Contacts of the helix formed by residues 75 - 90 (chain B) in PDB entry 2QU7
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 75 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASP* 2.8 22.1 + - - +
74B GLN* 1.3 75.8 - - - +
76B PRO* 1.3 78.5 - - - +
77B PHE* 2.8 26.7 + - - +
78B PHE* 2.8 31.6 + - + +
79B THR* 3.8 3.5 + - - +
228B GLN* 5.8 0.2 + - - -
251B ASN* 3.8 13.9 - - - +
252B HIS* 3.4 21.2 - - - +
253B LEU* 4.3 12.7 - - + +
279B ASP* 3.1 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLN 3.2 8.7 - - - +
75B ASN* 1.3 93.2 - - - +
77B PHE* 1.3 51.0 + - - +
78B PHE 3.2 0.2 - - - -
79B THR* 2.8 18.0 + - + +
80B GLU* 2.8 52.0 + - - +
252B HIS* 3.5 36.1 - - + +
253B LEU* 4.7 2.0 - - + -
280B ASP 5.7 2.0 - - - +
281B SER* 6.1 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 2.8 22.6 + - - +
76B PRO* 1.3 77.6 - - - +
78B PHE* 1.3 93.3 + + - +
80B GLU* 3.4 10.4 + - - +
81B VAL* 3.1 47.7 + - + +
146B LEU* 4.6 1.8 - - + -
147B ASP* 3.7 20.6 - - + -
279B ASP* 3.9 23.3 - - + +
296B GLN* 3.7 30.5 - - + -
298B VAL* 3.7 18.2 - - + -
301B MET* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 3.4 9.0 - + + -
71B VAL* 3.8 21.1 - - + -
72B PRO* 3.7 23.3 - - + -
73B ASP* 3.3 38.4 - - - +
75B ASN* 2.8 28.2 + - + +
77B PHE* 1.3 99.6 - + - +
79B THR* 1.3 56.7 + - + +
81B VAL* 3.4 4.0 + - - +
82B LEU* 2.8 28.4 + - - +
126B VAL* 3.7 31.2 - - + -
146B LEU* 4.5 6.3 - - + -
147B ASP* 3.8 18.8 - - + -
148B ARG* 4.4 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 3.7 21.0 + - - +
79A THR* 5.0 16.2 - - + -
74B GLN* 5.2 7.2 - - - +
75B ASN 4.2 9.0 - - - +
76B PRO* 2.8 23.2 + - + +
78B PHE* 1.3 73.6 - - + +
80B GLU* 1.3 60.4 + - - +
82B LEU* 3.4 16.5 - - + +
83B THR* 2.9 31.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
74A GLN* 4.3 10.1 - - - +
76B PRO* 2.8 37.3 + - + +
77B PHE* 3.8 7.2 - - - +
79B THR* 1.3 75.1 + - - +
81B VAL* 1.3 64.5 - - - +
83B THR* 3.5 7.5 + - - -
84B GLU* 3.4 22.7 + - - +
280B ASP 3.9 20.2 - - - +
281B SER* 5.1 4.5 - - - -
298B VAL* 4.0 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 4.7 3.1 - - + -
77B PHE* 3.1 45.3 + - + +
78B PHE* 3.7 6.5 - - - +
80B GLU* 1.3 74.1 - - - +
82B LEU* 1.3 65.7 + - - +
84B GLU* 3.1 3.8 + - - +
85B ILE* 2.9 40.2 + - + +
146B LEU* 3.9 20.6 - - + -
298B VAL* 3.9 23.6 - - + -
301B MET* 4.3 6.7 - - + -
302B GLY* 4.2 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 5.7 1.3 - - + +
99A ALA* 6.2 1.8 - - - -
100A SER* 5.9 9.2 - - - +
69B PHE* 3.7 15.7 - - + -
78B PHE 2.8 17.8 + - - +
79B THR* 3.4 17.9 - - + +
80B GLU 3.3 0.2 - - - -
81B VAL* 1.3 76.5 - - - +
