Contacts of the helix formed by residues 83 - 96 (chain X) in PDB entry 5A0Q
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 PRO 83 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X LEU* 3.7 26.0 - - + -
81X ILE 4.1 1.3 - - - +
82X LYS* 1.3 86.4 - - + +
84X TYR* 1.4 55.8 + - - +
86X LEU* 3.4 0.9 + - - +
87X MET* 3.1 22.0 + - - +
108X ILE* 3.2 13.8 - - + +
111X LEU 3.5 20.9 - - - +
112X ASP* 3.7 30.7 - - + +
113X PRO* 3.9 3.6 - - + -
119X PHE* 3.4 36.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 84 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97P TYR* 5.6 1.6 + - - -
101P GLN* 3.4 41.2 + - + +
82X LYS* 3.3 14.8 - - + -
83X PRO* 1.4 75.5 - - - +
85X THR* 1.3 66.3 + - - +
87X MET* 3.2 36.1 + - + +
88X SER* 3.0 21.8 + - - -
119X PHE* 4.2 23.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100P TYR* 3.2 52.0 + - + +
101P GLN 4.5 1.2 + - - -
102P GLU* 3.9 21.0 + - - +
73X TYR* 5.4 1.3 - - + -
79X ARG* 5.3 2.9 - - - +
81X ILE* 3.5 23.1 - - + -
82X LYS* 3.2 21.5 + - - +
84X TYR* 1.3 77.7 - - - +
86X LEU* 1.4 56.8 + - - +
88X SER* 3.2 3.6 + - - -
89X MET* 2.9 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X LEU* 3.8 30.5 - - + +
49X TYR 5.2 0.7 - - - +
50X ILE* 5.3 2.5 - - + -
66X LEU* 3.8 33.2 - - + -
70X LEU* 3.8 38.1 - - + -
81X ILE* 3.8 7.3 - - + +
82X LYS 3.1 12.9 + - - +
83X PRO 3.6 9.4 - - - +
84X TYR 3.3 0.2 - - - -
85X THR* 1.4 71.9 - - - +
87X MET* 1.4 63.9 + - - +
89X MET* 3.0 16.1 + - - +
90X VAL* 3.1 15.9 + - + +
108X ILE* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P GLN* 5.6 0.9 - - + -
83X PRO 3.1 12.5 + - - +
84X TYR* 3.3 40.6 - - + +
86X LEU* 1.4 77.5 - - - +
88X SER* 1.3 81.9 + - - +
90X VAL* 3.5 6.5 - - - +
91X ALA* 2.9 31.8 + - + +
108X ILE* 4.3 4.3 - - - -
119X PHE* 4.2 10.8 - - + -
121X CYS* 3.6 28.9 - - + -
122X SER 5.3 0.9 - - - +
123X LEU* 3.5 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P LEU 5.4 0.7 - - - -
99P VAL 3.5 17.5 - - - +
100P TYR 3.8 6.5 - - - -
101P GLN* 3.1 33.6 - - - +
57W GLN* 5.9 0.2 + - - -
84X TYR* 3.0 12.4 + - - -
85X THR 3.2 7.4 + - - -
87X MET* 1.3 88.1 - - - +
89X MET* 1.3 63.5 + - - +
91X ALA* 3.7 7.5 - - - +
92X ASN* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P VAL* 4.4 9.0 - - + -
100P TYR* 3.7 36.3 - - + -
66X LEU* 3.8 24.5 - - + -
69X ARG* 3.2 36.3 + - - +
70X LEU* 4.0 31.9 - - + -
73X TYR* 5.2 4.7 - - + -
81X ILE* 4.2 22.2 - - + -
85X THR 2.9 10.1 + - - +
86X LEU* 3.0 13.0 + - - +
88X SER* 1.3 77.6 - - - +
90X VAL* 1.4 58.3 + - - +
92X ASN* 3.7 1.0 + - - +
93X LEU* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X ILE* 4.5 9.2 - - + -
62X VAL* 4.3 20.6 - - + -
66X LEU* 3.6 36.6 - - + -
86X LEU 3.1 13.9 + - - +
87X MET* 3.5 11.0 - - - +
89X MET* 1.4 75.0 - - - +
91X ALA* 1.3 63.9 + - - +
92X ASN 3.4 0.2 - - - -
93X LEU* 3.6 7.2 - - + -
94X LEU* 3.1 29.4 + - + +
106X PRO* 4.7 10.3 - - + -
108X ILE* 5.3 3.6 - - + -
123X LEU* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54W MET* 3.5 22.1 - - + +
57W GLN* 6.1 0.4 - - - +
87X MET* 2.9 24.6 + - + +
88X SER* 3.7 9.6 - - - +
89X MET 3.3 0.6 - - - -
90X VAL* 1.3 75.4 - - - +
92X ASN* 1.3 62.0 + - - +
94X LEU* 4.1 1.8 - - - +
95X TYR* 3.2 25.1 + - - +
123X LEU* 3.3 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P LEU* 3.9 25.6 - - - +
99P VAL* 4.2 26.1 - - + +
54W MET* 4.0 15.1 - - + +
69X ARG* 4.2 10.4 - - - +
88X SER 3.0 16.3 + - - +
89X MET 4.0 2.7 - - - +
91X ALA* 1.3 75.5 - - - +
93X LEU* 1.4 61.9 + - - +
95X TYR* 3.4 11.7 + - - +
96X GLU* 3.4 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62X VAL* 4.2 21.3 - - + -
65X ARG* 4.0 33.4 - - + +
66X LEU* 4.1 19.3 - - + +
69X ARG* 3.5 37.2 - - - +
89X MET 3.0 19.2 + - - +
90X VAL* 3.7 9.6 - - + +
91X ALA 3.3 0.6 - - - -
92X ASN* 1.4 75.6 - - - +
94X LEU* 1.3 66.7 + - + +
96X GLU* 4.0 16.7 - - - +
97X LYS* 4.8 6.1 + - - +
102X TYR* 5.9 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62X VAL* 3.6 36.1 - - + -
90X VAL* 3.1 18.1 + - + +
91X ALA* 4.3 2.2 - - - +
93X LEU* 1.3 83.1 - - + +
95X TYR* 1.3 61.6 + - - +
96X GLU 3.1 2.6 + - - -
97X LYS* 2.9 27.3 + - - +
101X PRO* 5.0 2.3 - - - +
102X TYR* 4.9 23.3 + - + +
104X THR* 4.2 11.4 - - + +
106X PRO* 4.0 33.7 - - + -
123X LEU* 5.0 2.5 - - + -
124X ASP 4.2 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50W ALA* 3.8 18.6 - - + -
51W ASP* 3.6 22.3 + - - -
54W MET* 3.4 49.8 - - + +
55W THR* 3.9 5.5 + - - -
94W ILE* 3.5 26.4 - - + +
91X ALA 3.2 18.7 + - - +
92X ASN* 3.4 5.1 + - - +
94X LEU* 1.3 75.1 - - - +
96X GLU* 1.3 64.8 + - - +
97X LYS 3.2 2.8 + - - -
98X ARG* 3.4 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69X ARG* 3.2 30.1 + - - -
92X ASN* 3.4 26.2 + - - +
93X LEU* 4.0 14.4 - - - +
94X LEU 3.1 0.2 - - - -
95X TYR* 1.3 80.3 - - + +
97X LYS* 1.3 71.3 + - + +
98X ARG 3.5 3.6 + - - -
99X PHE* 4.9 1.6 + - - +
----------------------------------------------------------
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