Contacts of the helix formed by residues 59 - 69 (chain B) in PDB entry 2YTZ
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 GLY 59 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 2.7 27.4 + - - -
57B ALA 3.1 1.6 - - - -
58B THR* 1.3 77.7 - - - +
60B ILE* 1.3 54.3 + - - +
61B ARG 3.2 2.9 - - - -
62B GLY* 3.1 5.0 + - - -
63B ILE* 2.7 44.0 + - - +
76B LEU* 4.2 9.2 - - - +
87B MET* 4.1 8.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
8B GLU* 3.7 31.9 - - + +
11B ALA* 4.5 6.3 - - + +
13B ILE* 3.8 35.0 - - + +
28B TYR* 4.1 5.8 - - + -
36B ARG* 3.7 17.9 - - - +
58B THR* 3.1 21.7 + - - +
59B GLY* 1.3 76.6 - - - +
61B ARG* 1.3 70.6 + - - +
63B ILE* 3.2 6.2 + - - +
64B ARG* 2.9 51.4 + - + +
1002B SAH 3.4 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B MET* 4.6 2.2 - - - +
35B ASN* 2.9 30.1 + - - -
36B ARG* 3.7 30.7 - - + +
39B VAL* 4.0 5.7 - - - +
53B ASP* 3.0 29.6 - - - +
56B SER* 5.4 0.2 - - - -
59B GLY 3.2 0.8 - - - -
60B ILE* 1.3 82.2 - - - +
62B GLY* 1.3 59.8 + - - +
64B ARG* 3.4 4.8 + - - +
65B PHE* 3.2 40.5 + - + -
136B ASP* 3.1 34.3 + - - -
138B ASP* 3.0 29.8 + - - +
228B ARG* 3.1 7.5 - - - +
1002B SAH 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASP* 2.6 21.7 + - - -
59B GLY 3.1 3.7 + - - -
61B ARG* 1.3 72.3 - - - +
63B ILE* 1.3 65.1 + - - +
65B PHE* 2.9 25.4 + - - +
66B ALA* 3.1 10.6 + - - +
74B VAL* 3.7 7.5 - - - +
76B LEU* 3.7 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.9 23.1 - - + -
13B ILE* 4.7 7.9 - - + -
59B GLY* 2.7 37.8 + - - +
60B ILE* 3.4 9.2 - - - +
62B GLY* 1.3 70.7 - - - +
64B ARG* 1.3 63.6 + - - +
66B ALA* 3.2 11.0 + - - +
67B LEU* 3.1 23.7 + - + +
76B LEU* 4.3 3.1 - - + +
90B ASN* 3.7 7.4 - - + +
91B VAL* 3.4 52.7 - - + +
94B ASN* 3.9 19.7 - - + +
95B PHE* 4.4 5.2 - - + -
114B ILE* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 2.7 39.7 + - - +
9B GLY* 3.5 16.2 - - - +
11B ALA* 4.1 9.2 - - + -
33B ALA 3.8 0.8 + - - -
36B ARG* 3.7 14.1 - - + +
37B ASP* 2.7 34.1 + - - +
40B VAL* 4.3 16.3 - - + +
60B ILE* 2.9 45.7 + - + +
61B ARG 3.8 4.7 - - - +
63B ILE* 1.3 73.3 - - - +
65B PHE* 1.3 61.0 + - - +
67B LEU* 3.7 5.4 - - - +
68B GLU* 2.5 75.5 + - - +
69B THR* 3.9 1.0 + - - +
299B LEU* 4.4 2.0 - - - +
300B ALA* 3.9 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.6 37.7 - - + -
40B VAL* 4.3 11.7 - - + -
43B LEU* 3.5 23.3 - - + -
51B VAL* 4.2 17.9 - - + -
52B LEU 4.8 6.1 - - - -
53B ASP* 4.9 5.2 - - + -
61B ARG* 3.2 30.7 + - + -
62B GLY* 2.9 16.6 + - - +
64B ARG* 1.3 77.6 - - - +
66B ALA* 1.3 61.2 + - - +
69B THR* 2.4 36.3 + - + +
71B ALA* 3.9 3.5 - - - +
74B VAL* 4.3 12.6 - - + -
134B PHE* 3.9 17.9 - + - -
136B ASP* 3.6 17.5 - - + -
----------------------------------------------------------
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 GLY 3.1 10.0 + - - +
63B ILE* 3.4 10.5 - - - +
65B PHE* 1.3 77.8 - - - +
67B LEU* 1.3 59.3 + - - +
74B VAL* 4.2 17.6 - - + +
95B PHE* 3.5 25.0 - - + -
112B LYS* 2.6 39.7 + - + +
114B ILE* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 3.2 29.2 - - + +
11B ALA* 3.5 22.2 - - + -
63B ILE* 3.1 17.9 + - + +
64B ARG* 4.1 1.8 - - - +
66B ALA* 1.3 79.8 - - - +
68B GLU* 1.3 70.8 + - + +
69B THR 3.7 1.7 + - - +
94B ASN* 3.8 20.0 - - + +
95B PHE* 3.4 28.7 - - + -
112B LYS* 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 3.2 36.6 + - + -
40B VAL* 3.6 19.8 - - + +
44B ASN* 2.6 29.6 + - - +
64B ARG* 2.5 69.4 + - - +
67B LEU* 1.3 75.3 - - + +
69B THR* 1.3 50.0 + - - -
297B LEU* 5.0 8.4 - - + +
298B SER 3.8 13.6 + - - +
299B LEU* 4.4 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.5 37.7 - - + +
43B LEU* 3.8 19.9 - - + +
44B ASN* 3.9 0.9 - - - +
64B ARG 4.4 0.4 - - - +
65B PHE* 2.4 38.5 + - - +
67B LEU 3.5 1.4 - - - +
68B GLU* 1.3 82.5 - - - +
70B PRO* 1.3 67.0 - - - +
71B ALA* 3.0 14.5 + - - +
112B LYS* 2.7 32.2 + - - -
----------------------------------------------------------
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