Contacts of the helix formed by residues 69 - 89 (chain I) in PDB entry 1IBM
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 GLY 69 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249A C 3.6 12.5 + - - -
1371A G 3.1 24.3 + - - -
1372A U 3.0 5.7 + - - -
67I GLY 4.1 1.6 + - - -
68I GLY* 1.3 75.5 - - - -
70I LYS* 1.3 69.2 + - - -
72I GLY* 2.7 18.9 + - - +
73I GLN* 3.1 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248A A 2.8 50.6 + - + +
1249A C 3.7 25.9 + - - +
1289A A 5.5 3.3 - - - +
1290A G 5.9 2.0 - - - +
1372A U 3.7 3.4 + - - -
31I GLN* 5.2 0.2 + - - -
36I TYR* 2.9 45.5 + - + -
37I PHE* 4.2 17.6 - - + -
40I LEU* 3.9 27.6 - - + -
69I GLY* 1.3 68.0 - - - +
71I SER* 1.3 53.8 + - - +
73I GLN* 3.3 8.8 + - - +
74I ILE* 2.8 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372A U 2.9 28.7 + - - -
1373A G 2.5 30.8 + - - -
42I ARG* 3.3 24.6 + - - -
69I GLY 2.8 3.4 + - - -
70I LYS* 1.3 75.7 - - - +
72I GLY* 1.3 60.7 + - - -
74I ILE* 3.1 23.9 + - - +
75I ASP* 3.1 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 72 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1371A G 6.2 0.2 - - - -
1372A U 2.8 13.9 + - - -
10I ARG* 4.0 25.7 - - - +
11I LYS* 5.4 3.1 - - - -
13I ALA* 4.2 8.5 - - - -
69I GLY 2.7 14.8 + - - -
71I SER* 1.3 72.0 - - - +
73I GLN* 1.3 60.7 + - - -
75I ASP* 2.9 14.7 + - - +
76I ALA* 2.9 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249A C 2.5 34.2 + - - -
13I ALA* 4.2 3.9 - - - +
36I TYR* 2.5 36.6 + - - -
37I PHE* 4.8 5.2 - - + -
65I VAL* 3.1 34.5 + - + +
67I GLY 3.6 26.4 + - - +
69I GLY 3.2 16.6 - - - +
70I LYS* 3.4 8.5 - - - +
72I GLY* 1.3 71.8 - - - +
74I ILE* 1.3 56.0 + - - +
75I ASP 2.7 12.1 + - - -
76I ALA* 2.8 16.5 + - - +
77I ILE* 2.9 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I PHE* 3.7 33.8 - - + -
40I LEU* 4.7 10.3 - - + -
42I ARG* 4.1 20.0 - - + +
43I ALA* 3.7 48.2 - - + +
45I ALA* 4.6 2.6 - - + +
46I ALA* 3.4 27.7 + - + +
70I LYS* 2.8 36.7 + - + +
71I SER* 3.1 15.7 + - - +
73I GLN* 1.3 75.2 - - - +
75I ASP* 1.3 56.0 + - - +
77I ILE* 4.3 2.5 - - - -
78I LYS* 3.7 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ARG* 3.4 36.7 + - + +
42I ARG* 3.4 25.0 + - - +
71I SER 3.1 8.0 + - - +
72I GLY* 2.9 10.0 + - - +
73I GLN 2.7 4.0 + - - -
74I ILE* 1.3 74.4 - - - +
76I ALA* 1.3 65.2 + - - +
77I ILE 3.2 1.1 - - - -
78I LYS* 3.2 27.1 + - - +
79I LEU* 3.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I THR 3.9 0.2 - - - +
8I GLY* 3.3 30.3 - - - +
9I ARG* 3.9 4.5 - - - +
10I ARG* 4.2 7.5 - - - +
13I ALA* 3.9 13.7 - - + +
15I ALA* 3.7 12.6 - - + +
72I GLY 2.9 10.9 + - - +
73I GLN* 2.8 10.9 + - - +
75I ASP* 1.3 72.9 - - - +
77I ILE* 1.3 59.2 + - - +
79I LEU* 2.7 27.2 + - - +
80I GLY* 2.8 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ALA* 3.8 7.0 - - + -
17I VAL* 4.0 2.2 - - - +
28I VAL* 4.7 4.9 - - + -
33I PHE* 4.7 5.4 - - + -
37I PHE* 3.8 33.4 - - + -
46I ALA* 3.6 13.5 - - + -
63I ILE* 3.7 23.1 - - + -
65I VAL* 3.3 35.2 - - + -
73I GLN 2.9 13.5 + - - +
74I ILE* 4.0 3.4 - - - +
76I ALA* 1.3 76.0 - - - +
78I LYS* 1.3 56.6 + - - +
80I GLY* 2.9 4.0 + - - +
81I ILE* 2.8 59.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G GLN* 5.2 7.3 + - - -
42I ARG* 6.1 0.7 - - - +
45I ALA* 4.1 15.3 - - - +
46I ALA* 3.1 37.7 - - - +
48I GLU* 5.3 1.8 - - - +
49I PRO* 3.4 11.6 - - + +
74I ILE 3.7 4.2 + - - +
75I ASP* 3.2 30.2 + - - +
76I ALA 3.2 0.2 - - - -
77I ILE* 1.3 80.4 - - - +
79I LEU* 1.3 60.8 + - - +
81I ILE* 3.7 0.8 + - - -
82I ALA* 3.1 23.2 + - - +
99I LEU 5.8 0.6 + - - -
101I PHE* 3.2 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I GLY* 3.1 25.8 - - - +
