Contacts of the helix formed by residues 98 - 105 (chain O) in PDB entry 1VQM
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 LEU 98 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O LEU* 3.9 20.0 - - + -
14O LEU* 4.4 4.3 - - + -
26O TRP* 5.2 7.2 - - + -
29O VAL* 4.0 27.1 - - + -
33O LEU* 4.5 0.4 - - + -
59O VAL* 4.9 7.9 - - + -
60O VAL 4.2 5.4 - - - +
77O ALA* 3.2 15.5 - - + +
78O ALA* 3.1 37.3 + - - +
79O VAL* 4.1 23.3 - - + +
97O SER* 1.3 71.8 - - - +
99O GLU* 1.3 66.2 + - - +
101O ALA* 3.9 7.0 - - - -
102O ILE* 2.9 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O ARG* 4.6 16.4 + - - +
10O LEU* 3.8 32.8 - - + +
13O ASP* 5.7 3.8 - - - +
78O ALA 4.8 1.7 - - - +
79O VAL 4.9 6.0 - - - +
97O SER* 2.8 18.9 + - - +
98O LEU* 1.3 95.4 + - - +
100O GLN* 1.3 63.1 + - + +
102O ILE* 3.9 6.1 - - - +
103O GLU* 3.5 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95O ALA 4.8 2.4 + - - -
96O VAL* 3.3 28.6 - - + +
97O SER* 2.7 40.9 + - - +
99O GLU* 1.3 69.3 - - + +
101O ALA* 1.3 58.6 + - - +
103O GLU* 2.7 32.1 + - - +
104O ASN* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O TRP* 4.2 17.5 - - + -
57O THR* 5.2 6.5 - - + -
77O ALA* 4.0 24.0 - - + -
96O VAL* 3.7 6.3 - - + +
97O SER 3.0 10.9 + - - +
98O LEU* 3.9 4.9 - - - +
100O GLN* 1.3 79.3 - - - +
102O ILE* 1.3 63.0 + - - +
104O ASN* 3.2 6.2 + - - +
105O ASN* 2.9 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O LEU* 4.1 11.0 - - + -
13O ASP* 4.2 11.7 - - + +
14O LEU* 3.3 52.5 - - + +
17O ALA* 3.6 26.0 - - + -
26O TRP* 4.3 19.3 - - + +
98O LEU* 2.9 28.3 + - - +
99O GLU* 3.9 7.2 - - - +
101O ALA* 1.3 75.8 - - - +
103O GLU* 1.3 58.9 + - - +
106O PRO* 3.1 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O GLU 3.5 10.1 + - - +
100O GLN* 2.7 20.7 + - - +
102O ILE* 1.3 78.1 - - - +
104O ASN* 1.3 67.9 + - - +
105O ASN 3.2 3.2 + - - -
106O PRO* 3.6 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 104 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O VAL* 5.4 3.8 - - - +
100O GLN* 2.9 35.8 + - - +
101O ALA* 4.1 5.4 - - - +
103O GLU* 1.3 88.5 + - - +
105O ASN* 1.3 62.0 + - - +
106O PRO* 4.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O TRP* 3.1 16.4 + - + -
57O THR* 5.3 5.9 + - - +
101O ALA* 2.9 12.0 + - + +
102O ILE 3.6 3.6 - - - -
103O GLU 3.2 0.2 - - - -
104O ASN* 1.3 84.0 - - + +
106O PRO* 1.3 60.5 - - - +
107O GLU* 3.1 6.6 + - - +
108O GLY* 2.7 39.7 + - - -
109O SER* 3.0 45.0 + - - +
110O HIS 5.0 0.2 + - - -
111O VAL* 5.1 5.7 - - - +
----------------------------------------------------------
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