Contacts of the helix formed by residues 87 - 103 (chain D) in PDB entry 2VUU
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 87 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LEU* 3.7 16.7 - - + +
86D GLY* 1.3 65.7 - - - -
88D GLU* 1.3 64.6 + - - +
89D ILE* 3.0 19.8 + - - +
90D ALA* 3.1 26.3 + - + +
91D ILE* 3.0 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D THR* 2.9 39.5 + - - +
82D THR 3.7 16.8 - - - +
83D SER* 3.6 32.3 + - - -
86D GLY 3.0 9.0 + - - +
87D ASP* 1.3 70.9 + - - +
89D ILE* 1.3 53.3 + - + +
91D ILE* 4.4 7.0 - - + -
92D GLY* 2.6 34.8 + - - -
110D TYR* 5.1 2.9 + - - +
126D PRO 5.1 0.5 - - - +
127D MET* 4.5 10.2 - - - +
130D PRO* 4.4 24.6 - - + +
131D LYS* 3.0 23.8 + - + +
134D VAL* 3.8 4.2 - - + +
1353D NAP 4.1 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ASP* 3.1 10.3 + - - +
88D GLU* 1.3 74.7 - - - +
90D ALA* 1.3 62.6 + - - +
93D LYS* 2.8 58.8 + - + +
130D PRO* 3.4 43.7 - - + +
133D THR* 3.8 24.5 - - + +
134D VAL* 3.6 9.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
61D LEU* 5.0 7.6 - - + -
62D ASN* 5.2 6.7 - - - +
87D ASP* 3.1 30.7 + - + +
89D ILE* 1.3 79.9 - - - +
91D ILE* 1.3 58.1 + - - +
93D LYS* 3.8 6.4 - - - +
94D ASP* 3.0 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D LEU* 3.7 36.3 - - + +
61D LEU* 3.4 48.0 - - + +
62D ASN 4.8 1.1 - - - +
67D MET* 5.1 0.7 - - + -
81D THR* 4.0 9.2 - - + -
82D THR 5.8 0.9 - - - +
85D ALA* 3.8 27.4 - - + +
86D GLY 4.3 1.3 - - - +
87D ASP 3.0 19.0 + - - +
88D GLU* 3.9 4.7 - - - +
90D ALA* 1.3 74.4 - - - +
92D GLY* 1.3 61.5 + - - +
94D ASP* 3.0 9.1 + - - +
95D LEU* 2.8 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ILE* 5.8 0.4 - - - -
81D THR* 4.9 5.1 - - - +
88D GLU 2.6 23.8 + - - -
89D ILE 3.8 0.4 - - - -
91D ILE* 1.3 74.2 - - - +
93D LYS* 1.3 58.8 + - - +
95D LEU* 3.5 11.1 + - - +
96D ALA* 3.1 22.9 + - - +
108D TYR* 4.6 1.4 + - - -
110D TYR* 5.1 4.5 - - - -
134D VAL* 3.9 24.3 - - - +
138D VAL* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ILE* 2.8 41.4 + - + +
90D ALA* 3.8 6.1 - - - +
92D GLY* 1.3 69.4 - - - +
94D ASP* 1.3 62.0 + - - +
96D ALA* 3.1 3.8 + - - +
97D ASP* 2.9 37.6 + - - +
133D THR* 5.3 7.6 - - - +
134D VAL* 4.3 3.6 - - + +
137D TYR* 3.6 53.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ASN* 4.3 21.3 + - - -
64D VAL* 4.4 16.2 - - + +
67D MET* 3.3 29.5 - - + +
90D ALA* 3.0 24.3 + - - +
91D ILE* 3.0 9.3 + - - +
93D LYS* 1.3 78.0 - - - +
95D LEU* 1.3 57.3 + - - +
97D ASP* 3.2 12.1 + - - +
98D ALA* 2.8 29.5 + - - +
101D ARG* 5.2 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 4.0 24.7 - - + -
