Contacts of the helix formed by residues 73 - 93 in PDB entry 2IIL
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 73
.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70 GLU 4.6 2.3 + - - +
71 MET* 4.1 14.0 - - - +
72 ARG* 1.3 79.8 - - - +
74 VAL* 1.3 66.3 + - - +
75 THR* 3.9 17.5 - - + +
76 ASN* 2.8 33.4 + - - +
77 ILE* 3.1 12.3 + - - +
137 GLU* 5.9 0.7 - - - +
155 ALA* 5.1 0.4 - - - -
356 HIS* 6.1 3.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73 ASN* 1.3 70.8 - - - +
75 THR* 1.3 57.7 + - - +
77 ILE* 3.0 4.2 + - - +
78 LEU* 2.9 50.7 + - + +
133 LEU* 4.5 10.1 - - + -
134 ILE* 5.8 1.1 - - + -
137 GLU* 3.3 46.0 + - + +
150 PRO* 3.9 30.3 - - + +
151 ASN 4.5 2.2 - - - +
154 HIS 5.9 0.2 - - - -
155 ALA* 4.1 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73 ASN* 3.9 16.6 - - + +
74 VAL* 1.3 77.4 - - - +
76 ASN* 1.3 61.0 + - + +
78 LEU* 3.2 8.5 + - - +
79 ILE* 2.9 28.9 + - - +
134 ILE* 5.6 11.1 - - - +
137 GLU* 4.6 2.8 + - - -
261 ILE* 3.6 37.0 - - + +
264 MET* 4.4 6.1 - - - -
320 TYR* 3.6 28.0 - - + +
324 ASN* 4.9 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 76
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65 ILE* 3.6 11.7 - - + +
71 MET* 2.9 53.3 - - + +
72 ARG* 3.0 2.9 + - - -
73 ASN* 2.8 53.3 + - - +
75 THR* 1.3 79.3 - - - +
77 ILE* 1.3 59.0 + - - +
79 ILE* 3.3 12.8 - - + +
80 VAL* 3.2 21.8 + - - +
320 TYR* 3.5 14.9 + - - +
327 PHE* 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65 ILE* 5.8 2.5 - - + -
71 MET 5.2 0.7 - - - +
72 ARG* 4.4 24.5 - - + +
73 ASN 3.1 15.7 + - - +
74 VAL 3.0 7.9 + - - +
76 ASN* 1.3 82.1 - - - +
78 LEU* 1.3 64.1 + - + +
80 VAL* 3.1 28.3 - - + +
81 ASN 3.2 4.5 + - - -
152 ASN* 5.5 7.4 - - + +
155 ALA* 3.5 34.8 - - + +
156 TYR 4.4 1.3 - - - +
159 ILE* 3.3 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74 VAL* 2.9 53.1 + - + +
75 THR 3.7 5.4 - - - +
77 ILE* 1.3 76.9 - - + +
79 ILE* 1.3 59.2 + - - +
81 ASN* 3.2 6.9 + - + +
82 LEU* 2.9 31.7 + - + +
130 SER* 3.6 32.8 - - - +
133 LEU* 3.4 28.5 - - + -
134 ILE* 3.7 34.5 - - + -
159 ILE* 4.3 8.7 - - + -
162 ILE* 4.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61 LEU* 3.3 25.8 - - + -
65 ILE* 3.6 11.7 - - + -
75 THR 2.9 10.5 + - - +
76 ASN* 3.3 26.7 - - - +
78 LEU* 1.3 74.5 - - - +
80 VAL* 1.3 58.9 + - - +
82 LEU* 3.3 16.0 + - + +
83 SER* 2.8 32.8 + - - +
316 ASN* 4.7 2.7 - - + +
317 PRO* 4.7 6.3 - - + -
320 TYR* 3.0 62.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62 ILE* 3.7 30.7 - - + +
65 ILE* 3.3 33.9 - - + -
66 LEU* 5.8 0.7 - - + +
76 ASN 3.2 13.8 + - - +
77 ILE* 3.1 30.5 - - + +
78 LEU 3.3 0.2 - - - -
79 ILE* 1.3 75.1 - - - +
81 ASN* 1.3 53.8 + - + +
83 SER* 3.3 3.5 - - - -
84 PHE* 2.8 33.1 + - - +
159 ILE* 5.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 81
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77 ILE 3.2 12.4 + - - +
78 LEU* 3.2 10.0 + - - +
80 VAL* 1.3 75.7 - - + +
82 LEU* 1.3 53.0 + - - +
84 PHE* 3.1 7.1 + - - +
85 SER* 2.8 38.1 + - - -
126 VAL* 4.3 7.7 - - - +
130 SER* 3.6 9.9 + - - -
159 ILE* 4.0 19.8 + - + +
162 ILE* 3.5 35.4 - - - +
163 TRP* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78 LEU* 2.9 21.4 + - + +
79 ILE* 3.6 16.6 - - + +
81 ASN* 1.3 72.6 - - - +
83 SER* 1.3 52.2 + - - +
85 SER* 3.3 3.8 + - - -
86 ASP* 2.8 51.3 + - - +
126 VAL* 4.1 7.0 - - + +
127 SER* 3.8 31.0 - - - +
130 SER* 3.6 27.6 - - - +
131 LEU* 6.1 0.2 - - + -
134 ILE* 5.5 2.2 - - + -
268 ILE* 3.7 29.6 - - + -
