Contacts of the helix formed by residues 46 - 65 (chain A) in PDB entry 2B33
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 THR 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLY* 1.3 77.0 - - - -
47A ILE* 1.3 64.6 + - - +
48A GLU* 3.5 18.9 + - - +
49A GLU* 3.3 37.5 + - - +
50A LYS* 3.1 23.5 + - - +
87A ARG* 6.0 1.3 - - - -
80B THR* 5.8 9.0 - - + +
109B ALA 4.5 15.3 - - - +
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Residues in contact with ILE 47 (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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45A GLY 4.1 0.2 + - - -
46A THR* 1.3 71.6 - - - +
48A GLU* 1.3 68.9 + - - +
50A LYS* 3.5 10.9 + - + +
51A THR* 2.7 38.7 + - - -
79A THR* 6.2 0.2 - - + -
84A TYR* 3.8 44.9 - - + -
87A ARG* 3.8 45.8 - - + +
88A VAL* 4.0 9.4 - - + -
116A GLU* 4.3 13.2 - - + +
117A ILE* 4.2 27.1 - - + -
116B GLU* 5.6 0.2 - - - +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 3.2 21.4 - - - +
47A ILE* 1.3 85.1 - - - +
49A GLU* 1.3 57.1 + - + +
51A THR* 3.4 2.5 + - - -
52A GLU* 2.9 30.2 + - - +
87A ARG* 3.4 42.4 + - + +
90A GLU* 4.1 12.4 - - - +
91A VAL* 3.5 31.5 - - + +
94A ARG* 5.6 2.2 - - - +
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Residues in contact with GLU 49 (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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43A VAL* 4.0 16.3 - - + +
44A GLN 4.6 0.5 - - - +
45A GLY* 3.6 10.0 - - - -
46A THR* 3.3 37.3 + - - +
48A GLU* 1.3 79.4 - - + +
50A LYS* 1.3 60.7 + - - +
52A GLU* 3.6 17.7 - - - +
53A ARG* 3.3 21.5 + - - +
129A EDO 4.4 16.9 + - - -
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Residues in contact with LYS 50 (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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34A PRO* 3.6 25.6 - - + +
43A VAL* 3.5 31.0 - - + +
44A GLN* 4.2 0.2 - - - +
45A GLY 3.5 14.7 + - - +
46A THR 3.1 11.3 + - - +
47A ILE* 3.9 15.1 - - + +
48A GLU 3.3 0.2 - - - -
49A GLU* 1.3 74.1 - - - +
51A THR* 1.3 59.2 + - - +
53A ARG* 3.3 1.4 + - - -
54A VAL* 3.1 30.8 + - - +
116A GLU* 2.8 32.8 + - + +
117A ILE* 3.8 14.6 - - + -
114B ASN* 2.8 34.7 + - - +
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Residues in contact with THR 51 (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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47A ILE* 2.7 24.1 + - - +
48A GLU 3.7 3.8 - - - -
50A LYS* 1.3 73.4 - - - +
52A GLU* 1.3 60.4 + - - +
54A VAL* 3.4 6.5 + - - +
55A LEU* 2.9 50.9 + - + +
88A VAL* 3.6 41.6 - - + +
91A VAL* 3.9 18.8 - - + -
92A TYR* 5.1 0.4 - - + -
117A ILE* 4.3 7.3 - - + +
119A ILE* 4.6 7.0 - - + -
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Residues in contact with GLU 52 (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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48A GLU 2.9 18.2 + - - +
49A GLU* 3.6 18.9 - - - +
51A THR* 1.3 76.7 - - - +
53A ARG* 1.3 56.4 + - - +
55A LEU* 3.8 1.4 - - - -
56A GLU* 2.8 41.8 + - + +
91A VAL* 3.9 12.1 - - + +
95A TYR* 3.8 9.5 + - - +
130A EDO 2.7 35.0 + - - +
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Residues in contact with ARG 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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9A LYS 4.5 4.2 + - - -
34A PRO* 3.8 2.0 - - + -
35A ILE 3.5 31.8 + - - +
36A ASP* 3.9 16.0 + - - +
37A PRO* 3.6 21.0 - - - +
43A VAL* 3.6 29.6 - - + -
49A GLU 3.3 10.3 + - - +
50A LYS 3.6 8.5 - - - +
51A THR 3.3 0.2 - - - -
52A GLU* 1.3 78.1 - - - +
54A VAL* 1.3 59.0 + - - +
56A GLU* 3.2 30.1 + - - +
57A ASN* 2.9 58.6 + - - +
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Residues in contact with VAL 54 (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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32A GLN* 3.3 23.9 - - + +
33A ILE 3.6 10.5 - - - -
34A PRO* 3.5 30.1 - - + -
50A LYS 3.1 18.6 + - - +
51A THR* 3.7 9.0 - - - +
53A ARG* 1.3 76.3 - - - +
55A LEU* 1.3 57.9 + - + +
57A ASN* 3.3 5.1 + - - +
58A LEU* 2.9 26.6 + - + +
117A ILE* 3.9 14.6 - - + +
119A ILE* 3.6 36.6 - - + +
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Residues in contact with LEU 55 (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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51A THR* 2.9 39.0 + - + +
52A GLU 4.0 0.2 - - - +
54A VAL* 1.3 74.2 - - - +
56A GLU* 1.3 59.5 + - - +
58A LEU* 3.7 15.4 - - + +
59A LYS* 2.9 29.8 + - - +
69A LEU* 5.1 1.1 - - + +
91A VAL* 4.1 1.8 - - + +
