Contacts of the helix formed by residues 54 - 77 (chain M) 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 M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M ALA 3.5 6.4 - - - +
52M GLY 4.4 1.2 - - - -
53M ALA* 1.3 79.4 + - - +
55M LYS* 1.3 63.0 + - - +
56M GLU* 3.5 18.4 + - - +
57M LYS* 3.2 32.5 + - - +
58M LEU* 3.4 17.2 + - - +
97M TRP* 4.4 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M SER* 1.3 75.2 - - - +
56M GLU* 1.3 76.8 + - - +
58M LEU* 3.3 5.4 + - + +
59M ILE* 2.9 42.0 + - + +
96M SER* 5.3 1.4 + - - -
97M TRP* 3.6 67.8 - - + +
100M GLU* 2.9 41.4 + - - +
101M VAL* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M SER* 3.2 18.8 - - - +
55M LYS* 1.3 97.8 + - - +
57M LYS* 1.3 60.7 + - + +
59M ILE* 3.9 9.6 - - + +
60M LYS* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M GLU 4.0 8.0 + - - +
51M ALA* 3.6 21.1 - - - +
53M ALA* 4.0 23.8 - - + +
54M SER* 3.2 19.3 + - - +
55M LYS 3.3 0.2 - - - -
56M GLU* 1.3 80.4 - - + +
58M LEU* 1.3 57.0 + - - +
60M LYS* 3.7 6.7 - - - +
61M GLU* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M PRO* 4.3 18.6 - - + -
51M ALA* 3.1 32.9 + - + +
52M GLY* 3.8 9.9 - - - -
54M SER 3.4 5.6 + - - +
55M LYS* 3.3 8.5 + - + +
56M GLU 3.2 0.2 - - - -
57M LYS* 1.3 76.2 - - - +
59M ILE* 1.3 66.6 + - - +
61M GLU* 3.3 3.0 + - - +
62M TYR* 3.0 38.6 + - + -
88M VAL* 4.1 18.4 - - + -
90M GLN* 4.3 4.3 - - + +
91M MET* 3.8 28.9 - - + -
97M TRP* 4.2 22.4 - - + -
101M VAL* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M LYS* 2.9 36.3 + - + +
56M GLU* 3.9 9.2 - - + +
58M LEU* 1.3 72.6 - - - +
60M LYS* 1.3 59.6 + - - +
62M TYR* 3.1 5.6 + - - +
63M GLU* 2.9 41.1 + - - +
100M GLU* 3.6 31.2 - - + +
101M VAL* 4.0 27.6 - - + +
104M ALA* 3.9 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M GLU 3.0 18.8 + - - +
57M LYS* 3.7 9.0 - - - +
59M ILE* 1.3 76.9 - - - +
61M GLU* 1.3 61.6 + - - +
63M GLU* 3.1 27.8 + - - +
64M ARG* 3.0 44.8 + - - +
257P LYS* 4.5 25.6 + - - +
258P HIS 3.2 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M PRO* 3.8 22.8 - - + +
48M ARG* 2.4 65.8 + - - +
51M ALA* 3.7 16.3 - - + +
57M LYS 3.1 15.7 + - - +
58M LEU 3.3 5.4 + - - +
60M LYS* 1.3 76.5 - - - +
62M TYR* 1.3 57.2 + - - +
64M ARG* 3.1 14.1 + - - +
65M ILE* 2.9 38.3 + - + +
317M TYR* 3.7 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M TYR* 3.6 37.5 + + - -
47M PRO* 3.2 34.1 - - + +
58M LEU* 3.0 35.2 + - + -
59M ILE 3.6 6.7 - - - +
61M GLU* 1.3 76.5 - - + +
63M GLU* 1.3 54.3 + - + +
65M ILE* 3.7 9.5 + - + +
66M THR* 2.6 36.7 + - - -
85M THR* 3.6 16.4 - - + -
86M GLU 3.8 13.3 + - - -
88M VAL* 4.4 1.7 - - - +
