Contacts of the helix formed by residues 54 - 77 (chain I) in PDB entry 2I2X
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 SER 54 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I ALA 3.3 6.6 + - - +
52I GLY 4.3 1.2 - - - -
53I ALA* 1.3 79.5 - - - +
55I LYS* 1.3 64.5 + - - +
56I GLU* 3.5 15.9 + - - +
57I LYS* 3.3 29.6 + - - +
58I LEU* 3.2 17.2 + - - +
97I TRP* 4.5 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I SER* 1.3 74.1 - - - +
56I GLU* 1.3 84.9 + - - +
58I LEU* 3.2 7.3 + - + +
59I ILE* 3.0 39.3 + - + +
97I TRP* 3.6 71.6 - - + +
100I GLU* 2.6 43.9 + - - +
101I VAL* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I SER* 3.2 15.2 + - - +
55I LYS* 1.3 106.8 + - - +
57I LYS* 1.3 58.5 + - + +
59I ILE* 3.4 12.1 + - + +
60I LYS* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLU* 3.9 17.2 + - + +
51I ALA* 3.5 19.9 - - - +
53I ALA* 4.0 20.2 - - + +
54I SER* 3.3 17.2 + - - +
56I GLU* 1.3 77.0 - - + +
58I LEU* 1.3 58.4 + - - +
60I LYS* 3.4 7.9 + - - +
61I GLU* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I PRO* 4.2 24.7 - - + -
51I ALA* 3.2 27.3 + - + +
52I GLY* 3.8 8.3 - - - +
54I SER 3.2 8.1 + - - +
55I LYS* 3.2 10.5 + - + +
57I LYS* 1.3 73.2 - - - +
59I ILE* 1.3 66.0 + - - +
61I GLU* 3.4 2.9 + - - +
62I TYR* 3.0 41.7 + - + -
88I VAL* 4.1 12.8 - - + -
90I GLN* 4.3 6.5 - - - +
91I MET* 3.8 28.5 - - + -
97I TRP* 4.2 21.3 - - + -
101I VAL* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I LYS* 3.0 34.0 + - + +
56I GLU* 3.7 9.6 - - + +
57I LYS 3.3 0.2 - - - -
58I LEU* 1.3 75.5 - - - +
60I LYS* 1.3 53.0 + - - +
62I TYR* 3.3 3.5 + - - +
63I GLU* 2.8 59.0 + - - +
100I GLU* 3.7 33.4 - - + +
101I VAL* 4.0 28.3 - - + +
104I ALA* 3.9 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I GLU 3.1 14.0 + - - +
57I LYS* 3.4 13.0 - - - +
59I ILE* 1.3 76.4 - - - +
61I GLU* 1.3 63.5 + - - +
63I GLU* 3.0 24.4 + - + +
64I ARG* 2.9 41.5 + - - +
257L LYS* 3.3 43.5 + - - +
258L HIS* 3.2 38.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I PRO* 3.8 23.9 - - + +
48I ARG* 2.8 61.3 + - - +
51I ALA* 3.7 18.1 - - + +
57I LYS 3.0 17.1 + - - +
58I LEU* 3.7 5.2 - - - +
60I LYS* 1.3 76.6 - - - +
62I TYR* 1.3 57.9 + - + +
64I ARG* 3.3 11.1 + - - +
65I ILE* 3.0 39.3 + - + +
317I TYR* 3.5 12.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I TYR* 3.7 32.8 + + - -
47I PRO* 3.4 29.8 - - + +
58I LEU* 3.0 37.7 + - + +
59I ILE* 3.8 4.3 - - - +
61I GLU* 1.3 72.8 - - + +
63I GLU* 1.3 58.2 + - - +
65I ILE* 3.6 17.4 - - + +
66I THR* 2.7 39.1 + - - -
85I THR* 3.7 17.5 - - + +
86I GLU 3.9 10.3 + - - -
88I VAL* 4.4 1.7 - - - +
91I MET* 3.6 32.3 - - + -
