Contacts of the strand formed by residues 90 - 100 (chain E) in PDB entry 1VHA
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 TYR 90 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E SER 3.4 26.4 + - - -
1E LEU 5.2 1.1 - - - -
3E ARG* 3.5 37.3 + - + -
53E ALA* 4.6 11.0 - - + -
82E PHE* 4.8 0.2 - - - -
85E VAL* 3.2 32.0 + - + +
86E GLN* 2.6 37.0 + - - +
88E LYS* 3.6 34.3 - - + -
89E GLY* 1.3 78.4 - - - +
91E LYS* 1.3 55.1 + - - +
155E LEU* 3.9 24.7 - - + -
156E ILE* 3.2 16.6 - - - +
157E ARG* 3.5 27.8 + - - -
158E GLN* 4.4 1.6 - - - -
126F GLU* 4.7 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E PHE* 4.5 7.0 - - + -
86E GLN* 4.0 6.1 - - - +
90E TYR* 1.3 75.4 - - - +
92E ILE* 1.3 71.3 + - - +
155E LEU* 3.6 7.4 - - - -
156E ILE* 2.6 52.4 + - + +
157E ARG 3.9 15.5 - - - +
158E GLN* 4.0 35.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ILE* 4.0 25.1 - - + -
82E PHE* 3.9 24.5 - - + -
91E LYS* 1.3 88.1 - - - +
93E GLY* 1.3 64.0 + - - +
94E ASN* 3.3 25.8 - - - +
95E VAL* 4.2 8.5 - - + -
121E LEU* 3.9 24.0 - - + +
123E CYS* 4.3 23.0 - - + +
127E GLN* 3.2 17.4 + - - +
153E ALA* 5.8 0.2 - - + -
154E LEU 4.1 2.0 - - - +
155E LEU* 3.8 20.0 - - + -
156E ILE* 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D SER* 4.1 7.3 + - - -
2D ILE 5.4 2.9 - - - -
3D ARG* 3.7 3.3 + - - -
91E LYS 3.6 0.8 + - - -
92E ILE* 1.3 75.2 - - - +
94E ASN* 1.3 71.0 + - - +
127E GLN* 3.0 21.8 + - - +
154E LEU* 2.7 20.4 + - - -
156E ILE* 3.8 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ILE 4.2 0.7 - - - +
3D ARG* 3.2 29.8 - - - +
4D ILE* 2.9 52.6 + - - +
51D GLY 5.0 0.8 + - - -
52D ALA* 3.7 14.5 + - - +
92E ILE* 3.3 4.6 - - - +
93E GLY* 1.3 83.0 - - - +
95E VAL* 1.3 73.2 + - - +
127E GLN* 3.1 11.7 - - - +
153E ALA* 3.8 0.3 - - - -
154E LEU* 3.1 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ARG* 5.9 0.2 + - - -
51D GLY 4.8 0.2 - - - +
45E LEU* 3.7 31.9 - - + -
49E ILE* 4.5 0.7 - - + -
92E ILE* 4.2 17.0 - - + -
94E ASN* 1.3 86.6 + - - +
96E ASP* 1.3 62.5 + - - +
97E ILE* 5.1 2.2 - - + -
117E ILE* 4.7 1.6 - - + -
121E LEU* 4.4 11.9 - - + -
127E GLN 2.8 17.7 + - - +
128E VAL* 3.7 29.6 - - + -
129E ASN* 3.0 25.2 + - - +
152E VAL 3.5 6.1 - - - +
153E ALA* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE 4.2 7.9 - - - +
6D HIS* 3.1 25.4 + - - +
51D GLY* 3.3 21.6 - - - +
95E VAL* 1.3 76.1 - - - +
97E ILE* 1.3 63.6 + - - +
98E THR* 5.0 0.2 + - - -
129E ASN* 2.9 29.5 + - - +
131E LYS* 2.9 24.6 + - - -
150E GLU 4.1 0.3 - - - +
151E ALA* 3.5 3.0 - - - -
152E VAL* 3.2 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ALA* 4.2 17.9 - - + +
45E LEU* 3.8 29.8 - - + -
95E VAL* 5.1 4.0 - - + -
96E ASP* 1.3 79.4 + - - +
98E THR* 1.3 65.9 + - - +
99E ILE* 4.3 7.2 - - + -
117E ILE* 3.6 32.3 - - + -
129E ASN 3.0 12.9 + - - +
130E VAL* 3.5 13.1 - - + -
131E LYS* 2.9 29.3 + - - +
149E CYS* 3.3 25.6 - - - -
150E GLU 3.6 3.1 - - - +
151E ALA* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D HIS* 3.0 28.5 + - + +
7D GLY* 4.9 0.2 - - - -
8D PHE* 4.2 20.0 - - + +
96E ASP 5.0 0.2 + - - -
97E ILE* 1.3 70.7 - - - +
99E ILE* 1.3 60.6 + - - +
100E ILE* 3.7 6.3 + - + +
131E LYS* 3.1 33.7 + - + +
133E THR* 4.1 24.7 - - + -
149E CYS* 3.3 4.6 - - - -
150E GLU* 2.7 42.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E VAL* 5.2 7.9 - - + -
41E ALA* 4.4 6.5 - - + -
97E ILE* 4.3 4.9 - - + -
98E THR* 1.3 73.3 - - - +
100E ILE* 1.3 68.6 + - - +
101E ALA* 4.4 11.7 - - + -
106E MSE 4.4 23.3 - - + -
110E ILE* 4.8 2.2 - - + -
113E MSE 3.8 33.4 - - + -
130E VAL* 4.0 15.0 - - + -
131E LYS 2.9 13.6 + - - +
132E ALA* 3.3 10.9 - - + +
133E THR* 2.8 32.4 + - - +
147E ILE* 5.7 3.4 - - + -
148E ALA 3.9 8.5 - - - +
149E CYS* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PHE* 3.7 33.9 - - + -
8E PHE* 5.2 6.1 - - + -
98E THR* 3.9 13.0 - - + +
99E ILE* 1.3 74.6 - - - +
101E ALA* 1.3 62.9 + - - +
133E THR* 3.5 11.9 - - + +
135E THR* 3.6 31.0 - - + -
141E THR* 3.6 11.4 - - + +
148E ALA* 2.8 50.1 + - + +
149E CYS 4.8 0.7 - - - +
150E GLU* 4.3 21.5 - - + +
169E ACY 4.2 11.2 - - + -
----------------------------------------------------------
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