91M MET* 3.7 29.8 - - + -
101M VAL* 3.5 31.4 - - + -
104M ALA* 6.4 0.7 - - + -
105M GLN* 4.3 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M ILE* 2.9 25.5 + - - +
60M LYS* 3.1 34.9 + - + +
62M TYR* 1.3 75.9 - - - +
64M ARG* 1.3 64.4 + - - +
66M THR* 3.4 0.6 + - - -
67M THR* 2.8 30.6 + - - -
104M ALA* 3.5 30.0 - - + +
105M GLN* 5.8 0.9 - - - -
108M ILE* 3.7 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M ARG* 4.5 11.5 - - - +
60M LYS* 3.0 41.5 + - - +
61M GLU* 3.4 15.4 + - - +
63M GLU* 1.3 76.3 - - - +
65M ILE* 1.3 65.1 + - - +
67M THR* 3.7 3.8 - - - -
68M ASP* 2.8 29.9 + - - +
317M TYR* 3.5 31.9 - - + +
216P GLN* 5.6 5.7 + - - +
217P ASP* 4.4 17.0 + - - -
257P LYS* 4.3 12.9 - - - +
258P HIS* 2.7 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M TYR* 3.6 57.7 - - + -
47M PRO 4.6 5.6 - - - -
61M GLU* 2.9 29.7 + - + +
62M TYR* 3.8 18.8 - - + +
64M ARG* 1.3 79.6 - - - +
66M THR* 1.3 64.8 + - - +
68M ASP* 3.4 2.6 + - - +
69M VAL* 3.2 27.0 + - + +
105M GLN* 5.5 0.2 - - - +
317M TYR* 3.6 43.7 - - + -
326M VAL* 4.0 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M TYR 2.6 23.6 + - - -
63M GLU 3.9 3.8 - - - -
64M ARG 3.3 0.2 - - - -
65M ILE* 1.3 76.5 - - - +
67M THR* 1.3 61.3 + - - +
69M VAL* 3.4 2.6 + - - +
70M MET* 3.1 31.6 + - + +
83M LEU* 3.8 19.0 - - + +
105M GLN* 3.2 47.6 + - - +
108M ILE* 4.1 12.8 - - + -
109M MET* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M GLU* 2.8 22.1 + - - +
64M ARG* 3.7 4.7 - - - -
66M THR* 1.3 73.4 - - - +
68M ASP* 1.3 70.2 + - - +
71M GLU* 3.0 31.1 + - + +
108M ILE* 3.6 23.1 - - - +
112M TYR* 3.8 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M ARG* 2.8 23.3 + - - +
65M ILE 3.6 4.5 - - - +
67M THR* 1.3 78.0 - - - +
69M VAL* 1.3 61.3 + - - +
71M GLU* 3.9 1.5 - - - +
72M ARG* 3.2 11.8 + - - +
317M TYR* 2.5 27.7 + - - -
324M THR* 3.0 23.3 + - + -
326M VAL* 4.1 2.0 - - + -
327M GLN* 2.9 46.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M ILE* 3.8 20.6 - - + -
65M ILE* 3.2 19.1 + - + +
66M THR 3.7 5.4 - - - +
68M ASP* 1.3 71.4 - - - +
70M MET* 1.3 68.8 + - - +
72M ARG* 3.0 6.5 + - - +
73M MET* 2.9 33.9 + - + +
81M ILE* 3.4 33.4 - - + -
83M LEU* 4.1 15.5 - - + -
326M VAL* 3.8 23.1 - - + +
327M GLN* 5.0 0.9 - - - -
330M SER* 4.4 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M THR* 3.1 27.2 + - + +
69M VAL* 1.3 78.6 - - - +
71M GLU* 1.3 63.2 + - - +
73M MET* 3.4 4.3 + - - +
74M VAL* 3.2 27.4 + - - +
81M ILE* 3.9 10.8 - - + -
83M LEU* 3.9 26.5 - - - -
108M ILE* 4.6 1.3 - - + -
109M MET* 4.4 11.7 - - + +
112M TYR* 3.5 40.8 - - + -
118M ILE* 3.7 39.5 - - + -
