Contacts of the helix formed by residues 67 - 78 (chain E) in PDB entry 2VIG
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 PRO 67 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ILE* 4.1 14.8 - - + -
60E VAL* 4.3 10.1 - - + -
65E LEU 3.3 7.4 - - - +
66E PHE* 1.3 90.3 - - + +
68E ALA* 1.3 63.9 + - - +
70E GLN* 3.2 24.8 + - + +
71E VAL* 2.9 28.5 + - + +
112E THR* 3.7 24.2 - - - +
115E ILE* 3.9 16.6 - - + -
235E GLY 4.0 4.9 - - - +
502E EDO 3.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E PHE* 2.8 36.9 + - + +
67E PRO* 1.3 71.7 - - - +
69E ALA* 1.3 62.2 + - - +
71E VAL* 3.3 2.8 + - - +
72E LYS* 3.1 22.7 + - - +
502E EDO 4.0 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E PRO 3.4 0.6 - - - -
68E ALA* 1.3 78.2 - - - +
70E GLN* 1.3 76.6 + - - +
72E LYS* 3.4 6.7 + - - +
73E LYS* 3.1 39.0 + - - +
502E EDO 4.5 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E PHE* 3.9 4.9 - - + -
52E GLU* 3.8 25.9 + - + +
53E LEU* 4.0 19.1 - - + -
56E ILE* 3.2 33.8 - - + +
67E PRO* 3.3 17.5 - - + +
69E ALA* 1.3 86.3 + - - +
71E VAL* 1.3 63.7 + - - +
73E LYS* 3.3 9.9 + - - +
74E MET* 3.0 29.7 + - - +
112E THR* 5.2 0.7 - - - +
502E EDO 2.7 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E PHE* 4.0 24.5 - - + -
67E PRO* 2.9 35.7 + - + +
68E ALA* 3.3 4.9 + - - +
70E GLN* 1.3 76.4 - - - +
72E LYS* 1.3 56.8 + - - +
74E MET* 3.4 9.2 + - + +
75E GLY 2.9 22.2 + - - -
80E LEU* 3.4 24.7 - - + +
112E THR* 4.9 8.5 - - + -
115E ILE* 4.1 26.2 - - + -
146E GLY 5.1 4.5 - - - +
149E ILE* 4.4 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ALA 3.1 13.5 + - - +
69E ALA* 3.8 9.0 - - - +
70E GLN 3.3 0.2 - - - -
71E VAL* 1.3 73.3 - - - +
73E LYS* 1.3 61.6 + - - +
75E GLY* 3.0 3.5 + - - +
76E GLY* 2.9 23.7 + - - -
145E SER 3.8 4.0 - - - +
146E GLY* 3.9 22.6 + - - +
147E ASP* 3.5 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E PHE* 3.9 15.3 - - + -
52E GLU* 3.8 36.0 + - - +
69E ALA* 3.1 28.9 + - - +
70E GLN* 3.6 10.2 - - - +
72E LYS* 1.3 77.2 - - - +
74E MET* 1.3 60.1 + - - +
76E GLY* 3.2 11.7 + - - +
77E LEU* 3.2 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E PHE* 3.5 26.0 - - + -
53E LEU* 4.7 0.2 - - - -
70E GLN 3.0 21.3 + - - +
71E VAL* 3.5 11.7 - - + +
73E LYS* 1.3 73.0 - - - +
75E GLY* 1.3 65.5 + - - +
77E LEU* 3.0 15.1 + - - +
78E GLY 3.2 0.2 + - - -
79E LEU* 3.2 40.5 + - + -
80E LEU* 4.1 10.5 - - + -
105E ILE* 3.9 9.0 - - + -
112E THR* 3.0 38.4 - - + +
115E ILE* 6.4 0.2 - - + -
116E MET* 3.7 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E VAL 2.9 11.9 + - - -
72E LYS 3.0 2.6 + - - -
74E MET* 1.3 75.6 - - - +
76E GLY* 1.3 61.0 + - - +
78E GLY* 3.2 14.3 + - - -
80E LEU* 3.6 19.6 - - - +
144E THR 4.0 2.6 - - - +
145E SER* 3.3 38.7 - - - -
146E GLY 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LYS 2.9 12.7 + - - -
73E LYS* 3.2 7.0 + - - -
75E GLY* 1.3 75.7 - - - +
77E LEU* 1.3 61.1 + - - +
78E GLY 3.6 0.3 + - - -
145E SER* 3.6 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E THR* 5.0 18.2 - - + -
48E PHE* 3.4 43.3 - - + -
73E LYS* 3.2 10.5 + - + +
74E MET* 3.0 12.5 + - - +
76E GLY* 1.3 78.1 - - - +
78E GLY* 1.3 57.9 + - - +
79E LEU* 3.5 19.4 + - + +
91E ALA* 5.3 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E GLY 3.2 12.3 + - - -
76E GLY 3.4 1.0 - - - -
77E LEU* 1.3 79.6 - - - +
79E LEU* 1.3 64.0 + - - +
80E LEU 3.3 2.7 - - - -
81E ALA* 3.4 15.0 + - - +
82E MET* 3.4 17.4 + - - +
90E GLY* 5.8 0.7 - - - -
91E ALA* 3.8 17.8 - - - +
144E THR 5.1 5.2 - - - -
----------------------------------------------------------
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