Contacts of the helix formed by residues 39 - 54 (chain B) in PDB entry 3D9L
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 PHE 39 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.7 40.2 - - + -
3B ALA* 4.5 14.8 - - + -
4B VAL* 3.5 29.4 - - + -
36B ALA* 2.8 14.9 + - - +
38B LYS* 1.3 116.4 - - + +
40B TYR* 1.3 61.5 + - - -
41B LYS* 3.1 4.3 - - - +
42B HIS* 3.0 25.9 + + - +
43B VAL* 3.1 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA 3.4 3.1 + - - -
37B ILE 3.2 23.7 + - - +
38B LYS 3.3 8.9 - - - -
39B PHE* 1.3 75.9 - - - +
41B LYS* 1.3 98.5 + - + +
43B VAL* 3.6 3.1 - - - +
44B VAL* 3.0 30.1 + - + +
83B VAL* 3.6 36.7 - - + +
84B PHE* 3.6 28.7 - + + -
87B ARG* 4.0 8.3 - - + -
503B GOL 3.7 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS 5.2 0.2 + - - -
39B PHE 3.1 1.0 - - - -
40B TYR* 1.3 115.3 - - + +
42B HIS* 1.3 62.2 + - + +
44B VAL* 3.7 3.3 + - - +
45B GLN* 3.2 24.9 + - - +
87B ARG* 3.7 45.6 + - - +
503B GOL 4.4 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.4 31.6 - - + +
4B VAL* 3.9 21.8 - - + -
39B PHE* 3.0 24.6 + + - +
41B LYS* 1.3 80.3 - - + +
43B VAL* 1.3 60.4 + - - +
45B GLN* 3.2 8.0 + - + +
46B SER* 2.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 5.0 4.0 - - + +
7B PHE* 3.7 36.3 - - + -
33B ALA* 3.8 19.7 - - + +
36B ALA* 3.6 33.2 - - + +
39B PHE 3.1 10.9 + - - +
40B TYR* 3.6 7.9 - - - +
42B HIS* 1.3 75.1 - - + +
44B VAL* 1.3 58.9 + - + +
46B SER* 3.3 2.9 + - - -
47B VAL* 2.9 34.1 + - + +
69B ILE* 4.2 6.7 - - + -
84B PHE* 3.8 20.2 - - + -
88B PHE* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.0 21.7 + - + +
41B LYS 3.9 5.2 - - - +
43B VAL* 1.3 75.2 - - - +
45B GLN* 1.3 57.4 - - - +
47B VAL* 3.2 3.1 + - - +
48B GLU* 2.9 56.7 + - - +
84B PHE* 3.9 12.3 - - + -
87B ARG* 3.7 39.9 - - + +
88B PHE* 3.8 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS 3.2 15.9 + - - +
42B HIS* 3.5 11.4 - - + +
44B VAL* 1.3 77.8 - - - +
46B SER* 1.3 56.8 + - - +
48B GLU* 3.2 20.2 + - - +
49B LYS* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 4.7 2.8 - - - +
7B PHE* 3.8 12.1 - - - -
8B ASN* 2.7 32.3 + - - -
11B LEU* 3.4 12.3 - - - +
42B HIS 2.8 22.6 + - - -
43B VAL 3.5 4.7 - - - -
45B GLN* 1.3 73.4 - - - +
47B VAL* 1.3 63.4 + - - +
49B LYS* 3.5 7.7 + - - +
50B PHE* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.4 24.2 - - + -
11B LEU* 3.8 9.2 - - + -
43B VAL 2.9 19.5 + - - +
44B VAL 3.2 6.5 + - - +
46B SER* 1.3 74.8 - - - +
48B GLU* 1.3 59.1 + - - +
50B PHE* 3.3 4.3 + - + +
51B ILE* 3.0 38.0 + - + +
62B GLY* 4.3 5.2 - - - +
65B VAL* 3.9 17.9 - - + -
66B ILE* 3.6 31.2 - - + -
69B ILE* 4.2 3.1 - - + -
88B PHE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 2.9 40.0 + - + +
45B GLN* 3.6 18.7 + - - +
47B VAL* 1.3 77.4 - - + +
49B LYS* 1.3 56.0 + - - +
51B ILE* 3.4 8.4 + - - +
52B GLN* 3.0 28.2 + - - +
87B ARG 4.6 0.7 - - - +
88B PHE* 4.1 20.6 - - + +
91B ASN* 3.2 42.2 + - - +
95B THR* 3.7 20.8 + - + +
98B ASN* 4.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 5.8 3.5 + - - -
17A TYR* 5.1 8.9 + - - -
12B TYR* 6.3 1.2 - - - -
45B GLN* 2.9 24.5 + - + +
46B SER* 3.9 7.4 - - - +
48B GLU* 1.3 71.7 - - - +
50B PHE* 1.3 59.4 + - - +
52B GLN* 3.2 14.5 + - - +
53B LYS* 2.8 64.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.7 40.4 - - + -
12B TYR* 4.4 10.8 - + + -
14B LEU* 3.6 29.6 - - + -
15B ASN* 3.5 27.1 - - - -
46B SER 3.1 14.1 + - - +
47B VAL* 3.3 8.9 + - + +
49B LYS* 1.3 77.1 - - - +
51B ILE* 1.3 58.7 + - + +
53B LYS* 5.0 2.2 - - - -
54B CYS* 2.8 58.6 + - + +
58B TYR* 3.8 31.0 - + + -
62B GLY* 4.3 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.0 25.3 + - + +
48B GLU* 3.8 6.1 - - - +
50B PHE* 1.3 75.8 - - + +
52B GLN* 1.3 54.0 + - - +
54B CYS* 4.0 6.7 - - - -
59B LYS* 2.7 31.1 + - + +
62B GLY* 3.6 40.2 - - - +
66B ILE* 3.7 23.8 - - + -
95B THR* 3.7 29.6 - - + +
98B ASN* 3.7 10.6 - - + +
99B LEU* 3.5 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU 3.0 17.0 + - - +
49B LYS* 3.5 16.9 - - - +
50B PHE 3.2 0.2 - - - -
51B ILE* 1.3 78.6 - - - +
53B LYS* 1.3 67.8 + - + +
54B CYS 3.9 0.3 + - - +
59B LYS* 4.1 5.9 + - - -
98B ASN* 3.6 26.7 - - - +
101B ARG* 5.5 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 2.8 60.7 + - + +
50B PHE* 4.4 2.0 - - - +
52B GLN* 1.3 86.6 - - + +
54B CYS* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN* 5.2 3.6 - - - +
50B PHE* 2.8 53.0 + - + +
51B ILE* 4.0 5.4 - - - -
52B GLN 3.6 0.8 - - - +
53B LYS* 1.3 77.9 - - - +
55B LYS* 1.3 75.7 + - - +
56B PRO* 3.8 1.2 - - - +
58B TYR* 3.7 27.6 - - + -
59B LYS* 3.3 31.9 + - - -
----------------------------------------------------------
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