Contacts of the helix formed by residues 61 - 75 (chain B) in PDB entry 4DQ0
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 ASN 61 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASP* 3.0 37.7 + - - -
142A PRO* 3.7 2.2 - - - +
143A CYS* 3.7 21.3 + - - +
59B ASP* 2.9 14.7 + - - +
60B LYS* 1.3 85.2 - - + +
62B ALA* 1.3 65.2 + - - +
63B MET* 3.1 19.0 + - - +
64B SER* 2.8 33.3 + - - -
65B ILE* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS 3.4 6.1 + - - -
61B ASN* 1.3 72.1 + - - +
63B MET* 1.3 58.1 + - + +
65B ILE* 3.3 1.9 + - - +
66B ALA* 2.8 30.9 + - - +
84B VAL* 3.8 23.5 - - + +
110D ALA* 3.8 31.4 - - + +
111D LYS* 4.0 13.2 - - - +
114D PRO* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASP* 3.4 39.0 - - - +
138A THR* 3.9 13.5 - - - +
139A ALA* 3.7 30.3 - - - +
142A PRO* 4.0 13.9 - - + +
152A LYS* 6.5 0.4 - - + -
61B ASN* 3.1 6.8 + - - +
62B ALA* 1.3 75.5 - - + +
64B SER* 1.3 65.9 + - - +
66B ALA* 3.3 8.5 + - - +
67B ASN* 3.1 21.8 + - - +
114D PRO* 4.8 15.0 - - + +
155D GLU* 5.0 11.0 - - - +
159D TYR* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PRO* 3.8 14.7 - - - +
143A CYS 3.7 16.3 + - - -
144A THR* 4.1 10.4 - - - +
40B GLY 3.6 23.9 + - - -
41B ASN* 4.2 4.7 - - - +
59B ASP* 4.5 2.2 - - - -
61B ASN* 2.8 27.0 + - - -
63B MET* 1.3 71.5 - - - +
65B ILE* 1.3 64.8 + - - +
67B ASN* 3.1 17.6 + - - +
68B VAL* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B CYS* 4.0 16.4 - - - -
40B GLY 5.4 0.2 - - - +
57B ALA 4.1 7.2 - - - +
59B ASP* 3.8 25.4 - - + +
61B ASN 3.0 18.9 + - - +
62B ALA 3.6 7.0 - - - +
63B MET 3.3 0.2 - - - -
64B SER* 1.3 75.4 - - - +
66B ALA* 1.3 63.2 + - - +
68B VAL* 3.1 9.6 + - + +
69B GLU* 3.0 20.4 + - + +
82B THR* 3.7 19.1 - - + +
83B ARG 3.9 14.1 - - - +
84B VAL* 3.7 20.6 - - + -
111D LYS* 3.6 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA 2.8 20.4 + - - +
63B MET 3.6 5.8 - - - +
64B SER 3.3 0.2 - - - -
65B ILE* 1.3 74.1 - - - +
67B ASN* 1.3 58.3 + - - +
69B GLU* 3.2 9.6 + - - +
70B ARG* 2.9 27.4 + - - +
111D LYS* 3.5 24.2 - - - +
114D PRO* 3.8 27.6 - - + -
115D GLY 5.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PRO* 5.9 3.8 - - + -
13B TYR 5.4 0.8 + - - -
15B LEU* 3.9 18.4 - - - +
41B ASN* 4.8 6.3 + - - +
63B MET 3.1 10.7 + - - +
64B SER* 3.1 13.0 + - - +
66B ALA* 1.3 78.5 - - - +
68B VAL* 1.3 57.6 + - - +
70B ARG* 2.9 41.5 + - - +
71B ILE* 3.0 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B CYS* 5.2 2.9 - - - -
40B GLY 5.1 1.8 - - - +
41B ASN 3.7 23.6 - - - +
42B GLY* 4.0 13.5 - - - +
45B SER* 5.7 0.7 - - - -
46B LEU* 4.5 9.5 - - + +
57B ALA* 5.2 4.5 - - + -
64B SER 3.2 15.0 + - - +
65B ILE* 3.1 14.2 + - + +
67B ASN* 1.3 76.3 - - + +
69B GLU* 1.3 56.9 + - - +
71B ILE* 3.3 7.7 + - - +
72B LYS* 2.8 29.0 + - + +
80B LEU* 3.8 23.3 - - + -
82B THR* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 3.0 14.0 + - + +
66B ALA* 3.6 11.0 - - - +
68B VAL* 1.3 76.2 - - - +
70B ARG* 1.3 62.5 + - - +
72B LYS* 3.6 29.1 + - - +
73B SER* 3.1 25.6 + - - -
82B THR* 2.3 46.0 + - + +
111D LYS* 4.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TYR* 4.0 19.6 + - - +
66B ALA 2.9 13.8 + - - +
67B ASN* 2.9 34.1 + - - +
69B GLU* 1.3 77.8 - - - +
71B ILE* 1.3 72.8 + - - +
73B SER* 3.4 5.5 + - - -
74B ILE* 3.1 51.1 + - + +
115D GLY* 6.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 4.2 4.5 - - + -
13B TYR* 3.6 60.1 - - + -
15B LEU* 4.2 3.4 - - + -
41B ASN 5.7 0.7 - - - +
46B LEU* 3.9 34.5 - - + -
67B ASN* 3.0 34.3 + - - +
68B VAL* 3.8 4.7 - - - +
70B ARG* 1.3 80.9 - - - +
72B LYS* 1.3 61.7 + - - +
73B SER 3.1 1.8 - - - -
74B ILE* 3.2 5.7 + - - +
75B GLU* 2.9 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 5.0 0.2 - - - +
68B VAL* 2.8 22.5 + - + +
69B GLU* 3.6 32.8 + - - +
70B ARG 3.4 0.2 - - - -
71B ILE* 1.3 73.2 - - - +
73B SER* 1.3 60.1 + - - +
76B ASN* 2.9 23.9 + - - -
77B LEU* 2.9 46.3 + - + +
78B ASP* 4.4 8.3 + - - +
80B LEU* 2.8 39.7 + - + +
81B HIS* 4.5 12.7 - - - +
82B THR* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU 3.1 17.7 + - - -
70B ARG* 3.8 5.2 - - - -
71B ILE 3.1 0.2 - - - -
72B LYS* 1.3 76.7 - - - +
74B ILE* 1.3 67.4 + - - +
76B ASN* 3.7 13.8 + - - +
91D THR* 5.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 4.4 6.7 - - - +
13B TYR* 3.4 29.4 - - + +
70B ARG* 3.1 46.8 + - + +
71B ILE 3.8 3.6 - - - +
73B SER* 1.3 79.8 - - - +
75B GLU* 1.3 62.0 + - - +
76B ASN* 3.3 9.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ILE* 5.2 5.7 - - - +
4B ARG* 3.0 31.0 + - - +
8B TYR* 2.7 34.0 + - - -
9B PHE* 4.0 15.0 - - + -
12B LYS* 2.7 6.7 + - - -
13B TYR* 2.3 33.1 + - - +
71B ILE* 2.9 20.0 + - + +
74B ILE* 1.3 79.3 - - - +
76B ASN* 1.3 72.6 + - - +
77B LEU* 3.4 21.2 + - + +
----------------------------------------------------------
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