Contacts of the helix formed by residues 45 - 57 (chain A) in PDB entry 1VLH
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 THR 45 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 1.3 77.3 - - - +
46A LEU* 1.3 66.2 + - - +
47A GLU* 3.5 5.5 + - - +
48A GLU* 2.6 46.4 + - - +
49A ARG* 2.9 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.4 45.6 - - + +
35A THR 4.0 13.0 - - - -
36A GLU* 4.1 13.7 - - + +
45A THR* 1.3 72.7 - - - +
47A GLU* 1.3 58.8 + - + +
49A ARG* 3.3 23.3 + - - +
50A LYS* 3.0 26.9 + - - +
67A VAL* 4.0 13.3 - - + +
68A HIS 4.3 4.9 - - - +
69A HIS* 3.2 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.1 5.9 + - - +
46A LEU* 1.3 78.2 - - - +
48A GLU* 1.3 64.8 + - - +
50A LYS* 3.3 37.4 + - - +
51A LYS* 3.1 52.1 + - + +
67A VAL* 4.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET 4.5 1.6 - - - +
44A PHE* 3.2 26.9 - - + -
45A THR* 2.6 54.4 + - - +
47A GLU* 1.3 75.0 - - - +
49A ARG* 1.3 62.3 + - - +
51A LYS* 3.5 6.9 + - - +
52A LEU* 3.1 26.5 + - - +
155A LYS* 4.4 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 2.8 33.5 + - - +
9A PHE 3.1 27.8 - - - +
10A ASP* 3.6 13.0 + - - +
11A PRO* 5.3 0.4 - - + -
34A VAL* 3.8 16.5 - - + +
35A THR 4.4 3.2 + - - -
36A GLU* 5.6 2.2 - - - +
42A CYS* 3.5 32.1 - - - +
44A PHE* 2.7 40.9 + - + -
45A THR* 2.9 10.3 + - - +
46A LEU* 3.5 39.5 - - - +
48A GLU* 1.3 74.8 - - - +
50A LYS* 1.3 65.3 + - - +
52A LEU* 3.4 8.8 + - + +
53A ILE* 3.1 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.1 10.4 - - + +
46A LEU 3.0 13.5 + - - +
47A GLU* 3.3 34.0 + - - +
49A ARG* 1.3 73.0 - - - +
51A LYS* 1.3 61.4 + - - +
53A ILE* 3.2 4.2 + - - +
54A GLU* 2.9 60.7 + - - +
65A VAL* 4.1 25.1 - - + +
66A ASP* 4.6 4.8 + - - +
67A VAL* 3.8 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 3.1 42.8 + - - +
48A GLU* 3.8 6.3 - - - +
50A LYS* 1.3 75.1 - - - +
52A LEU* 1.3 65.7 + - - +
54A GLU* 3.4 17.1 + - - +
55A GLU* 3.0 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 4.2 19.1 - - + -
12A ILE* 5.0 3.1 - - + +
44A PHE* 4.9 11.7 - - + -
48A GLU 3.1 16.5 + - - +
49A ARG* 3.7 11.9 - - + +
50A LYS 3.3 0.2 - - - -
51A LYS* 1.3 75.5 - - - +
53A ILE* 1.3 60.9 + - + +
55A GLU* 3.1 20.0 + - - +
56A VAL* 2.9 32.1 + - - +
147A GLU* 3.5 35.4 - - + +
148A VAL* 4.1 19.3 - - + +
151A ALA* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.6 29.2 - - + +
12A ILE* 4.0 26.7 - - + -
32A VAL* 4.1 10.8 - - + -
34A VAL* 3.5 27.6 - - + -
49A ARG 3.1 16.7 + - - +
50A LYS 3.5 5.8 - - - +
52A LEU* 1.3 80.2 - - + +
54A GLU* 1.3 55.9 + - - +
56A VAL* 3.6 7.1 - - - +
57A LEU* 2.8 55.0 + - + +
65A VAL* 3.6 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 2.9 51.5 + - - +
51A LYS* 3.7 16.9 - - - +
53A ILE* 1.3 75.3 - - - +
55A GLU* 1.3 62.5 + - - +
57A LEU* 3.9 1.7 - - - +
58A SER* 3.2 25.6 + - - -
65A VAL* 3.6 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 3.0 18.1 + - + +
52A LEU* 3.3 18.6 - - - +
54A GLU* 1.3 75.0 - - - +
56A VAL* 1.3 63.9 + - - +
58A SER* 3.2 21.6 + - - -
147A GLU* 3.7 39.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 4.2 7.0 - - + -
17A VAL* 3.7 32.3 - - + -
52A LEU 2.9 22.2 + - - +
53A ILE* 3.6 6.7 - - - +
55A GLU* 1.3 78.2 - - - +
57A LEU* 1.3 64.9 + - + +
58A SER* 3.2 5.1 + - - -
145A PRO* 3.9 22.2 - - + -
147A GLU* 3.9 32.0 - - + +
148A VAL* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 4.7 2.5 - - + -
17A VAL* 4.8 10.8 - - + -
20A ILE* 4.1 20.2 - - + -
32A VAL* 3.9 10.8 - - + -
53A ILE* 2.8 43.0 + - + +
54A GLU* 3.9 2.9 - - - +
56A VAL* 1.3 83.6 - - + +
58A SER* 1.3 57.5 + - - +
59A ASP 3.4 2.5 - - - -
60A LEU* 2.8 49.2 + - + +
63A VAL* 3.7 31.1 - - + +
65A VAL* 4.2 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