Contacts of the helix formed by residues 86 - 105 (chain X) in PDB entry 2CE2
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 86 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14X VAL* 6.1 0.2 - - + -
83X ALA* 2.9 14.4 + - + +
84X ILE 3.4 1.6 - - - -
85X ASN* 1.3 87.1 + - - +
87X THR* 1.3 65.1 + - - +
88X LYS* 3.4 12.5 + - - +
89X SER* 2.8 61.1 + - - +
90X PHE 3.4 2.8 + - - -
124X THR* 3.4 0.8 + - - -
125X VAL* 4.1 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86X ASN* 1.3 69.7 + - - +
88X LYS* 1.3 66.4 + - - +
90X PHE* 3.1 7.5 + - + +
91X GLU* 3.0 41.6 + - + +
124X THR* 3.1 28.7 + - - +
125X VAL* 3.9 13.5 - - + +
129X GLN* 6.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86X ASN* 3.3 9.7 + - - +
87X THR* 1.3 78.3 - - - +
89X SER* 1.3 63.1 + - - +
91X GLU* 3.2 19.8 + - + +
92X ASP* 2.6 60.9 + - - +
95X GLN* 5.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X ALA* 3.9 17.9 + - - +
12X GLY 5.7 0.7 - - - -
14X VAL* 3.4 27.8 - - - -
81X VAL 4.8 0.5 - - - +
82X PHE* 3.6 8.4 - - - +
83X ALA 2.9 23.3 + - - -
86X ASN* 2.8 36.1 + - - +
88X LYS* 1.3 77.5 - - - +
90X PHE* 1.3 60.6 + - - +
92X ASP* 3.5 15.0 + - - +
93X ILE* 3.5 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82X PHE* 3.6 32.8 - + + -
86X ASN 3.4 0.2 + - - -
87X THR* 3.1 13.5 + - + +
89X SER* 1.3 79.3 + - - +
91X GLU* 1.3 69.7 + - + +
93X ILE* 3.1 20.3 + - + +
113X LEU* 4.9 0.2 - - + -
125X VAL* 3.6 35.2 - - + -
129X GLN* 3.9 44.9 - - + -
130X ALA* 4.1 16.2 - - + -
133X LEU* 3.6 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87X THR* 3.0 34.6 + - + +
88X LYS* 3.6 24.2 - - + +
90X PHE* 1.3 81.5 - - + +
92X ASP* 1.3 58.4 + - - +
93X ILE 3.3 0.7 + - - -
94X HIS* 3.0 33.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X ALA* 3.4 21.6 - - + +
88X LYS* 2.6 51.0 + - - +
89X SER* 3.5 9.9 - - - +
90X PHE 3.2 0.4 - - - -
91X GLU* 1.3 75.7 - - - +
93X ILE* 1.3 67.9 + - - +
94X HIS* 5.1 0.9 - - - -
95X GLN* 2.7 50.3 + - - +
96X TYR* 3.9 12.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10X GLY* 5.3 0.2 - - - -
11X ALA 6.0 0.2 - - - +
80X CYS* 3.9 16.8 - - + +
81X VAL 3.5 43.1 - - - +
82X PHE* 3.9 16.6 - - + +
89X SER 3.7 8.1 - - - +
90X PHE* 3.1 18.8 + - + +
92X ASP* 1.3 76.4 - - - +
94X HIS* 1.3 63.9 + - - +
96X TYR* 2.9 23.8 + - + +
97X ARG* 3.0 13.6 + - + +
113X LEU* 4.0 13.0 - - + -
133X LEU* 3.9 14.4 - - + -
137X TYR* 3.9 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 94 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90X PHE 4.7 0.2 + - - -
91X GLU* 3.0 26.8 + - + -
92X ASP* 2.8 4.4 + - - -
93X ILE* 1.3 77.0 - - - +
95X GLN* 1.3 64.2 + - + +
97X ARG* 3.9 1.1 - - - +
98X GLU* 2.8 50.0 + - + +
133X LEU* 5.5 2.0 - - + +
137X TYR* 3.5 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88X LYS* 5.2 1.0 - - - +
92X ASP* 2.7 55.7 + - - +
94X HIS* 1.3 83.0 - - + +
96X TYR* 1.3 92.4 + - + +
98X GLU* 3.8 4.6 - - - +
99X GLN* 3.1 28.2 + - - +
102X ARG* 4.6 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X VAL* 3.9 25.4 - - + -
