Contacts of the helix formed by residues 88 - 105 (chain D) in PDB entry 2WY2
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 ASP 88 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 4.0 2.6 - - - +
83D LEU* 3.0 40.5 + - + +
86D LYS* 3.3 12.4 - - + +
87D VAL* 1.3 72.4 - - - +
89D GLY* 1.3 66.3 + - - +
90D LEU* 3.5 9.9 + - - +
91D GLY* 3.1 21.9 + - - -
92D VAL* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 4.2 1.6 - - - -
22D LYS* 4.0 14.8 - - - +
23D MET* 3.5 34.4 - - - +
26D GLN* 3.9 5.8 - - - -
87D VAL 3.1 10.1 + - - -
88D ASP* 1.3 72.2 + - - +
90D LEU* 1.3 61.2 + - - +
93D LEU* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D GLN* 3.5 40.5 - - + +
30D TYR* 4.1 28.5 - - + +
88D ASP* 3.3 7.8 + - - +
89D GLY* 1.3 74.8 - - - +
91D GLY* 1.3 59.0 + - - +
93D LEU* 3.2 11.7 + - + +
94D LYS* 2.9 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D LEU* 3.9 15.6 - - - +
88D ASP* 3.1 27.0 + - - -
90D LEU* 1.3 77.6 - - - +
92D VAL* 1.3 60.8 + - - +
94D LYS* 3.3 13.3 + - - +
95D ALA* 3.1 21.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
19D LEU* 4.0 17.5 - - + -
23D MET* 3.9 26.7 - - + -
55D LEU* 4.0 17.0 - - + +
79D ILE* 4.0 26.2 - - + -
83D LEU* 3.9 28.5 - - + +
88D ASP 3.1 17.2 + - - +
89D GLY 4.3 0.2 - - - +
91D GLY* 1.3 72.4 - - - +
93D LEU* 1.3 67.0 + - - +
95D ALA* 3.2 7.3 + - + +
96D ALA* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.2 22.0 - - + -
23D MET* 4.0 11.3 - - + +
26D GLN* 4.0 11.2 - - + +
27D ALA* 3.7 32.1 - - + +
30D TYR* 5.8 0.4 - - + -
32D VAL* 4.2 14.1 - - + -
34D VAL* 4.2 16.4 - - + -
36D ILE* 4.3 13.0 - - + -
89D GLY 3.1 19.5 + - - +
90D LEU* 3.4 11.9 - - + +
92D VAL* 1.3 76.0 - - - +
94D LYS* 1.3 62.7 + - + +
96D ALA* 3.2 4.4 + - - +
97D VAL* 3.1 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D LEU* 2.9 48.8 + - + +
91D GLY* 3.5 13.2 - - - +
93D LEU* 1.3 77.6 - - + +
95D ALA* 1.3 57.3 + - - +
97D VAL* 3.5 6.3 + - - +
98D ALA* 3.0 28.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
55D LEU* 5.6 4.3 - - + -
77D GLU* 4.8 11.9 - - - +
83D LEU* 5.1 7.6 - - + -
91D GLY 3.1 12.7 + - - +
92D VAL* 3.2 12.7 + - + +
94D LYS* 1.3 76.2 - - - +
96D ALA* 1.3 57.7 + - - +
98D ALA* 3.4 7.0 + - - +
99D ALA* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 3.8 36.8 - - + -
23D MET* 4.9 0.4 - - + -
53D VAL* 4.1 6.3 - - + +
55D LEU* 4.1 15.7 - - + +
92D VAL 3.0 13.3 + - - +
93D LEU* 3.5 9.4 - - - +
95D ALA* 1.3 75.1 - - - +
97D VAL* 1.3 65.0 + - - +
99D ALA* 3.3 7.1 + - - +
100D ILE* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 5.3 1.3 - - + -
32D VAL* 4.2 26.0 - - + -
34D VAL* 5.1 7.0 - - + -
93D LEU* 3.1 27.4 + - + +
94D LYS* 3.9 5.8 - - - +
96D ALA* 1.3 74.6 - - + +
98D ALA* 1.3 63.6 + - - +
100D ILE* 3.1 14.4 + - + +
101D LYS* 3.0 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LYS 3.0 18.5 + - - +
95D ALA* 3.5 8.7 - - - +
97D VAL* 1.3 78.2 - - - +
99D ALA* 1.3 57.1 + - - +
101D LYS* 3.1 10.2 + - - +
102D LYS* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D VAL* 3.9 19.3 - - + -
75D PRO* 4.3 10.1 - - + +
77D GLU* 3.4 28.3 - - + +
95D ALA 3.0 15.9 + - - +
96D ALA* 3.3 6.0 + - - +
98D ALA* 1.3 75.8 - - - +
100D ILE* 1.3 62.2 + - - +
102D LYS* 4.0 6.1 - - - +
103D ALA* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LYS* 4.0 42.8 - - + +
6D ILE* 4.7 7.9 - - + -
34D VAL* 5.5 1.6 - - + -
52D ASP* 4.5 12.1 - - + +
53D VAL* 3.8 28.5 - - + -
75D PRO* 5.2 1.6 - - - -
96D ALA 3.1 15.0 + - - +
97D VAL* 3.1 16.5 + - + +
99D ALA* 1.3 75.2 - - - +
101D LYS* 1.3 63.1 + - + +
103D ALA* 3.2 7.4 + - - +
104D ALA* 3.0 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D VAL* 3.0 30.9 + - + +
98D ALA* 3.7 9.4 - - - +
100D ILE* 1.3 74.3 - - + +
102D LYS* 1.3 63.7 + - - +
103D ALA 2.9 5.6 + - - -
104D ALA* 3.0 16.0 + - - +
105D ALA* 3.3 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ALA 2.8 20.9 + - - +
99D ALA* 4.2 5.8 - - - +
101D LYS* 1.3 73.4 - - - +
103D ALA* 1.3 57.6 + - - +
105D ALA* 3.4 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D PRO* 4.2 25.8 - - + -
99D ALA 3.1 18.9 + - - +
100D ILE* 3.4 7.2 - - - +
101D LYS 2.9 1.2 + - - -
102D LYS* 1.3 75.4 - - - +
104D ALA* 1.3 58.0 + - - +
105D ALA 3.1 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ILE* 3.0 17.6 + - + +
101D LYS* 3.0 6.0 + - - +
103D ALA* 1.3 74.7 - - - +
105D ALA* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LYS 3.3 9.8 + - - +
102D LYS* 3.4 23.2 - - - +
103D ALA 3.1 4.3 + - - +
104D ALA* 1.3 83.6 - - - +
----------------------------------------------------------
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