Contacts of the helix formed by residues 75 - 87 (chain B) in PDB entry 6R7Y
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 75 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLN* 5.6 1.6 + - - -
51B LEU* 3.8 16.7 - - - +
74B ALA* 1.3 76.4 - - - +
76B LYS* 1.3 62.7 + - - +
77B ILE* 3.4 4.5 - - - +
78B ARG* 3.2 16.1 + - - +
79B MET* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 1.3 76.2 - - - +
77B ILE* 1.3 69.0 + - + +
79B MET* 3.3 8.6 + - - +
80B LEU* 3.1 31.3 + - + +
113B ASP 4.0 7.3 + - - -
114B ASN* 3.7 12.1 - - - +
115B ASN 3.5 41.7 - - - +
116B ASP* 3.8 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 4.6 3.5 - - - +
76B LYS* 1.3 80.7 - - + +
78B ARG* 1.3 58.0 + - - +
80B LEU* 3.4 8.6 + - + +
81B LEU* 3.0 41.4 + - + +
102B TYR* 3.7 31.9 - - + +
105B ARG* 5.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 3.3 22.5 - - - +
48B ALA 3.4 22.6 + - - -
49B GLN* 3.4 42.3 - - - +
50B LEU* 4.4 4.2 - - + +
74B ALA* 3.8 15.7 - - + -
75B SER* 3.2 26.3 + - - +
77B ILE* 1.3 79.6 - - - +
79B MET* 1.3 56.7 + - - +
81B LEU* 3.4 15.5 + - - +
82B GLY* 2.9 28.4 + - - +
127B ILE* 5.4 0.8 - - - +
131B GLU* 3.3 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 5.1 3.4 - - + -
50B LEU* 5.7 0.7 - - - -
74B ALA* 3.6 27.4 - - + +
75B SER 3.0 16.4 + - - +
76B LYS* 3.3 8.2 + - - +
78B ARG* 1.3 75.1 - - - +
80B LEU* 1.3 61.6 + - + +
82B GLY* 3.6 1.8 - - - -
83B ALA* 2.8 28.6 + - - +
119B LEU* 3.8 17.2 - - + +
124B CYS* 3.5 49.1 - - + +
127B ILE* 3.9 19.6 - - + +
128B ILE* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 3.1 21.3 + - + +
77B ILE* 3.8 7.4 - - + +
79B MET* 1.3 75.0 - - + +
81B LEU* 1.3 59.9 + - - +
83B ALA* 3.2 4.0 + - - +
84B GLU* 3.0 24.3 + - - +
100B PHE* 3.8 27.4 - - + -
102B TYR* 3.7 35.7 - - + +
105B ARG* 4.7 2.5 - - - +
111B PHE* 4.3 23.6 - - + -
118B PHE* 4.5 9.6 - - + -
119B LEU* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 5.8 1.4 + - - -
49B GLN* 6.0 4.3 - - - +
77B ILE* 3.0 34.6 + - + +
78B ARG* 3.7 18.8 - - - +
80B LEU* 1.3 75.3 - - - +
82B GLY* 1.3 62.0 + - - +
84B GLU* 3.3 10.4 + - + +
85B ALA* 3.2 18.5 + - - +
102B TYR* 4.2 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 5.9 0.4 - - - -
78B ARG* 2.9 26.8 + - - +
79B MET 3.6 3.4 - - - -
81B LEU* 1.3 75.6 - - - +
83B ALA* 1.3 57.9 + - - +
85B ALA* 3.1 4.6 + - - +
86B VAL* 3.0 31.9 + - - +
127B ILE* 3.8 19.8 - - - +
131B GLU* 3.9 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET 2.8 17.0 + - - +
80B LEU* 3.2 8.0 + - - +
82B GLY* 1.3 72.3 - - - +
84B GLU* 1.3 66.3 + - - +
86B VAL* 4.5 0.7 - - - +
87B GLY* 3.2 18.0 + - - -
88B LEU* 3.6 24.0 + - + -
100B PHE* 3.7 25.5 - - + +
119B LEU* 4.2 7.2 - - + -
127B ILE* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A GLN* 6.5 0.9 - - + -
80B LEU 3.0 13.0 + - - +
81B LEU* 3.5 14.4 - - + +
82B GLY 3.2 0.4 - - - -
83B ALA* 1.3 78.4 - - - +
85B ALA* 1.3 61.7 + - - +
86B VAL 3.6 0.2 + - - -
87B GLY* 3.8 6.9 + - - -
100B PHE* 3.9 17.6 - - - +
101B THR* 4.8 2.9 - - + -
102B TYR* 4.5 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 5.3 7.2 - - - +
81B LEU 3.2 9.2 + - - +
82B GLY 3.1 9.0 + - - +
84B GLU* 1.3 81.6 - - - +
86B VAL* 1.3 62.9 + - + +
130B HIS* 4.9 8.3 + - + +
131B GLU* 4.1 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY 3.0 18.1 + - - +
83B ALA* 4.4 2.2 - - - +
85B ALA* 1.3 79.4 - - - +
87B GLY* 1.3 61.4 + - - +
88B LEU* 4.2 16.2 - - + +
126B PHE* 3.6 29.6 - - + -
127B ILE* 4.0 20.0 - - + -
130B HIS* 3.6 42.4 - - + +
131B GLU* 5.2 0.2 - - - +
277B MET* 4.8 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA 3.2 9.5 + - - -
84B GLU 3.8 5.1 + - - -
85B ALA 3.5 1.2 - - - -
86B VAL* 1.3 84.5 - - - +
88B LEU* 1.3 68.6 + - - +
89B VAL* 3.6 3.6 + - - +
99B ALA* 5.5 6.1 - - - +
100B PHE 5.2 5.4 - - - -
277B MET* 3.5 24.8 - - - +
----------------------------------------------------------
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