83B THR* 1.3 57.7 + - - +
85B ILE* 3.1 5.8 + - - +
86B SER* 2.7 41.3 + - - -
96B VAL* 3.4 32.8 - - + +
98B VAL* 3.4 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 3.5 28.6 + - - +
102A GLU* 4.7 16.9 + - + +
79B THR 2.9 18.0 + - - -
80B GLU* 3.8 7.9 - - - -
81B VAL 3.2 0.4 - - - -
82B LEU* 1.3 79.8 - - - +
84B GLU* 1.3 60.3 + - + +
86B SER* 3.6 6.9 - - - -
87B HIS* 3.0 28.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
80B GLU 3.4 10.6 + - - +
81B VAL 3.1 8.3 + - - +
83B THR* 1.3 80.9 - - - +
85B ILE* 1.3 66.6 + - - +
87B HIS* 3.3 18.0 + - - +
88B GLU* 3.2 22.5 + - - +
298B VAL* 4.1 2.2 - - + +
299B LYS* 3.3 54.6 + - + +
302B GLY* 3.8 18.5 - - - +
303B GLN* 3.6 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 5.7 0.7 - - + -
69B PHE* 4.7 12.6 - - + -
81B VAL* 2.9 35.1 + - + +
82B LEU* 3.5 8.1 - - - +
84B GLU* 1.3 74.7 - - - +
86B SER* 1.3 58.0 + - - +
88B GLU* 3.2 4.3 + - - +
89B CYS* 2.9 41.4 + - - +
96B VAL* 3.8 22.0 - - + -
124B ILE* 4.1 23.8 - - + -
146B LEU* 4.1 8.1 - - + -
302B GLY* 3.5 26.0 - - - +
305B ALA* 4.0 17.9 - - + -
306B ALA* 4.0 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A SER 5.4 1.7 + - - -
107A LYS* 4.3 11.8 + - - -
82B LEU* 2.7 26.0 + - - -
83B THR* 3.6 8.5 - - - -
85B ILE* 1.3 74.3 - - - +
87B HIS* 1.3 62.7 + - - +
89B CYS* 3.2 1.4 + - - +
90B GLN* 3.1 37.4 + - - +
94B LEU 4.8 0.7 - - - +
95B HIS* 5.9 0.2 - - - -
96B VAL* 3.8 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR* 3.0 18.7 + - + +
84B GLU* 3.3 19.3 + - - +
86B SER* 1.3 76.0 - - - +
88B GLU* 1.3 68.1 + - + +
90B GLN* 3.5 24.9 + - - +
91B LYS* 3.5 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 3.2 8.3 + - - +
85B ILE 3.2 3.3 + - - +
87B HIS* 1.3 83.3 - - + +
89B CYS* 1.3 59.2 + - - +
91B LYS* 2.9 55.6 + - - +
92B HIS* 4.2 15.8 + - + -
302B GLY 5.1 1.1 - - - +
303B GLN* 4.7 17.4 - - + +
306B ALA* 3.5 30.3 - - + -
307B LYS* 4.4 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.7 24.9 - - - -
85B ILE* 2.9 33.4 + - - +
86B SER 3.9 2.5 - - - +
88B GLU* 1.3 72.0 - - - +
90B GLN* 1.3 62.8 + - - +
91B LYS 3.0 5.6 - - - -
92B HIS* 2.9 20.5 + - - +
94B LEU* 3.1 37.7 + - + +
96B VAL* 4.3 8.5 - - + -
306B ALA* 4.0 15.0 - - - -
309B ILE* 4.3 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 3.3 38.6 + - + +
86B SER* 3.1 25.9 + - - +
87B HIS* 3.5 24.7 + - - +
89B CYS* 1.3 76.8 - - - +
91B LYS* 1.3 61.3 + - + +
93B HIS* 3.0 20.7 + - - +
94B LEU 3.3 14.2 + - - +
95B HIS* 5.4 3.8 - - + +
----------------------------------------------------------
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