120M CYS* 4.2 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M THR* 3.0 22.1 + - + +
68M ASP* 3.9 4.5 - - - +
70M MET* 1.3 78.7 - - - +
72M ARG* 1.3 63.7 + - - +
74M VAL* 3.2 8.9 - - - +
75M GLN* 3.1 54.7 + - + +
112M TYR* 2.6 36.9 + - - +
116M TYR* 5.0 3.5 + - - -
327M GLN* 4.8 5.6 - - - +
234O LEU* 4.7 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M ASP 3.2 15.3 + - - +
69M VAL* 3.0 5.2 + - - +
71M GLU* 1.3 80.7 - - - +
73M MET* 1.3 65.8 + - - +
75M GLN* 3.1 17.5 + - - +
76M VAL* 3.2 19.6 + - + +
78M PHE* 5.8 0.2 - - + -
322M GLY 3.4 26.7 + - - -
323M GLY* 4.9 0.2 - - - -
327M GLN* 3.7 61.5 + - + +
328M CYS* 4.2 3.6 - - - +
330M SER* 4.6 4.0 - - - +
331M GLU* 2.7 35.3 + - + +
292O THR* 4.2 10.9 + - - -
296O SER* 3.5 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M PRO* 3.9 2.5 - - + -
69M VAL* 2.9 24.9 + - + +
70M MET 3.6 3.1 - - - +
71M GLU 3.2 0.2 - - - -
72M ARG* 1.3 77.3 - - - +
74M VAL* 1.3 57.2 + - - +
76M VAL 3.5 0.2 + - - -
77M GLY 3.0 8.3 + - - -
78M PHE* 3.0 67.6 + - + -
80M ALA 3.4 21.5 - - - +
81M ILE* 3.6 30.5 - - + -
118M ILE* 3.6 18.4 - - + -
330M SER* 4.2 20.2 - - - +
331M GLU* 5.0 0.7 - - - -
334M ALA* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M MET 3.2 12.5 + - - +
71M GLU* 3.2 22.4 - - - +
73M MET* 1.3 75.5 - - - +
75M GLN* 1.3 61.7 + - - +
76M VAL 3.3 0.6 + - - -
77M GLY* 3.6 2.3 + - - -
112M TYR* 4.2 3.4 - - + -
116M TYR* 3.6 45.8 - - + +
118M ILE* 4.3 15.5 - - + -
233O LEU* 4.1 6.4 - - - +
234O LEU* 3.9 22.7 - - + +
16P TYR* 3.3 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M GLU* 3.1 47.1 + - + +
72M ARG* 3.1 12.3 + - - +
74M VAL* 1.3 77.2 - - - +
76M VAL* 1.3 62.0 + - + +
77M GLY 3.5 0.2 - - - -
232O GLY* 3.1 23.4 - - - -
233O LEU* 2.7 29.8 + - - +
234O LEU* 2.9 44.8 + - + +
235O ASN* 3.3 17.9 + - - +
298O VAL* 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72M ARG* 3.2 19.0 + - - +
75M GLN* 1.3 82.8 - - + +
77M GLY* 1.3 59.0 + - - +
78M PHE* 3.5 29.2 - - + -
331M GLU* 3.7 10.5 - - - +
335M TYR* 3.3 28.3 - - + +
232O GLY* 6.0 0.9 - - - -
233O LEU* 3.5 8.5 - - - +
296O SER* 3.4 25.1 - - - +
297O ASP 3.6 9.6 - - - +
298O VAL* 4.5 6.2 - - + +
363O ARG* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73M MET 3.0 3.4 + - - -
74M VAL 3.6 0.4 + - - -
75M GLN 3.5 0.6 - - - -
76M VAL* 1.3 81.2 - - - +
78M PHE* 1.3 62.7 + - - +
233O LEU* 3.5 9.8 - - - +
363O ARG* 3.7 4.4 + - - -
13P LEU* 3.5 11.8 - - - +
14P THR 3.0 43.4 + - - -
16P TYR* 3.7 10.5 - - - -
----------------------------------------------------------
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