Contacts of the helix formed by residues 41 - 52 (chain A) in PDB entry 3L6D
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 SER 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 3.0 30.0 + - - +
40A ARG* 1.3 79.5 + - - +
42A PRO* 1.4 68.9 - - - +
43A GLY* 3.0 6.2 + - - -
44A LYS* 3.1 10.6 + - - -
45A ALA 4.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 4.0 6.2 - - + +
40A ARG 3.5 10.5 - - - +
41A SER* 1.4 81.7 - - - +
43A GLY* 1.3 64.7 + - - +
45A ALA* 3.0 24.9 + - + +
46A ALA* 3.6 3.8 + - - +
55A LEU* 5.0 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 3.0 7.0 + - - +
42A PRO* 1.3 77.0 - - - +
44A LYS* 1.3 55.6 + - - -
46A ALA* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 2.5 37.0 - - + +
18A GLY* 5.0 3.8 - - - -
19A ALA* 6.2 0.6 - - - +
22A THR* 3.2 35.6 - - + +
39A ASN* 4.1 12.3 - - - +
41A SER* 3.1 8.5 + - - -
43A GLY* 1.3 70.2 - - - +
45A ALA* 1.3 62.9 + - - +
46A ALA 3.1 0.6 + - - -
47A ALA* 4.4 9.9 + - + +
48A LEU* 4.3 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.8 14.3 - - + +
37A ILE* 3.6 22.7 - - + -
39A ASN* 5.2 0.9 - - + -
41A SER 4.1 2.0 + - - +
42A PRO* 3.0 16.4 + - + +
44A LYS* 1.3 79.8 - - - +
46A ALA* 1.3 58.4 + - - +
47A ALA 3.4 0.4 - - - -
48A LEU* 3.2 4.0 + - - +
49A VAL* 2.8 34.3 + - + +
55A LEU* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO 3.6 3.8 + - - +
43A GLY* 3.0 18.5 + - - +
44A LYS 3.1 0.8 - - - -
45A ALA* 1.3 77.1 - - - +
47A ALA* 1.3 58.1 + - - +
49A VAL* 3.3 5.9 + - - +
50A ALA* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 6.5 1.6 - - + -
26A GLN* 5.3 9.4 - - - +
44A LYS* 4.4 9.5 + - + +
46A ALA* 1.3 77.6 - - - +
48A LEU* 1.3 54.4 + - + +
50A ALA* 3.1 8.6 + - - +
51A ALA* 2.7 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.8 36.6 - - + -
22A THR* 4.3 18.2 - - + +
25A ALA* 4.0 14.1 - - + -
26A GLN* 3.4 44.6 - - + +
29A LEU* 4.0 12.7 - - + +
37A ILE* 3.7 13.5 - - + -
44A LYS 4.3 8.9 + - - +
45A ALA 3.2 8.4 + - - +
47A ALA* 1.3 78.7 - - + +
49A VAL* 1.3 58.9 + - - +
51A ALA* 3.2 6.8 + - + +
52A GLY 3.0 6.4 + - - -
53A ALA* 2.9 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 4.4 5.8 - - + -
45A ALA* 2.8 27.8 + - + +
46A ALA* 3.7 6.5 - - - +
48A LEU* 1.3 69.4 - - - +
50A ALA* 1.3 69.5 + - - +
52A GLY* 3.0 14.6 + - - -
53A ALA 3.6 18.5 - - - +
55A LEU* 3.8 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 3.0 13.8 + - - +
47A ALA* 3.4 11.0 - - - +
49A VAL* 1.3 78.2 - - - +
51A ALA* 1.3 61.8 + - - +
52A GLY* 3.2 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN* 5.8 3.8 - - + -
29A LEU* 4.0 25.1 - - + +
47A ALA 2.7 20.2 + - - +
48A LEU* 3.5 11.4 - - + +
49A VAL 3.2 0.2 - - - -
50A ALA* 1.3 72.1 - - - +
52A GLY* 1.3 55.5 + - - +
53A ALA 3.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 5.8 1.4 - - - -
29A LEU* 3.9 12.1 - - - +
35A VAL 4.5 1.9 + - - +
49A VAL 3.0 11.6 + - - -
50A ALA 3.2 2.0 - - - -
51A ALA* 1.3 79.3 - - - +
53A ALA* 1.3 67.0 + - - +
54A HIS* 3.8 1.4 + - - +
----------------------------------------------------------
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