Contacts of the helix formed by residues 88 - 100 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F PHE* 3.6 32.0 - - + -
8F LEU* 4.2 6.3 - - + -
11F ALA* 3.6 29.2 - - + -
12F MET* 3.8 22.7 - - + +
15F HIS* 3.7 17.5 - - + +
40F THR* 4.4 8.5 - - + -
55F ILE* 4.1 23.1 - - + -
85F SER 4.8 1.6 - - - -
86F SER 4.3 0.4 - - - +
87F ASP* 1.3 73.4 + - - +
89F THR* 1.3 63.9 + - - +
90F ALA 3.3 2.2 - - - -
91F SER* 3.1 9.2 + - - -
92F VAL* 3.0 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F HIS* 3.2 28.1 - - + +
87F ASP* 2.5 31.8 + - - -
88F ILE* 1.3 76.2 - - - +
90F ALA* 1.3 58.0 + - - +
92F VAL* 3.2 4.7 + - - +
93F ASN* 2.9 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ILE* 4.5 13.7 - - + +
82F ALA* 3.7 39.0 - - + +
83F LEU* 4.1 8.3 - - + +
87F ASP 4.4 2.6 + - - +
88F ILE 3.3 0.6 - - - -
89F THR* 1.3 77.4 - - - +
91F SER* 1.3 66.7 + - - +
93F ASN* 3.4 7.4 + - - +
94F CYS* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F TYR 4.8 0.7 + - - -
54F GLY* 4.5 0.9 - - - -
55F ILE* 4.0 32.0 + - - +
56F LEU* 4.4 7.6 + - - +
58F ILE* 4.7 6.5 - - - +
82F ALA 4.9 0.4 + - - -
83F LEU* 3.6 41.2 + - - +
88F ILE* 3.1 12.6 + - - -
90F ALA* 1.3 80.0 - - - +
92F VAL* 1.3 51.6 + - - +
94F CYS* 3.4 3.3 + - - +
95F ALA* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F MET* 5.0 0.9 - - + -
15F HIS* 3.7 30.1 - - + +
17F LEU* 3.7 37.2 - - + +
55F ILE* 5.3 4.0 - - + -
56F LEU* 5.6 1.8 - - + -
88F ILE* 3.0 45.4 + - + +
89F THR 3.6 4.5 - - - +
91F SER* 1.3 75.9 - - - +
93F ASN* 1.3 60.9 + - - +
94F CYS 3.2 0.2 - - - -
95F ALA* 3.4 6.7 + - - +
96F LYS* 3.0 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F THR* 2.9 37.5 + - - +
90F ALA* 3.9 6.7 - - - +
92F VAL* 1.3 79.0 - - - +
94F CYS* 1.3 57.8 + - - +
96F LYS* 3.5 20.0 + - - +
97F LYS* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F ILE* 3.6 31.6 - - + -
63F TRP* 3.9 4.3 - - - -
76F CYS* 2.1 52.0 - - + -
78F ILE* 4.5 6.3 - - + -
83F LEU* 4.7 6.3 - - + -
90F ALA 3.0 18.4 + - - +
91F SER* 3.8 5.4 - - - +
93F ASN* 1.3 77.9 - - - +
95F ALA* 1.3 57.7 + - - +
97F LYS* 3.3 2.8 + - - +
98F ILE* 3.0 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LEU* 5.5 2.5 - - + -
28F TRP* 4.3 12.8 - - + -
56F LEU* 3.7 25.8 - - + -
58F ILE* 5.0 1.3 - - + +
91F SER 2.8 17.7 + - - +
92F VAL* 3.9 6.5 - - - +
93F ASN 3.4 0.2 - - - -
94F CYS* 1.3 73.1 - - - +
96F LYS* 1.3 58.8 + - - +
98F ILE* 3.2 11.1 + - - +
99F VAL* 2.8 35.9 + - - +
108F TRP* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F HIS 2.5 32.2 + - - -
16F GLY* 4.0 11.4 + - - -
17F LEU* 4.0 15.7 - - + +
20F TYR* 2.8 58.3 + - + +
92F VAL* 3.0 24.5 + - + +
93F ASN* 3.5 21.9 + - - +
95F ALA* 1.3 73.7 - - - +
97F LYS* 1.3 64.2 + - - +
100F SER* 2.9 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F TRP* 4.0 21.8 - - + -
75F LEU* 4.1 20.0 - - + +
76F CYS* 4.0 17.0 - - + -
93F ASN 3.1 14.6 + - - +
94F CYS 3.3 8.9 + - - +
96F LYS* 1.3 73.2 - - - +
98F ILE* 1.3 62.4 + - - +
100F SER* 3.2 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E TYR* 5.5 2.9 - - + -
138E LEU* 4.6 6.7 - - + -
58F ILE* 3.4 39.3 - - + -
63F TRP* 3.7 51.4 - - + +
94F CYS* 3.0 18.2 + - - +
95F ALA* 3.2 8.2 + - - +
97F LYS* 1.3 77.3 - - - +
99F VAL* 1.3 62.6 + - - +
100F SER 4.3 3.6 - - - +
101F ASP* 5.7 0.2 - - - +
104F GLY* 4.4 4.0 - - - +
107F ALA* 4.3 21.1 - - + -
108F TRP* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TYR* 4.0 9.9 - - + -
21F ARG* 4.0 16.2 - - + -
23F TYR* 3.7 24.7 - - + -
28F TRP* 3.5 23.1 - - + -
95F ALA 2.8 23.2 + - - +
98F ILE* 1.3 72.0 - - - +
100F SER* 1.3 67.1 + - - +
101F ASP* 2.7 17.8 + - - +
104F GLY* 3.5 31.2 - - - -
105F MET* 4.1 1.8 - - + +
108F TRP* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TYR* 3.2 5.9 + - - -
21F ARG* 2.9 25.2 + - - +
96F LYS 2.9 21.2 + - - -
97F LYS* 3.2 31.2 + - - +
98F ILE 4.3 4.2 - - - +
99F VAL* 1.3 70.6 - - - +
101F ASP* 1.4 64.5 - - - +
----------------------------------------------------------
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