101I VAL* 3.6 30.7 - - + -
104I ALA* 6.2 0.7 - - + -
105I GLN* 4.3 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ILE* 2.8 35.6 + - - +
60I LYS* 3.0 28.7 + - + +
62I TYR* 1.3 69.8 - - - +
64I ARG* 1.3 65.3 + - + +
66I THR* 3.3 1.4 + - - -
67I THR* 2.9 30.3 + - - -
104I ALA* 3.6 28.8 - - + +
105I GLN* 5.8 0.7 - - - -
108I ILE* 3.7 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I ARG* 4.1 14.2 - - - +
60I LYS* 2.9 38.3 + - + +
61I GLU* 3.5 15.0 + - - +
63I GLU* 1.3 75.6 - - + +
65I ILE* 1.3 65.8 + - - +
67I THR* 3.6 3.9 - - - -
68I ASP* 2.8 29.3 + - - +
317I TYR* 3.3 30.5 - - + +
215L ASN* 5.8 2.0 - - - +
216L GLN* 3.9 20.4 - - - +
217L ASP* 4.2 17.0 + - - -
257L LYS* 5.0 3.8 - - - +
258L HIS* 2.8 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I TYR* 3.5 52.0 - - + -
46I ALA 4.9 3.8 - - - +
47I PRO* 5.0 1.6 - - + -
61I GLU* 3.0 29.3 + - + +
62I TYR* 3.6 28.3 - - + +
64I ARG* 1.3 78.4 - - - +
66I THR* 1.3 66.9 + - - +
68I ASP* 3.2 2.1 + - - +
69I VAL* 3.1 25.0 + - + +
317I TYR* 3.7 41.5 - - + -
326I VAL* 4.1 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I TYR 2.7 25.5 + - - -
63I GLU 3.8 2.9 - - - -
65I ILE* 1.3 71.0 - - - +
67I THR* 1.3 63.8 + - - +
69I VAL* 3.3 3.5 + - - +
70I MET* 3.0 25.3 + - + +
83I LEU* 3.9 14.4 - - + -
105I GLN* 3.2 46.4 + - - +
108I ILE* 3.9 20.0 - - + -
109I MET* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I GLU 2.9 21.1 + - - -
64I ARG* 3.7 4.7 - - - -
66I THR* 1.3 72.3 - - - +
68I ASP* 1.3 71.9 + - - +
70I MET* 3.5 1.7 + - - +
71I GLU* 3.0 30.0 + - + +
108I ILE* 3.3 28.2 - - - +
112I TYR* 4.0 15.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I ARG* 2.8 22.3 + - - +
65I ILE 3.8 3.4 - - - +
67I THR* 1.3 80.0 - - - +
69I VAL* 1.3 60.5 + - - +
71I GLU* 3.7 2.3 - - - +
72I ARG* 3.1 13.5 + - - +
317I TYR* 2.6 25.4 + - - -
324I THR* 3.5 19.7 + - + +
326I VAL* 4.2 1.3 - - + -
327I GLN* 3.1 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I ILE* 3.8 19.3 - - + -
65I ILE* 3.1 20.6 + - + +
66I THR 3.7 6.5 - - - +
67I THR 3.3 0.2 - - - -
68I ASP* 1.3 72.4 - - - +
70I MET* 1.3 70.4 + - - +
72I ARG* 3.1 7.4 + - - +
73I MET* 3.0 24.2 + - + +
81I ILE* 3.7 32.3 - - + -
83I LEU* 4.3 14.1 - - + -
326I VAL* 3.7 32.3 - - + +
327I GLN* 5.0 1.1 - - - -
330I SER* 4.4 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I THR* 3.0 29.9 + - + +
69I VAL* 1.3 76.8 - - - +
71I GLU* 1.3 62.5 - - - +
73I MET* 3.3 6.4 + - - +
74I VAL* 3.2 27.7 + - - +
81I ILE* 3.8 26.0 - - + -
83I LEU* 3.9 17.3 - - - -
108I ILE* 4.5 1.6 - - + -
109I MET* 4.2 11.7 - - + -
112I TYR* 3.5 40.6 - - + -
118I ILE* 3.8 26.2 - - + +