92A TYR* 3.8 25.6 - - + +
95A TYR* 3.7 43.7 - - + -
96A PHE* 3.8 26.2 - - + -
119A ILE* 3.9 20.6 - - + -
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Residues in contact with GLU 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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52A GLU* 2.8 30.6 + - + +
53A ARG* 3.3 28.2 + - - +
55A LEU* 1.3 73.2 - - - +
57A ASN* 1.3 60.5 + - - +
59A LYS* 3.5 18.1 + - - +
60A ALA* 3.0 30.1 + - - +
95A TYR* 2.8 29.4 + - - +
130A EDO 5.1 0.7 + - - -
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Residues in contact with ASN 57 (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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10A ALA* 3.7 4.6 - - - +
11A PRO* 3.4 24.5 - - + +
32A GLN* 3.4 18.0 + - + +
33A ILE 3.1 22.4 + - - -
35A ILE 3.0 21.6 + - - +
37A PRO* 3.6 7.1 - - - +
53A ARG* 2.9 39.2 + - - +
54A VAL* 3.5 5.1 - - - +
56A GLU* 1.3 76.1 - - - +
58A LEU* 1.3 63.6 + - - +
60A ALA* 3.4 4.4 + - - +
61A ILE* 3.1 30.5 + - - +
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Residues in contact with LEU 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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29A VAL* 3.6 36.1 - - + -
32A GLN* 3.9 12.2 - - + +
54A VAL* 2.9 17.8 + - + +
55A LEU* 3.7 19.1 - - + +
56A GLU 3.4 0.2 - - - -
57A ASN* 1.3 75.9 - - - +
59A LYS* 1.3 57.4 + - - +
61A ILE* 3.3 4.7 + - - +
62A LEU* 3.1 44.3 + - + +
69A LEU* 5.0 1.6 - - + -
72A VAL* 5.3 0.2 - - + -
75A VAL* 5.4 0.9 - - + -
96A PHE* 3.9 27.4 - - + -
119A ILE* 4.5 15.9 - - + +
121A ALA* 4.0 23.6 - - + +
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU 2.9 18.2 + - - +
56A GLU* 3.7 20.1 + - - +
58A LEU* 1.3 74.5 - - - +
60A ALA* 1.3 59.3 + - - +
62A LEU* 3.5 11.2 + - + +
63A GLU* 3.0 63.0 + - + +
69A LEU* 4.0 33.0 - - + +
95A TYR* 4.2 15.0 - - + -
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A THR* 4.1 2.8 + - - +
9A LYS* 3.5 42.5 - - + +
10A ALA* 4.4 0.7 - - + +
56A GLU 3.0 17.5 + - - +
57A ASN 3.6 4.9 - - - +
59A LYS* 1.3 77.4 - - - +
61A ILE* 1.3 57.6 + - - +
63A GLU* 3.5 8.1 + - - +
64A ALA* 2.9 30.4 + - - +
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Residues in contact with ILE 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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5A VAL* 3.7 10.6 - - + +
7A THR* 4.3 9.2 - - + -
10A ALA* 3.5 17.9 - - + -
19A GLN* 3.9 18.2 - - + +
20A ALA* 3.4 32.8 - - + -
27A MET* 3.9 3.2 - - - +
29A VAL* 4.0 15.3 - - + -
32A GLN* 3.2 44.2 - - + +
57A ASN 3.1 13.2 + - - +
58A LEU 3.6 5.8 - - - +
60A ALA* 1.3 72.8 - - - +
62A LEU* 1.3 68.0 + - - +
64A ALA* 3.3 10.0 + - - +
65A GLY 3.3 7.8 + - - -
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Residues in contact with LEU 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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27A MET* 3.9 18.7 - - - +
29A VAL* 4.2 8.3 - - + -
58A LEU* 3.1 31.3 + - + +
59A LYS* 3.7 5.4 - - - +
61A ILE* 1.3 78.4 - - - +
63A GLU* 1.3 60.1 + - + +
65A GLY* 3.2 6.4 + - - -
67A PHE* 2.8 38.9 + - + +
68A SER* 3.9 12.1 - - - +
69A LEU* 3.6 29.8 - - + -
72A VAL* 3.7 19.5 - - + -
121A ALA* 6.0 0.4 - - + -
123A ALA* 3.8 29.2 - - + -
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Residues in contact with GLU 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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59A LYS* 3.0 52.9 + - + +
60A ALA* 4.0 6.4 - - - +
62A LEU* 1.3 77.0 - - + +
64A ALA* 1.3 59.7 + - - +
65A GLY 3.3 0.4 + - - -
66A GLY* 3.5 10.0 + - - -
67A PHE 3.2 14.4 - - - +
68A SER* 4.8 9.9 - - - -
69A LEU* 5.9 0.5 + - - +
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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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5A VAL* 3.7 13.2 - - + +
6A GLU 5.1 1.6 - - - +
7A THR* 3.6 29.6 - - + +
60A ALA 2.9 18.0 + - - +
61A ILE 3.3 6.2 + - - +
63A GLU* 1.3 77.1 - - - +
65A GLY* 1.3 57.3 + - - +
66A GLY 3.5 0.8 + - - -
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Residues in contact with GLY 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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5A VAL* 3.9 11.8 - - - +
22A VAL* 4.6 4.9 - - - +
27A MET* 3.8 14.3 - - - +
61A ILE 3.3 3.4 + - - -
62A LEU 3.2 7.2 + - - -
64A ALA* 1.3 79.9 - - - +
66A GLY* 1.3 58.6 + - - +
67A PHE* 3.4 18.5 - - - -
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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