Contacts of the helix formed by residues 62 - 73 (chain B) in PDB entry 2YXE
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 ALA 62 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ASP* 3.6 12.1 - - - +
50B THR* 3.7 28.7 - - - -
51B PRO* 3.9 13.2 - - + +
61B SER* 1.3 77.4 - - - +
63B ILE* 1.3 66.6 + - - +
64B HIS* 3.8 23.3 - - + +
65B MET* 3.0 16.4 + - + +
66B VAL* 3.1 11.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
10B VAL* 3.9 19.1 - - + -
11B ILE* 4.5 11.9 - - + -
14B LEU* 3.8 19.1 - - + +
29B LEU* 4.6 5.8 - - + -
34B ARG* 3.6 29.1 - - - +
46B ALA 4.0 2.9 - - - +
47B TYR* 3.8 46.7 - - + -
48B VAL 4.2 4.5 - - - +
49B ASP* 3.1 11.2 + - - +
61B SER 3.6 1.4 + - - -
62B ALA* 1.3 70.2 - - - +
64B HIS* 1.3 63.5 + - - +
65B MET 3.2 0.2 + - - -
66B VAL* 3.3 4.8 + - - +
67B GLY* 2.9 20.8 + - - -
90B TYR* 4.4 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 5.0 0.2 + - - -
14B LEU* 3.5 30.2 - - + +
19B TYR* 3.6 45.3 + + + +
49B ASP* 2.6 41.5 + - - +
62B ALA* 3.8 17.0 - - + +
63B ILE* 1.3 73.2 - - - +
65B MET* 1.3 72.2 + - + +
67B GLY 3.9 0.2 - - - -
68B MET* 2.9 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B SER* 4.2 10.5 - - - -
62B ALA* 3.0 15.7 + - + +
64B HIS* 1.3 90.6 - - + +
66B VAL* 1.3 66.8 + - - +
68B MET* 4.1 22.0 - - + +
69B MET* 2.8 44.0 + - - +
184B LEU* 4.5 11.9 - - - -
202B VAL* 4.0 21.8 - - + -
204B PHE* 3.5 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.3 6.1 - - + -
34B ARG* 4.6 0.7 - - - +
60B ILE* 5.8 0.2 - - + -
61B SER* 4.1 18.4 - - - +
62B ALA 3.1 12.2 + - - +
63B ILE* 3.7 6.5 - - - +
65B MET* 1.3 75.3 - - - +
67B GLY* 1.3 65.1 + - - +
69B MET* 3.7 1.6 - - - +
70B CYS* 3.0 30.5 + - - -
90B TYR* 4.1 34.1 - - + -
91B HIS* 3.9 40.3 - - + +
94B VAL* 4.3 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 5.1 0.2 - - - -
20B ILE* 3.5 26.2 - - - +
25B VAL* 4.0 3.0 - - - +
29B LEU* 3.9 14.8 - - - +
63B ILE 2.9 16.4 + - - -
64B HIS 3.9 0.9 - - - -
66B VAL* 1.3 76.3 - - - +
68B MET* 1.3 63.3 + - - +
70B CYS* 3.2 6.1 + - - +
71B GLU* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.2 57.0 + - + +
20B ILE* 4.2 0.2 - - - +
64B HIS* 2.9 22.8 + - + +
65B MET* 3.8 23.1 - - + +
67B GLY* 1.3 77.2 - - - +
69B MET* 1.3 56.8 + - - +
71B GLU* 3.2 3.8 + - + +
72B LEU* 2.8 53.3 + - + +
184B LEU* 5.0 4.9 - - - -
199B CYS 5.5 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B SER* 5.5 0.7 - - - -
65B MET* 2.8 37.3 + - - +
66B VAL 3.7 3.4 - - - +
68B MET* 1.3 72.4 - - - +
70B CYS* 1.3 56.5 - - - +
72B LEU* 3.3 2.0 + - - -
73B LEU* 3.0 29.7 + - - +
91B HIS* 3.9 21.5 - - + +
151B TYR* 4.1 19.7 - - + -
152B THR 3.4 25.6 - - - +
153B THR* 5.0 0.7 - - - -
174B LEU* 3.3 36.5 - - + +
184B LEU* 4.4 14.8 - - + -
204B PHE* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 4.0 16.0 - - + +
66B VAL* 3.0 19.0 + - - -
67B GLY* 3.2 9.2 + - - +
69B MET* 1.3 75.3 - - - +
71B GLU* 1.3 64.1 + - - +
73B LEU* 3.5 9.1 + - - +
74B ASP* 3.6 7.4 + - - -
75B LEU* 4.0 19.5 + - - +
91B HIS* 4.0 17.5 - - - -
94B VAL* 3.7 30.3 - - - -
95B THR* 4.8 3.4 - - - -
98B ILE* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR 3.8 5.4 - - - +
20B ILE* 3.5 17.1 - - + -
21B LYS* 2.6 37.7 + - + +
22B SER* 2.6 36.2 + - - -
25B VAL* 3.5 15.8 - - + +
67B GLY 3.1 17.9 + - - +
68B MET* 3.5 7.6 - - + +
70B CYS* 1.3 73.9 - - - +
72B LEU* 1.3 68.5 + - + +
74B ASP* 3.1 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 2.8 43.1 + - + +
69B MET 3.3 3.1 + - - +
71B GLU* 1.3 74.6 - - + +
73B LEU* 1.3 59.6 + - - +
74B ASP* 3.4 5.7 + - - +
172B LYS* 5.1 0.5 - - - +
174B LEU* 3.9 16.6 - - + -
184B LEU* 3.8 29.6 - - + -
186B LEU* 3.6 29.6 - - + +
197B LYS* 6.3 1.3 - - + -
199B CYS* 4.3 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B MET 3.0 17.0 + - - +
70B CYS* 3.9 6.1 - - - +
71B GLU 3.1 0.4 - - - -
72B LEU* 1.3 75.7 - - - +
74B ASP* 1.3 58.9 + - - +
75B LEU* 3.3 27.1 - - + -
81B VAL* 4.5 0.2 - - + -
91B HIS* 6.3 1.1 - - + -
149B ARG* 2.7 51.4 + - + -
150B ILE 3.5 20.9 - - - +
151B TYR* 3.4 34.8 - - + -
172B LYS* 3.8 20.0 - - + +
173B LEU 4.5 0.4 - - - -
174B LEU* 3.7 21.1 - - + +
186B LEU* 4.8 2.0 - - + -
----------------------------------------------------------
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