60D LEU* 4.3 4.5 - - + -
67D MET* 3.5 29.8 - - + -
70D LEU* 4.9 2.2 - - + -
71D PHE* 3.4 23.9 - - + -
79D ILE* 3.5 27.6 - - + -
81D THR* 3.9 20.0 - - + -
91D ILE* 2.8 29.1 + - + +
92D GLY* 3.7 5.4 - - - +
94D ASP* 1.3 74.2 - - - +
96D ALA* 1.3 57.3 + - - +
98D ALA* 3.2 1.6 + - - -
99D ALA* 2.9 27.2 + - - +
108D TYR* 3.4 12.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
92D GLY 3.1 14.9 + - - +
93D LYS 3.5 8.1 - - - +
95D LEU* 1.3 77.2 - - - +
97D ASP* 1.3 57.9 + - - +
99D ALA 3.5 0.5 + - - -
100D LYS* 3.0 27.7 + - - +
108D TYR* 3.5 8.5 + - - +
137D TYR* 4.0 8.3 - - + -
138D VAL* 3.9 26.2 - - + -
141D LEU* 3.5 18.1 - - + +
143D LEU* 3.6 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LYS* 2.9 24.3 + - - +
94D ASP* 3.5 13.9 + - - +
96D ALA* 1.3 74.5 - - - +
98D ALA* 1.3 60.5 + - - +
100D LYS* 3.3 5.4 + - - +
101D ARG* 2.9 49.2 + - - +
137D TYR* 2.8 27.1 + - - -
141D LEU* 3.6 13.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
64D VAL* 6.3 0.2 - - + -
67D MET* 3.7 22.2 - - + +
68D ASP* 4.2 8.0 - - - +
71D PHE* 3.3 28.7 - - + +
94D ASP 2.8 16.2 + - - +
95D LEU 3.4 0.4 - - - +
97D ASP* 1.3 76.3 - - - +
99D ALA* 1.3 63.3 + - - +
101D ARG* 3.1 18.7 + - - +
102D ALA* 2.9 22.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
71D PHE* 3.5 21.7 - - + -
95D LEU 2.9 11.0 + - - +
96D ALA 3.7 4.3 - - - +
98D ALA* 1.3 77.3 - - - +
100D LYS* 1.3 60.7 + - - +
102D ALA* 3.3 12.5 + - - +
103D GLY* 3.4 8.7 + - - -
105D ILE* 3.7 15.6 - - + +
108D TYR* 3.2 40.2 - - + -
143D LEU* 4.4 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ALA 3.0 17.1 + - - +
97D ASP* 3.5 7.2 - - - +
99D ALA* 1.3 75.6 - - - +
101D ARG* 1.3 62.9 + - + +
103D GLY* 3.1 14.8 + - - -
141D LEU* 3.7 54.0 + - + +
143D LEU* 3.8 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D VAL* 3.4 30.1 - - - +
68D ASP* 3.1 30.2 + - - +
94D ASP 5.2 0.4 + - - -
97D ASP* 2.9 33.6 + - - +
98D ALA* 3.5 18.9 - - - +
100D LYS* 1.3 74.7 - - + +
102D ALA* 1.3 65.3 + - - +
103D GLY* 3.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASP 5.8 0.2 - - - +
71D PHE* 3.6 39.7 - - + +
72D GLU* 5.5 1.1 - - - -
98D ALA 2.9 8.1 + - - +
99D ALA 3.4 10.5 - - - +
100D LYS 3.2 0.2 - - - -
101D ARG* 1.3 76.8 - - - +
103D GLY* 1.3 57.5 + - - +
104D THR* 3.0 24.2 + - - +
105D ILE* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ALA 3.4 4.0 + - - -
100D LYS* 3.1 13.9 + - - -
101D ARG 3.1 4.5 - - - -
102D ALA* 1.3 76.7 - - - +
104D THR* 1.3 62.2 + - - +
105D ILE 3.6 3.5 - - - +
----------------------------------------------------------
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