120I CYS* 3.8 26.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I THR* 3.0 21.7 + - + +
68I ASP* 3.7 6.7 - - - +
70I MET* 1.3 77.4 - - - +
72I ARG* 1.3 62.7 + - - +
74I VAL* 3.3 8.5 - - - +
75I GLN* 3.1 56.0 + - + +
112I TYR* 2.6 36.3 + - - +
116I TYR* 4.9 4.8 + - - -
327I GLN* 4.9 5.8 - - - +
234K LEU* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I ASP 3.1 13.8 + - - +
69I VAL 3.1 9.4 + - - +
71I GLU* 1.3 75.0 - - - +
73I MET* 1.3 65.5 + - - +
75I GLN* 3.3 16.1 + - - -
76I VAL* 3.3 20.1 + - + +
78I PHE* 4.6 0.8 - - + -
322I GLY 2.9 28.5 + - - -
323I GLY* 5.0 0.2 - - - -
327I GLN* 3.6 66.4 + - + +
328I CYS* 4.6 2.0 - - - +
330I SER* 4.4 7.0 - - - +
331I GLU* 2.9 30.2 + - + +
292K THR* 4.7 5.3 + - - -
295K HIS 4.7 0.2 - - - -
296K SER* 3.5 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I PRO* 3.7 2.7 - - + -
69I VAL* 3.0 16.8 + - + +
70I MET* 3.6 6.1 - - - +
72I ARG* 1.3 78.1 - - - +
74I VAL* 1.3 57.0 + - - +
76I VAL 3.5 0.2 + - - -
77I GLY 3.1 6.9 + - - -
78I PHE* 3.1 52.8 + - + +
80I ALA 3.5 23.6 - - - +
81I ILE* 3.5 35.4 - - + -
118I ILE* 3.5 20.2 - - + -
330I SER* 4.2 20.9 - - - +
331I GLU 5.0 0.4 - - - -
334I ALA* 3.3 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I MET 3.2 12.7 + - - +
71I GLU* 3.3 20.9 - - - +
73I MET* 1.3 76.2 - - - +
75I GLN* 1.3 64.1 + - + +
76I VAL 3.4 0.5 + - - -
77I GLY 3.7 0.9 + - - -
112I TYR* 4.2 7.4 - - + -
116I TYR* 3.8 40.6 - - + +
118I ILE* 4.3 14.6 - - + -
233K LEU* 4.1 5.4 - - - +
234K LEU* 3.5 27.0 - - + +
16L TYR* 3.2 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I GLU* 3.1 47.8 + - + +
72I ARG* 3.3 12.1 + - - +
74I VAL* 1.3 78.6 - - + +
76I VAL* 1.3 62.3 + - + +
232K GLY* 3.1 24.5 - - - -
233K LEU* 2.8 30.6 + - - +
234K LEU* 3.0 42.0 + - - +
235K ASN* 3.2 17.6 + - - +
296K SER* 5.9 0.2 - - - +
298K VAL* 5.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ARG* 3.3 19.9 + - - +
74I VAL 3.2 0.2 - - - -
75I GLN* 1.3 82.0 - - + +
77I GLY* 1.3 60.0 + - - +
78I PHE* 3.4 28.3 - - + -
331I GLU* 3.6 10.1 - - - +
335I TYR* 3.4 28.3 - - + +
232K GLY* 6.0 0.7 - - - -
233K LEU* 3.7 6.3 - - - -
296K SER* 3.6 23.1 - - - +
297K ASP 3.7 9.0 - - - +
298K VAL* 4.6 6.3 - - + -
363K ARG* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I MET 3.1 4.6 + - - -
74I VAL 3.7 1.0 + - - -
75I GLN 3.6 0.2 - - - -
76I VAL* 1.3 80.4 - - - +
78I PHE* 1.3 63.9 + - - +
233K LEU* 3.5 10.2 - - - +
363K ARG* 3.9 4.9 - - - -
13L LEU* 3.4 9.7 - - - +
14L THR 2.9 46.7 + - - -
16L TYR* 3.7 7.6 - - - -
----------------------------------------------------------
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