Contacts of the helix formed by residues 79 - 94 (chain B) in PDB entry 2VDY
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 SER 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASN 5.1 8.1 + - - -
75B LEU* 4.6 12.4 - - - +
80B GLU* 1.3 64.4 + - - +
81B THR* 3.5 13.5 + - - -
82B GLU* 3.4 39.5 + - - +
83B ILE* 3.4 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 4.7 3.6 - - - +
57B LEU* 4.1 4.0 - - - +
64B ARG* 3.0 47.3 + - - +
68B LEU* 3.5 9.8 - - + +
75B LEU* 4.4 6.6 - - + +
79B SER* 1.3 71.9 - - - +
81B THR* 1.3 68.3 - - + +
83B ILE* 3.0 22.4 + - + +
84B HIS* 3.2 44.0 + - + +
311B ARG* 3.2 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 3.5 12.6 + - - -
80B GLU* 1.3 79.4 - - + +
82B GLU* 1.3 58.8 + - - +
84B HIS* 3.6 6.0 + - + +
85B GLN* 3.1 40.2 + - - +
128B TYR* 3.8 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.4 17.3 - - + +
79B SER* 3.4 33.1 + - - +
80B GLU 3.2 0.6 - - - -
81B THR* 1.3 76.0 + - - +
83B ILE* 1.3 60.1 + - + +
85B GLN* 3.9 16.3 - - - +
86B GLY 3.1 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.5 12.1 - - + +
53B ALA* 5.4 1.1 - - + -
68B LEU* 5.1 10.3 - - + -
73B PHE* 3.7 64.2 - - + -
74B ASN 5.6 2.7 - - - +
75B LEU* 4.2 14.8 - - + -
79B SER 3.4 17.7 - - - +
80B GLU* 3.0 15.8 + - - +
82B GLU* 1.3 77.3 - - + +
84B HIS* 1.3 67.4 + - + +
86B GLY* 3.1 14.7 + - - -
87B PHE* 3.2 23.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 3.1 28.7 - - + -
56B SER* 3.5 10.9 + - - -
57B LEU* 3.5 32.8 - - + +
68B LEU* 5.4 1.9 - - + +
80B GLU* 3.2 46.3 + - + +
81B THR* 4.2 2.5 - - + +
83B ILE* 1.3 79.3 - - + +
85B GLN* 1.3 60.7 + - - +
87B PHE* 3.3 2.5 + - - +
88B GLN* 3.0 26.9 + - - +
128B TYR* 3.6 35.0 - + + +
129B TYR* 2.8 29.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR* 3.1 29.0 + - - +
82B GLU* 3.9 17.8 - - - +
83B ILE 3.3 0.2 - - - -
84B HIS* 1.3 75.8 - - - +
86B GLY* 1.3 55.8 + - - +
88B GLN* 3.4 14.2 + - - +
89B HIS* 2.8 47.4 + - + +
127B HIS* 5.4 4.3 - - + -
128B TYR* 3.7 19.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.8 23.6 - - - -
82B GLU 3.1 8.0 + - - -
83B ILE 3.1 10.0 + - - -
85B GLN* 1.3 77.9 - - - +
87B PHE* 1.3 59.6 + - - +
89B HIS* 3.4 10.6 + - - +
90B LEU* 3.2 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.8 2.2 - - + -
21B ASN* 3.5 34.1 - - - -
46B VAL* 4.8 2.2 - - + -
49B SER* 3.6 18.4 - - - -
50B MET* 3.6 45.2 - - + +
53B ALA* 3.6 13.9 - - + -
73B PHE* 3.6 22.4 - + - -
83B ILE* 3.2 27.3 + - + -
84B HIS 3.3 4.2 + - - +
86B GLY* 1.3 73.5 - - - +
88B GLN* 1.3 60.2 + - - +
90B LEU* 3.9 13.9 - - + -
91B HIS* 3.1 28.6 + - - +
128B TYR 4.3 2.2 - - - +
129B TYR* 3.6 34.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B HIS 3.0 11.9 + - - +
85B GLN* 3.5 21.2 - - - +
86B GLY 3.3 0.2 - - - -
87B PHE* 1.3 75.8 - - - +
89B HIS* 1.3 66.1 + - - +
91B HIS* 3.5 4.6 + - - +
92B GLN* 3.1 61.6 + - + +
127B HIS* 2.8 44.7 + - - +
128B TYR* 3.3 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLN* 2.8 30.7 + - + +
86B GLY* 3.4 13.0 - - - +
88B GLN* 1.3 85.1 - - - +
90B LEU* 1.3 65.9 + - + +
92B GLN* 3.3 11.9 + - - +
93B LEU* 3.0 40.6 + - + +
370B THR* 5.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 5.9 5.6 - - + -
21B ASN* 4.5 10.3 - - - +
46B VAL* 3.9 23.8 - - + -
50B MET* 4.4 6.1 - - + -
86B GLY* 3.2 23.2 + - - +
87B PHE* 3.8 27.6 - - + +
88B GLN 3.4 0.2 - - - -
89B HIS* 1.3 79.9 - - + +
91B HIS* 1.3 57.9 + - - +
93B LEU* 3.4 2.7 + - - +
94B PHE* 3.0 33.5 + - - +
105B MET* 5.0 3.1 - - - +
370B THR* 3.8 34.1 - - + +
372B SER* 3.4 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B MET* 3.9 14.1 - - + -
87B PHE 3.1 19.1 + - - +
88B GLN* 3.9 6.1 + - - +
89B HIS 3.3 0.2 - - - -
90B LEU* 1.3 77.5 - - - +
92B GLN* 1.3 68.6 + - + +
93B LEU 3.7 0.2 + - - -
94B PHE* 3.8 16.3 + - - +
95B ALA* 4.4 4.7 - - - +
105B MET* 3.0 38.9 + - + +
106B GLY* 3.9 10.8 - - - -
107B ASN* 4.3 8.3 + - - +
128B TYR 5.2 3.2 + - - +
129B TYR* 3.8 13.7 + - - -
130B GLU* 3.3 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLN* 3.1 50.0 + - + +
89B HIS* 3.9 11.0 + - - +
91B HIS* 1.3 85.7 - - + +
93B LEU* 1.3 63.1 + - + +
95B ALA* 3.9 15.0 - - - +
130B GLU* 5.5 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B HIS* 3.0 27.7 + - + +
90B LEU* 4.0 3.6 - - - +
92B GLN* 1.3 75.7 - - + +
94B PHE* 1.3 54.4 + - - +
95B ALA 3.0 13.5 + - - +
96B LYS* 5.7 1.6 - - - -
103B MET* 3.7 14.0 - - - +
367B ASP* 5.7 4.9 - - - +
369B PHE* 3.6 51.8 - - + -
370B THR* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU 3.0 18.2 + - - +
91B HIS 4.0 5.3 - - - +
92B GLN 3.5 0.6 - - - -
93B LEU* 1.3 73.6 - - - +
95B ALA* 1.3 58.6 + - - +
103B MET* 3.6 36.9 - - + +
104B THR 3.8 2.9 - - - -
105B MET* 3.6 40.5 + - + +
179B ILE* 3.7 25.1 - - + -
180B PHE 3.6 20.2 - - - -
181B PHE* 3.9 26.0 - + + -
367B ASP* 4.1 15.0 - - - -
374B LEU* 3.8 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