Contacts of the helix formed by residues 41 - 50 (chain H) 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 GLY 41 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H LEU 3.5 1.4 + - - -
40H LYS* 1.3 74.4 - - - +
42H LEU* 1.3 69.5 + - - +
43H ILE 3.4 2.2 - - - -
44H ALA* 3.3 4.5 + - - +
45H GLU* 3.0 32.7 + - - -
1353H NAP 5.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H GLY* 1.3 72.9 - - - +
43H ILE* 1.3 76.6 + - + +
45H GLU* 3.2 9.0 + - - +
46H GLU* 2.9 35.4 + - + +
712P LEU* 4.3 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 43 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H THR* 3.7 42.8 - - + +
19H ALA* 4.3 12.1 - - + -
23H ARG* 4.0 19.7 - - - +
41H GLY 3.4 0.4 - - - -
42H LEU* 1.3 82.6 - - + +
44H ALA* 1.3 67.5 + - - +
46H GLU* 2.9 14.3 + - - +
47H LEU* 2.8 37.7 + - + +
1353H NAP 5.3 6.3 - - - +
711P SER* 6.0 0.2 - - - -
712P LEU 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H THR* 3.7 16.8 - - + +
36H VAL* 5.4 1.8 - - + -
38H SER 3.7 12.6 - - - +
39H LEU* 3.3 35.0 - - + +
40H LYS 4.2 1.3 - - - +
41H GLY* 3.3 11.3 + - - +
42H LEU 3.3 0.4 - - - -
43H ILE* 1.3 80.0 - - - +
45H GLU* 1.3 58.5 + - - +
47H LEU* 3.2 4.8 + - - +
48H GLN* 2.8 29.8 + - - +
55H LEU* 4.1 6.8 - - - +
1353H NAP 5.1 1.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H LEU 3.8 13.3 - - - +
40H LYS* 4.3 2.6 - - - -
41H GLY 3.0 30.5 + - - +
42H LEU* 3.7 6.3 - - - +
44H ALA* 1.3 76.9 - - - +
46H GLU* 1.3 62.2 - - - +
48H GLN* 3.5 12.3 + - - +
49H ALA* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H ARG* 2.6 51.2 + - - +
42H LEU* 2.9 15.2 + - + +
43H ILE* 2.9 19.1 + - - +
45H GLU* 1.3 76.8 - - - +
47H LEU* 1.3 68.9 + - + +
49H ALA* 2.9 23.7 + - + +
50H ILE* 3.2 12.9 + - + +
710P LEU 4.7 1.2 - - - +
711P SER* 4.0 2.3 - - - -
712P LEU* 3.4 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ALA* 3.4 44.6 - - + +
14H THR* 4.0 6.7 - - + +
19H ALA* 4.5 11.7 - - + +
22H ILE* 3.6 30.5 - - + -
23H ARG* 4.8 4.3 - - + -
36H VAL* 5.0 0.2 - - + -
43H ILE* 2.8 33.0 + - + +
44H ALA* 3.6 5.8 - - - +
46H GLU* 1.3 76.6 - - - +
48H GLN* 1.3 64.8 + - - +
50H ILE* 3.1 30.2 + - + +
53H VAL* 3.5 17.3 - - + +
55H LEU* 4.5 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H LEU* 4.0 31.0 - - - +
44H ALA 2.8 17.6 + - - +
45H GLU* 3.5 13.8 - - - +
46H GLU 3.1 0.2 - - - -
47H LEU* 1.3 79.6 - - - +
49H ALA* 1.3 64.1 + - - +
50H ILE 3.4 6.9 - - - +
53H VAL* 4.5 5.7 - - - +
55H LEU* 3.8 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H GLU 3.1 10.3 + - - +
46H GLU* 2.9 14.5 + - - +
48H GLN* 1.3 79.0 - - - +
50H ILE* 1.3 64.3 + - + +
51H PRO* 3.1 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ILE* 4.2 12.6 - - + -
23H ARG* 4.4 19.1 - - + +
26H ALA* 3.4 28.7 - - + -
27H ALA 5.5 0.2 - - - +
46H GLU* 3.6 15.0 - - + +
47H LEU* 3.1 37.8 + - + +
48H GLN 3.4 8.7 - - - +
49H ALA* 1.3 76.1 - - + +
51H PRO* 1.3 78.4 - - + +
52H ASN 4.4 2.2 - - - +
53H VAL* 3.5 17.3 + - + +
----------------------------------------------------------
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