Contacts of the helix formed by residues 52 - 72 (chain A) in PDB entry 2IAI
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A MSE 3.9 21.5 - - - -
50A VAL* 3.3 16.8 + - - +
51A THR* 1.3 82.2 + - - +
53A LYS* 1.3 65.3 + - - -
54A GLU 3.3 4.2 + - - -
55A GLU* 3.4 9.5 + - - +
56A LEU* 3.5 8.4 + - - +
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.6 15.3 - - + -
27A TYR* 2.9 53.3 + - + +
28A ASP* 3.1 17.2 + - - +
30A THR* 2.7 31.6 + - + +
31A SER* 5.2 2.5 - - - -
32A MSE 3.6 12.6 - - + +
35A LEU* 3.9 14.1 - - + -
52A GLY* 1.3 71.4 - - - -
54A GLU* 1.3 68.9 + - - +
56A LEU* 3.2 11.5 + - - +
57A LEU 2.9 18.4 + - - -
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.1 23.8 + - + +
52A GLY 3.3 1.2 - - - -
53A LYS* 1.3 78.0 - - - +
55A GLU* 1.3 58.7 + - - +
57A LEU* 3.2 3.3 + - + +
58A ARG* 2.8 28.1 + - - +
114A THR* 3.8 23.0 + - - +
115A GLY* 3.8 5.1 + - - -
116A THR* 2.6 42.9 + - + +
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.8 17.3 - - + -
51A THR* 4.0 18.9 + - + +
52A GLY 3.4 9.7 + - - +
53A LYS 3.2 0.4 - - - -
54A GLU* 1.3 79.3 - - - +
56A LEU* 1.3 56.8 + - - +
58A ARG* 2.8 38.4 + - - +
59A ARG* 2.8 67.9 + - - +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.2 26.0 - - + -
15A LEU* 3.5 33.1 - - + +
18A ALA* 3.9 13.0 - - + -
22A PHE* 4.1 13.0 - - + -
32A MSE 5.3 2.0 - - + -
35A LEU* 3.9 28.0 - - + -
46A ILE* 5.4 0.9 - - + -
50A VAL* 3.8 29.8 - - + -
52A GLY 3.5 14.0 + - - +
53A LYS* 3.2 7.9 + - - +
55A GLU* 1.3 72.7 - - - +
57A LEU* 1.3 66.3 + - - +
59A ARG* 3.2 7.3 + - - +
60A ALA* 3.0 19.4 + - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.8 15.6 - - + -
27A TYR* 3.6 51.1 - - + -
53A LYS 2.9 6.5 + - - -
54A GLU* 3.2 7.4 + - + +
56A LEU* 1.3 75.4 - - - +
58A ARG* 1.3 58.1 + - - +
60A ALA* 3.1 4.6 + - + +
61A VAL* 2.8 47.5 + - + +
106A LEU* 4.7 15.3 - - + +
110A VAL* 5.0 7.6 - - + -
114A THR* 5.0 0.9 - - - -
116A THR* 4.3 12.1 - - + -
117A GLU* 3.8 28.9 - - + +
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLU 2.8 14.2 + - - +
55A GLU* 2.8 47.3 + - - +
56A LEU 3.3 0.2 - - - -
57A LEU* 1.3 77.6 - - - +
59A ARG* 1.3 75.5 + - - +
61A VAL* 3.7 2.1 - - - +
62A SER* 2.9 46.9 + - - -
116A THR* 3.6 28.9 - - + +
119A TRP* 4.5 17.2 - - + -
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.1 22.8 - - + +
49A HIS* 3.0 29.5 + - - +
50A VAL* 3.5 19.2 - - - +
55A GLU* 2.8 42.1 + - - +
56A LEU* 3.2 13.8 + - - +
58A ARG* 1.3 91.9 - - - +
60A ALA* 1.3 61.7 + - - +
62A SER* 3.9 4.9 - - - -
63A ARG* 3.1 22.9 + - - +
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.1 2.4 - - + +
19A VAL* 3.7 28.7 - - + -
22A PHE* 5.6 0.4 - - + -
56A LEU 3.0 13.4 + - - +
57A LEU* 3.5 9.4 - - - +
59A ARG* 1.3 76.9 - - - +
61A VAL* 1.3 63.6 + - + +
63A ARG* 3.2 13.5 + - - +
64A ALA 3.3 9.2 + - - -
103A TYR* 3.6 23.5 - - + +
106A LEU* 4.1 15.5 - - + -
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 2.8 43.8 + - + +
58A ARG* 3.7 10.5 - - - +
60A ALA* 1.3 71.4 - - - +
62A SER* 1.3 62.5 + - - +
64A ALA* 3.3 7.2 + - - +
65A LEU* 2.9 34.1 + - - +
103A TYR 5.0 0.4 - - - +
106A LEU* 4.4 3.6 - - + -
107A LEU* 4.0 36.6 - - + +
110A VAL* 4.2 10.8 - - + -
116A THR* 4.3 7.4 - - + -
119A TRP* 4.3 8.7 - - + -
120A ALA* 4.0 18.4 - - + -
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Residues in contact with SER 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 2.9 33.0 + - - -
59A ARG* 3.9 5.4 - - - -
61A VAL* 1.3 77.7 - - - +
63A ARG* 1.3 55.3 + - - +