9I ARG 4.2 9.2 - - - +
75I ASP 3.0 9.2 + - - +
76I ALA* 2.7 23.1 + - - +
78I LYS* 1.3 69.9 - - - +
80I GLY* 1.3 58.1 + - - +
82I ALA* 2.9 6.2 + - - +
83I ARG* 2.7 63.9 + - + +
101I PHE 2.9 33.4 - - - +
102I LEU* 4.1 4.0 - - - -
103I THR 3.6 24.7 - - - +
104I ARG* 4.3 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLY* 3.8 4.0 - - - -
7I THR 2.7 29.1 + - - -
17I VAL* 3.2 13.7 - - - -
76I ALA 2.8 13.9 + - - -
77I ILE 2.9 0.8 + - - -
79I LEU* 1.3 75.6 - - - +
81I ILE* 1.3 54.9 + - - -
82I ALA 2.9 0.3 + - - -
83I ARG 2.9 1.1 + - - -
84I ALA* 2.5 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I VAL* 3.6 22.8 - - + +
19I LEU* 4.2 8.7 - - + +
46I ALA 3.6 13.2 - - - +
47I LEU* 3.7 22.2 - - + -
49I PRO* 3.4 21.5 - - + -
50I LEU* 3.5 29.4 - - + -
61I ALA* 5.8 2.5 - - + -
63I ILE* 4.0 6.3 - - + -
77I ILE* 2.8 43.8 + - + +
80I GLY* 1.3 71.8 - - - -
82I ALA* 1.3 56.9 + - - +
84I ALA* 4.3 1.8 - - - -
85I LEU* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I PRO* 3.9 5.4 - - + -
78I LYS 3.1 13.8 + - - +
79I LEU 2.9 10.6 + - - +
81I ILE* 1.3 76.9 - - - +
83I ARG* 1.3 65.2 + - - +
85I LEU* 3.3 5.5 + - - +
86I VAL* 3.2 23.7 + - - +
96I LEU* 3.8 15.5 - - + +
101I PHE* 3.8 30.5 - - + -
102I LEU* 3.6 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118A C 2.8 43.0 + - - -
1119A C 3.2 20.7 + - - -
1179A A 4.6 11.7 + - - -
5I TYR 4.0 2.2 - - - +
6I GLY* 3.8 9.4 - - - -
7I THR* 4.2 21.8 - - - +
8I GLY* 4.4 1.4 - - - +
9I ARG* 4.4 5.5 - - - +
79I LEU* 2.7 45.8 + - + +
80I GLY 3.6 4.9 - - - +
82I ALA* 1.3 69.8 - - - +
84I ALA* 1.3 56.7 - - - +
86I VAL* 2.7 26.4 + - - +
87I GLN* 2.9 11.3 + - - +
102I LEU* 3.6 21.1 - - + +
104I ARG* 5.6 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I TYR* 4.3 1.4 - - - +
5I TYR* 2.9 38.4 - - - +
6I GLY* 3.2 3.7 - - - +
17I VAL* 4.2 5.2 - - + +
19I LEU* 3.7 22.9 - - + -
80I GLY 2.5 23.2 + - - +
81I ILE* 4.3 1.8 - - - +
83I ARG* 1.3 70.8 - - - +
85I LEU* 1.3 55.3 + - - +
86I VAL 2.6 1.7 + - - -
87I GLN* 2.6 26.2 + - - +
88I TYR* 3.1 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU* 3.5 14.3 - - + +
49I PRO 3.5 20.0 - - - +
50I LEU* 3.7 23.3 - - + -
53I VAL* 3.3 27.4 - - + -
55I ALA* 4.2 11.0 - - + -
59I PHE* 4.4 11.2 - - + -
81I ILE 2.9 18.1 + - - +
82I ALA 3.3 7.2 - - - +
84I ALA* 1.3 76.9 - - - +
86I VAL* 1.3 57.6 + - - +
88I TYR* 4.1 5.8 - - - +
89I ASN 2.9 20.3 + - - +
92I TYR* 3.2 31.2 - - + -
96I LEU* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I ALA 3.2 15.0 + - - +
83I ARG* 2.7 12.8 + - - +
84I ALA 2.6 4.9 + - - -
85I LEU* 1.3 75.0 - - - +
87I GLN* 1.3 64.6 + - - +
88I TYR 3.1 1.3 - - - -
89I ASN 3.4 3.8 - - - +
90I PRO* 3.1 26.6 - - + +
92I TYR* 4.7 3.4 - - + -
93I ARG* 3.3 52.0 - - + +
96I LEU* 4.8 2.7 - - + -
102I LEU* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I TYR* 4.3 6.9 - - + -
5I TYR* 2.9 38.8 - - + +
83I ARG 2.9 6.5 + - - +
84I ALA 2.6 15.2 + - - +
86I VAL* 1.3 73.6 - - - +
88I TYR* 1.3 65.3 + - - +
90I PRO* 4.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I TYR* 3.0 62.5 - + + -
58I ARG* 3.5 17.6 + - - -
59I PHE* 3.1 35.7 - + + -
84I ALA 3.1 3.8 + - - +
85I LEU* 4.1 7.9 - - + +
86I VAL 3.1 0.2 - - - -
87I GLN* 1.3 86.0 - - - +
89I ASN* 1.3 73.5 + - + +
90I PRO* 3.3 8.5 - - - +
92I TYR* 4.0 25.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I LEU 2.9 18.2 + - - +
86I VAL* 3.2 3.9 - - - -
88I TYR* 1.3 100.9 - - + +
90I PRO* 1.3 59.4 - - - +
91I ASP* 2.6 44.7 - - - +
92I TYR* 3.1 50.7 - - + +
----------------------------------------------------------
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