316 ASN* 3.9 20.6 - - + +
317 PRO* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58 ASN* 2.7 44.2 + - - +
61 LEU* 4.2 9.4 - - - -
62 ILE* 3.3 20.8 + - - +
79 ILE* 2.8 21.1 + - - +
80 VAL* 3.3 9.6 - - - -
82 LEU* 1.3 71.2 - - - +
84 PHE* 1.3 55.9 + - - +
86 ASP* 3.4 2.8 + - - +
87 LEU* 3.0 31.9 + - - +
317 PRO* 5.6 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62 ILE* 4.2 20.4 - - + +
80 VAL* 2.8 17.2 + - + +
81 ASN* 3.4 10.5 - - - +
83 SER* 1.3 71.3 + - - +
85 SER* 1.3 61.7 + - - +
87 LEU* 3.0 23.1 + - + +
88 LEU* 3.0 48.5 + - + +
163 TRP* 3.4 35.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 ASN* 2.8 22.7 + - - -
82 LEU* 3.7 4.5 - - - -
84 PHE* 1.3 73.1 - - - +
86 ASP* 1.3 52.0 + - - +
88 LEU* 3.2 11.9 + - - +
89 VAL* 2.9 35.6 + - - +
119 VAL* 5.2 0.2 - - - +
122 VAL* 5.4 3.8 - - - +
123 SER* 4.3 5.9 - - - -
126 VAL* 3.1 46.0 - - - +
163 TRP* 3.9 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58 ASN* 2.9 36.4 + - - +
82 LEU* 2.8 26.8 + - - +
83 SER 3.5 0.2 - - - +
85 SER* 1.3 71.7 - - - +
87 LEU* 1.3 57.8 + - - +
89 VAL* 3.3 9.3 - - - +
90 ALA* 3.0 24.7 + - - +
123 SER* 5.0 6.4 - - - +
126 VAL* 5.7 0.5 - - - +
312 SER* 3.7 13.3 + - - +
313 THR* 2.8 38.1 - - + +
316 ASN* 4.0 8.3 + - - -
317 PRO* 3.7 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54 GLY 4.4 0.9 - - - +
55 VAL* 3.8 22.0 - - + +
58 ASN* 3.6 20.2 - - + -
59 LEU* 3.7 22.7 - - + +
62 ILE* 4.2 28.3 - - + -
83 SER 3.0 19.5 + - - +
84 PHE* 3.0 18.1 + - + +
86 ASP* 1.3 71.0 - - - +
88 LEU* 1.3 64.7 + - + +
90 ALA* 3.3 4.8 + - - +
91 ILE* 2.9 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84 PHE* 3.0 70.7 + - + +
85 SER* 3.2 11.0 + - - +
87 LEU* 1.3 75.7 - - + +
89 VAL* 1.3 55.2 + - - +
91 ILE* 3.9 7.4 - - + -
92 MET* 2.6 71.0 + - + +
119 VAL* 3.0 17.5 - - + +
122 VAL* 5.1 7.6 - - + -
163 TRP* 4.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85 SER 2.9 18.9 + - - +
86 ASP* 3.3 17.5 - - - +
88 LEU* 1.3 70.4 - - - +
90 ALA* 1.3 52.8 + - - +
93 CYS* 2.9 32.1 + - - -
94 LEU* 2.8 37.6 + - + -
119 VAL* 3.3 8.8 - - - +
120 GLN* 3.4 20.6 - - - +
123 SER* 3.1 25.4 - - - +
313 THR* 3.1 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51 ILE* 3.8 15.4 - - + +
54 GLY 4.8 0.9 - - - -
55 VAL* 4.0 32.1 - - + +
86 ASP 3.0 14.0 + - - +
87 LEU* 3.3 7.8 + - - +
89 VAL* 1.3 77.6 - - - +
91 ILE* 1.3 57.9 + - + +
94 LEU* 3.2 35.2 - - + +
95 PRO* 3.2 8.8 - - - +
313 THR* 4.3 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51 ILE* 5.9 0.4 - - - -
55 VAL* 6.5 0.7 - - + -
87 LEU* 2.9 26.2 + - + +
88 LEU* 3.7 14.8 - - + +
90 ALA* 1.3 72.7 - - - +
92 MET* 1.3 73.5 + - + +
95 PRO* 3.0 24.1 - - + +
96 PHE* 3.9 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 92
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88 LEU* 2.6 57.0 + - + +
91 ILE* 1.3 81.3 - - + +
93 CYS* 1.3 54.8 + - - -
96 PHE* 2.8 24.1 - - - -
115 LEU* 3.0 28.2 - - + +
118 PHE* 5.5 6.7 - - - -
119 VAL* 3.2 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 93
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88 LEU 3.7 0.2 + - - -
89 VAL* 2.9 57.1 + - - -
92 MET* 1.3 71.2 - - - +
94 LEU* 1.3 63.0 + - - +
95 PRO* 3.3 3.4 - - - -
96 PHE* 3.2 6.9 + - - +
97 THR 2.9 24.1 + - - -
115 LEU 3.5 6.7 - - - +
116 ASN* 2.9 40.2 - - - +
119 VAL* 3.7 2.2 - - + -
120 GLN* 3.6 21.5 - - - -
310 MET* 5.8 0.7 - - - -
----------------------------------------------------------
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