65A LEU* 3.9 2.2 - - - -
66A ASP* 2.8 49.1 + - - +
119A TRP* 4.1 24.1 - - - -
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 5.5 4.5 - - + -
59A ARG 3.1 14.6 + - - +
60A ALA 3.2 8.9 + - - +
62A SER* 1.3 75.4 - - - +
64A ALA* 1.3 62.3 + - - +
66A ASP* 3.9 6.3 - - - +
67A GLU* 3.2 30.9 + - + +
100A GLU* 2.8 41.0 + - - +
103A TYR* 3.7 35.0 - - + -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA 3.3 3.6 + - - +
61A VAL 3.3 7.4 + - - +
63A ARG* 1.3 75.3 - - - +
65A LEU* 1.3 65.7 + - - +
67A GLU* 3.2 6.4 + - - +
68A LEU* 3.1 28.8 + - - +
96A VAL* 5.0 0.7 - - - +
100A GLU* 5.3 2.5 - - - -
103A TYR* 3.6 38.1 - - + +
104A VAL* 3.9 16.6 - - + +
107A LEU* 4.1 13.5 - - + -
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL 2.9 25.0 + - - +
62A SER* 3.9 3.6 - - - +
64A ALA* 1.3 75.9 - - - +
66A ASP* 1.3 60.5 + - - +
68A LEU* 4.5 6.5 - - + +
69A PHE* 2.9 49.6 + - + +
107A LEU* 3.7 29.8 - - + -
119A TRP* 4.1 16.6 - - + -
120A ALA* 4.1 18.2 - - + -
123A ARG* 3.8 34.8 - - + +
124A ARG* 4.2 12.3 - - + +
127A PHE* 5.8 1.1 - - + -
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A SER* 2.8 34.0 + - - +
63A ARG* 3.9 5.9 - - - +
64A ALA 3.3 0.2 - - - -
65A LEU* 1.3 80.5 - - - +
67A GLU* 1.3 62.3 + - - +
69A PHE* 4.3 3.3 - - - +
70A GLY* 2.9 27.0 + - - -
119A TRP* 6.1 0.7 - - - -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ARG* 3.2 20.5 + - + +
64A ALA 3.7 7.2 - - - +
65A LEU 3.2 0.6 - - - -
66A ASP* 1.3 83.1 - - - +
68A LEU* 1.3 62.7 + - - +
70A GLY* 3.4 2.1 + - - -
71A ILE* 3.4 21.1 + - - +
92A ARG* 5.2 5.7 + - - -
96A VAL* 3.8 29.8 - - + +
100A GLU* 4.0 29.1 - - + +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ALA 3.1 20.3 + - - +
65A LEU* 3.8 7.9 - - + +
67A GLU* 1.3 73.2 - - - +
69A PHE* 1.3 66.4 + - + +
71A ILE* 3.1 33.8 + - + +
72A LEU 3.9 0.3 + - - -
93A MSE 4.5 16.2 - - + +
96A VAL* 4.1 20.6 - - + -
97A LEU* 5.7 0.9 - - + +
104A VAL* 4.9 15.0 - - + -
107A LEU* 3.9 25.6 - - + -
108A LEU* 6.4 0.9 - - + -
124A ARG* 6.0 0.9 - - + -
127A PHE* 3.3 41.0 - - + -
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 2.9 40.8 + - + +
66A ASP* 4.3 2.9 - - - +
68A LEU* 1.3 74.1 - - + +
70A GLY* 1.3 64.5 + - - +
72A LEU* 3.0 29.8 + - + +
73A ASP* 4.0 7.4 + - - +
123A ARG* 3.2 70.0 - - - +
126A GLU* 4.0 16.8 - - + -
127A PHE* 3.6 30.1 - + + -
130A ARG* 4.4 18.1 + - - -
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP 2.9 21.6 + - - -
67A GLU* 3.8 2.9 - - - -
68A LEU 3.1 0.8 - - - -
69A PHE* 1.3 76.0 - - - +
71A ILE* 1.3 65.4 + - - +
72A LEU 3.2 0.7 + - - -
73A ASP* 3.4 12.4 + - - +
74A GLU* 3.4 18.8 + - - +
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Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLU 3.4 10.3 + - - +
68A LEU* 3.1 21.9 + - + +
70A GLY* 1.3 76.7 - - - +
72A LEU* 1.3 63.1 + - + +
74A GLU* 3.1 25.1 + - - +
77A ALA* 3.2 9.5 - - - +
88A TYR* 4.6 1.6 - - + -
89A VAL* 4.0 27.6 - - + +
92A ARG* 3.6 57.9 - - + +
93A MSE 3.7 19.1 - - + +
96A VAL* 3.9 14.8 - - + -
127A PHE* 5.1 0.9 - - + -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.0 15.5 + - + +
71A ILE* 1.3 78.7 - - + +
73A ASP* 1.3 59.9 + - - +
74A GLU 3.5 0.2 - - - -
77A ALA* 3.6 10.7 - - - +
78A ARG* 3.3 21.3 - - - +
89A VAL* 4.0 29.6 - - + -
127A PHE* 3.8 37.9 - - + -
130A ARG* 3.7 60.0 + - + +
131A VAL* 4.2 7.6 - - + -
134A LEU* 4.7 7.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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