10X GLY* 3.5 37.2 + - - -
11X ALA* 3.5 22.9 - - - +
12X GLY 4.7 0.7 + - - -
58X THR* 6.0 0.9 - - - -
60X GLY* 5.7 4.9 - - - -
80X CYS* 4.7 5.2 - - + -
92X ASP* 3.6 21.6 + - + -
93X ILE* 2.9 12.1 + - + +
95X GLN* 1.3 110.1 + - + +
97X ARG* 1.3 65.6 + - - +
99X GLN* 3.3 15.3 + - - +
100X ILE* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80X CYS* 4.5 7.3 - - - -
93X ILE* 3.0 14.2 + - + +
94X HIS* 4.2 2.5 - - - +
96X TYR* 1.3 76.7 - - - +
98X GLU* 1.3 60.9 + - - +
100X ILE* 3.0 10.3 + - - +
101X LYS* 2.7 61.3 + - + +
107X ASP* 3.0 29.3 + - - +
109X VAL 4.8 4.0 + - - +
111X MET* 3.4 40.2 - - + +
137X TYR* 3.7 60.7 + - + +
139X ILE* 4.4 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94X HIS* 2.8 41.8 + - + +
95X GLN* 3.8 5.8 - - - +
97X ARG* 1.3 85.6 - - - +
99X GLN* 1.3 60.6 + - - +
101X LYS* 2.4 43.4 + - - +
102X ARG* 3.1 37.5 + - - +
137X TYR* 4.8 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X VAL* 5.7 0.9 - - - +
63X GLU* 5.5 8.9 + - - +
72X MET* 3.4 25.0 - - + +
95X GLN 3.1 18.5 + - - +
96X TYR* 3.7 15.1 - - - +
98X GLU* 1.3 75.4 - - - +
100X ILE* 1.3 59.2 + - - +
102X ARG* 3.4 30.3 + - - +
103X VAL* 3.0 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X VAL* 3.7 20.2 - - + -
72X MET* 3.7 12.3 - - + -
78X PHE* 3.2 63.9 - - + -
80X CYS* 4.0 9.6 - - - -
96X TYR 3.0 14.8 + - - +
97X ARG 3.0 7.0 + - - +
99X GLN* 1.3 74.6 - - - +
101X LYS* 1.3 65.2 + - - +
103X VAL* 3.3 6.1 + - - +
104X LYS* 2.9 24.0 + - + +
109X VAL* 3.8 7.4 - - + -
111X MET* 3.0 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97X ARG* 2.7 53.9 + - + +
98X GLU* 2.4 43.8 + - - +
100X ILE* 1.3 73.6 - - - +
102X ARG* 1.3 57.7 + - + +
105X ASP* 2.9 23.6 + - - -
106X SER 3.1 28.2 + - - +
107X ASP* 3.6 25.2 + - - +
109X VAL* 4.7 1.6 - - + -
111X MET* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95X GLN 4.6 3.4 + - - -
98X GLU* 3.1 21.4 + - - +
99X GLN* 3.4 48.9 + - - +
100X ILE 3.1 0.2 - - - -
101X LYS* 1.3 77.7 - - + +
103X VAL* 1.3 65.1 + - + +
105X ASP* 3.1 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69X ASP* 5.8 2.2 - - - +
72X MET* 3.2 47.6 - - + +
73X ARG* 4.6 19.1 - - + +
78X PHE* 4.8 0.9 - - + -
99X GLN* 3.0 27.0 + - + +
100X ILE* 3.3 17.0 - - + +
102X ARG* 1.3 80.5 - - + +
104X LYS* 1.3 67.5 + - + +
105X ASP* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72X MET 3.3 24.0 - - - +
73X ARG 3.0 22.2 + - - +
74X THR* 4.1 2.8 - - - +
75X GLY 2.8 29.0 + - - +
76X GLU* 4.9 3.0 - - - +
78X PHE* 4.0 15.7 - - + -
100X ILE 2.9 19.6 + - - +
103X VAL* 1.3 78.5 - - + +
105X ASP* 1.3 70.7 + - - +
106X SER* 3.2 6.4 + - - -
109X VAL* 3.7 27.1 - - + -
110X PRO* 6.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101X LYS 2.9 11.8 + - - -
102X ARG* 3.1 11.3 + - - +
103X VAL 3.3 0.9 - - - +
104X LYS* 1.3 79.4 - - - +
106X SER* 1.3 58.8 + - - +
----------------------------------------------------------
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