8.6 + - - +
96D LYS* 1.3 75.5 - - - +
98D ILE* 1.3 63.1 + - - +
99D VAL 4.4 2.4 - - - -
100D SER* 4.6 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C TYR* 5.6 4.5 - - + -
138C LEU* 4.6 5.8 - - + -
58D ILE* 3.4 46.2 - - + -
63D TRP* 3.6 44.9 - - + +
94D CYS 3.0 21.3 + - - +
95D ALA* 3.3 5.4 + - - +
97D LYS* 1.3 77.4 - - - +
99D VAL* 1.3 56.3 + - - +
100D SER* 3.3 10.2 + - - -
104D GLY 4.1 4.5 - - - +
107D ALA* 3.8 28.7 - - + +
108D TRP* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D TYR* 3.4 10.2 + - + -
21D ARG* 3.0 19.0 + - - -
23D TYR* 3.9 28.7 - - + -
28D TRP* 3.6 25.4 - - + -
95D ALA 2.8 18.8 + - - +
96D LYS 2.8 19.1 - - - +
97D LYS 4.4 0.2 - - - -
98D ILE* 1.3 69.7 - - - +
100D SER* 1.3 59.4 + - - +
104D GLY* 3.5 19.3 - - - +
105D MET* 3.8 4.7 - - + -
108D TRP* 3.4 31.4 - - + -
----------------------------------------------------------
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