Contacts of the helix formed by residues 56 - 70 (chain B) in PDB entry 4LQL
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 56 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 5.0 9.2 - - + -
55B THR* 1.3 86.4 + - - +
57B ALA* 1.3 69.8 + - - +
58B ASP* 3.5 9.8 + - - +
59B SER* 2.7 32.7 + - - -
60B ILE* 3.8 7.3 + - - +
88B ASN* 3.7 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 1.3 81.8 - - - +
58B ASP* 1.3 77.0 + - - +
60B ILE* 2.9 10.9 + - - +
61B THR* 3.1 17.9 + - - +
87B LYS 5.7 1.3 - - - +
88B ASN* 4.1 20.1 - - - +
177E LYS* 4.7 21.5 - - - +
205E THR* 5.4 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 4.1 7.6 + - - +
57B ALA* 1.3 80.1 - - - +
59B SER* 1.3 58.9 + - - +
60B ILE 3.1 0.5 + - - -
61B THR* 3.1 9.1 + - - -
62B LYS* 2.7 37.3 + - + +
175E HIS* 5.3 8.7 - - - -
177E LYS* 5.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.5 17.0 - - - +
53B VAL 3.7 16.8 + - - -
54B ALA* 5.6 1.3 - - - -
55B THR* 4.3 6.7 + - - -
56B THR* 2.7 37.6 + - - -
58B ASP* 1.3 73.1 - - - +
60B ILE* 1.3 60.8 + - - +
62B LYS* 4.9 3.1 - - - +
63B PHE* 3.9 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 6.3 1.6 - - + -
54B ALA* 3.5 34.3 - - + +
55B THR 4.4 0.7 - - - +
56B THR 3.8 7.8 + - - +
57B ALA 2.9 6.3 + - - -
59B SER* 1.3 73.2 - - - +
61B THR* 1.3 61.6 + - - +
63B PHE* 2.9 32.9 + - + +
64B MET* 3.1 16.1 + - + +
84B SER* 6.0 0.2 - - - -
88B ASN* 3.2 30.1 - - + +
89B TRP* 3.4 61.0 - - + +
92B GLY* 5.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 3.1 15.3 + - - +
58B ASP* 3.1 11.1 + - - -
60B ILE* 1.3 76.4 - - - +
62B LYS* 1.3 64.7 + - - +
64B MET* 3.5 3.3 + - - +
65B LYS* 3.2 24.9 + - + +
88B ASN 5.3 1.9 + - - -
91B ARG* 3.8 23.0 - - + +
92B GLY* 3.5 26.6 + - - -
95B LEU* 6.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASP* 2.7 23.6 + - + +
59B SER* 4.9 2.7 - - - +
61B THR* 1.3 74.3 - - - +
63B PHE* 1.3 53.4 - - - +
65B LYS* 2.8 31.8 + - - +
66B GLU* 3.2 13.6 + - + +
71E ASP* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TRP* 4.0 14.9 - + - -
12B VAL* 4.4 23.3 - - + -
51B LYS* 5.1 9.0 - - + -
52B LEU* 5.0 10.5 - - + +
59B SER 3.9 12.8 + - - +
60B ILE* 2.9 19.5 + - + +
62B LYS* 1.3 73.1 - - - +
64B MET* 1.3 70.6 + - + +
65B LYS 3.2 0.9 + - - -
66B GLU* 3.2 16.9 + - - +
67B ALA* 3.3 12.6 + - + +
76B VAL* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 3.1 17.0 + - + +
61B THR 4.0 6.7 - - - +
63B PHE* 1.3 86.3 - - + +
65B LYS* 1.3 58.6 + - - +
67B ALA* 3.7 7.5 + - - +
68B ASN* 3.1 30.4 + - - +
76B VAL* 5.7 4.3 - - + -
89B TRP* 5.6 4.9 - - + -
92B GLY 3.0 30.7 - - - +
93B THR* 5.3 1.1 - - - +
95B LEU* 4.4 4.6 - - + +
96B LEU* 4.2 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 3.2 18.2 + - + +
62B LYS* 2.8 18.2 + - - +
64B MET* 1.3 75.3 - - - +
66B GLU* 1.3 60.5 + - + -
68B ASN* 3.8 13.2 - - - +
69B TYR* 3.5 10.4 + - - +
95B LEU* 5.5 10.8 - - + -
68E ASN 4.3 18.3 - - - +
69E TYR* 3.3 24.4 - - + +
71E ASP* 4.6 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TRP* 4.0 16.2 - - + -
62B LYS* 3.2 13.0 + - + +
63B PHE* 3.2 6.9 + - - +
65B LYS* 1.3 72.0 - - + +
67B ALA* 1.3 59.3 + - - +
68B ASN 3.0 2.2 - - - -
69B TYR 3.0 0.5 + - - -
70B ASN* 2.5 41.0 + - + +
69E TYR* 3.1 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TRP* 3.4 29.8 - - + -
63B PHE* 3.3 10.9 + - + +
64B MET* 3.7 7.6 + - - +
65B LYS 3.5 0.2 - - - -
66B GLU* 1.3 77.5 - - - +
68B ASN* 1.3 54.1 - - - +
70B ASN 4.2 0.8 + - - -
73B VAL* 4.1 6.8 - - + +
76B VAL* 4.5 15.9 - - + -
96B LEU* 4.6 4.9 - - + -
98B LYS* 2.6 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET 3.1 15.7 + - - +
65B LYS* 3.8 13.3 - - - +
66B GLU 3.0 0.4 - - - -
67B ALA* 1.3 80.5 - - - +
69B TYR* 1.3 61.6 + - + +
70B ASN 3.6 0.2 + - - -
71B ASP* 4.0 9.4 - - - +
95B LEU* 2.6 27.9 + - - +
96B LEU* 3.7 9.0 - - - +
97B GLN* 3.3 40.0 + - + +
98B LYS* 4.0 11.5 + - - +
65E LYS* 5.1 9.6 - - + +
68E ASN* 5.1 15.6 - - + +
97E GLN* 5.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS 3.5 2.9 + - - +
66B GLU* 3.0 3.1 + - - +
68B ASN* 1.3 78.4 - - + +
70B ASN* 1.3 60.8 + - + +
71B ASP* 3.1 15.3 + - - +
65E LYS* 3.8 18.6 - - + -
66E GLU* 3.8 36.2 + - + +
68E ASN* 6.4 0.7 - - + -
69E TYR* 3.3 73.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TRP* 4.3 21.3 - - + -
66B GLU* 2.5 26.3 + - + +
68B ASN 3.4 0.4 - - - -
69B TYR* 1.3 73.1 - - + +
71B ASP* 1.3 49.1 + - - +
72B ASP* 2.7 22.4 - - - -
73B VAL* 2.4 42.1 + - + +
98B LYS* 3.7 3.5 + - - -
----------------------------------------------------------
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