Contacts of the helix formed by residues 67 - 80 (chain Q) in PDB entry 5XS0
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 GLU 67 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Q SER* 3.7 16.1 + - - +
65Q TYR* 3.7 28.5 + - + -
66Q ILE* 1.3 79.1 - - - +
68Q GLY* 1.3 67.5 + - - +
69Q HIS* 3.1 32.9 - - + +
70Q ARG* 3.1 32.4 + - + +
71Q VAL* 3.3 8.8 + - - +
152Q LYS* 5.1 0.4 - - - +
167R LEU 4.9 0.6 - - - +
169R LYS* 3.3 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q ILE 3.7 1.0 + - - -
67Q GLU* 1.3 72.9 - - - +
69Q HIS* 1.3 63.6 + - - +
71Q VAL* 2.9 15.7 + - - +
72Q ILE* 3.0 21.2 + - - +
148Q THR* 4.5 16.2 - - - +
152Q LYS* 4.3 18.0 - - - +
167R LEU* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Q GLU* 3.1 38.9 - - + +
68Q GLY* 1.3 73.4 - - - +
70Q ARG* 1.3 83.5 + - + +
72Q ILE* 3.4 2.4 + - - -
73Q ASN* 2.9 41.9 + - - +
164R ASN* 3.1 35.5 + - - +
165R CYS* 5.9 0.7 - - - -
167R LEU* 3.6 42.6 + - + +
168R ASP* 3.8 33.1 + - + -
169R LYS 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195P ASP* 5.0 1.3 - - - +
50Q GLU 3.6 17.0 + - - -
51Q TYR* 3.2 50.3 + - + +
52Q ILE 5.0 0.6 + - - -
53Q SER* 3.4 18.0 + - - -
66Q ILE* 3.7 11.4 - - + -
67Q GLU* 3.1 30.8 + - + +
69Q HIS* 1.3 99.9 + - + +
71Q VAL* 1.3 57.2 + - - +
73Q ASN* 3.4 6.7 + - - +
74Q LEU* 2.9 34.8 + - - +
168R ASP* 4.9 4.6 + - - -
170R ASP* 4.8 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q ILE* 3.7 26.7 - - + -
67Q GLU 3.5 13.7 - - - +
68Q GLY 2.9 6.7 + - - +
70Q ARG* 1.3 72.5 - - - +
72Q ILE* 1.3 62.4 + - + +
74Q LEU* 3.3 9.1 + - + +
75Q ALA* 2.9 28.4 + - - +
151Q LEU* 6.0 0.7 - - + -
152Q LYS* 4.1 30.5 - - + -
155Q LEU* 3.6 32.1 - - + -
162Q LEU* 4.3 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Q GLY* 3.0 18.5 + - - +
69Q HIS* 3.7 2.7 - - - +
71Q VAL* 1.3 76.9 - - + +
73Q ASN* 1.3 56.6 + - - +
75Q ALA* 3.3 5.8 + - - +
76Q ASN* 2.9 48.8 + - - +
84Q TRP* 4.3 7.6 - - + -
151Q LEU* 4.6 19.3 - - + -
155Q LEU* 5.5 0.7 - - + -
156R ARG* 4.2 4.5 - - + +
157R SER* 3.5 39.9 - - - +
164R ASN* 3.3 33.4 - - - +
167R LEU* 5.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195P ASP* 3.7 23.9 + - + +
69Q HIS* 2.9 32.4 + - - +
70Q ARG* 3.8 6.1 - - - +
71Q VAL 3.3 0.2 - - - -
72Q ILE* 1.3 76.1 - - - +
74Q LEU* 1.3 64.1 + - - +
76Q ASN* 3.3 5.3 + - - +
77Q GLU* 2.9 31.0 + - + +
46R ARG* 6.1 1.4 - - - +
159R GLY* 4.6 4.0 - - - -
160R ASN* 3.2 39.8 + - - +
164R ASN* 3.4 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192P LYS* 3.6 31.8 - - + -
195P ASP* 4.1 14.5 + - - +
47Q LEU* 4.3 11.7 - - + -
51Q TYR* 4.1 17.0 - - + -
66Q ILE* 4.9 12.6 - - + -
70Q ARG 2.9 24.3 + - - +
71Q VAL* 3.5 13.7 - - + +
73Q ASN* 1.3 77.0 - - - +
75Q ALA* 1.3 56.9 + - - +
77Q GLU* 3.3 4.3 + - - +
78Q MET* 2.9 35.9 + - + +
161Q ALA 3.6 23.1 - - - +
162Q LEU* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71Q VAL 2.9 17.5 + - - +
72Q ILE 3.8 0.2 - - - +
74Q LEU* 1.3 73.6 - - - +
76Q ASN* 1.3 60.2 + - - +
78Q MET* 4.4 0.2 - - - -
79Q PHE* 2.9 37.6 + - + -
84Q TRP* 3.5 38.4 - - + -
155Q LEU* 4.1 18.4 - - + -
162Q LEU* 3.7 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 76 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Q ILE* 2.9 29.7 + - - +
73Q ASN* 3.8 7.8 + - - +
75Q ALA* 1.3 74.6 - - - +
77Q GLU* 1.3 62.1 + - + +
80Q GLY* 2.8 27.7 + - - -
81Q TYR* 3.4 18.5 - - - +
84Q TRP* 3.1 18.1 + - - +
40R GLN* 3.1 14.3 + - - +
121R HIS* 5.0 0.3 + - - -
157R SER 3.3 21.8 + - - +
158R PHE* 3.4 23.1 + - - +
159R GLY* 3.6 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192P LYS* 6.0 0.2 - - - -
195P ASP* 3.5 39.4 - - + +
196P LEU* 3.8 17.4 - - - +
197P GLU* 4.5 15.1 + - + +
200P VAL* 4.6 0.3 - - - +
201P GLU* 5.2 3.1 + - - +
204P ARG* 3.4 14.6 + - - -
73Q ASN* 2.9 21.6 + - + +
74Q LEU* 3.9 3.6 - - - +
76Q ASN* 1.3 82.2 - - + +
78Q MET* 1.3 63.7 + - + +
40R GLN* 4.5 9.1 + - - +
44R ARG* 2.8 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192P LYS* 5.5 3.8 - - - -
197P GLU* 4.2 13.9 - - + +
200P VAL* 3.6 3.5 - - + +
204P ARG* 2.6 18.8 + - - -
39Q ILE* 3.5 50.2 - - + +
42Q ALA* 3.8 26.7 - - + +
43Q LEU* 3.6 38.8 - - + -
74Q LEU* 2.9 26.4 + - + +
75Q ALA 3.3 3.1 + - - +
77Q GLU* 1.3 78.2 - - + +
79Q PHE* 1.3 70.9 + - + +
161Q ALA* 4.6 7.0 - - + -
162Q LEU* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P TYR* 3.9 14.6 - + - -
204P ARG* 3.4 20.4 + - - +
31Q TYR* 3.5 19.1 + - - +
35Q GLU* 4.8 1.8 - - - +
39Q ILE* 4.2 13.2 - - + -
43Q LEU* 4.5 5.4 - - + -
75Q ALA* 2.9 19.8 + - + +
78Q MET* 1.3 86.4 - - + +
80Q GLY* 1.3 58.8 + - - +
82Q ASN* 4.7 0.3 - - - +
83Q GLY* 3.3 34.6 + - - +
84Q TRP* 3.8 17.9 - + + +
115Q LEU* 3.6 34.8 - - + -
116Q LYS* 5.4 1.4 - - - -
155Q LEU* 4.9 2.2 - - + -
158Q PHE* 4.3 13.0 - + + -
162Q LEU* 3.6 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204P ARG* 3.3 17.3 - - - +
76Q ASN* 2.8 22.4 + - - -
79Q PHE* 1.3 78.4 - - - +
81Q TYR* 1.3 66.1 + - - -
82Q ASN* 3.0 8.6 + - - -
83Q GLY 3.1 4.5 + - - -
84Q TRP* 3.1 20.4 - - - -
36R TYR* 4.3 3.1 - - - -
40R GLN* 3.4 5.2 - - - -
----------------------------------------------------------
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