Contacts of the helix formed by residues 56 - 77 (chain A) in PDB entry 4MD4
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 ALA 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 4.0 11.4 - - + +
39A LYS* 3.4 34.3 - - + +
40A GLU* 4.0 0.2 - - - -
41A THR* 3.7 21.5 - - - +
54A PHE* 3.2 12.7 + - - -
55A GLU* 1.3 76.7 + - - +
57A GLN* 1.3 62.6 + - - +
59A ALA* 3.0 21.7 + - - +
60A LEU* 3.7 9.2 + - - +
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 5.0 12.8 + - - +
55A GLU* 3.0 26.4 + - + +
56A ALA* 1.3 77.9 - - - +
58A GLY* 1.3 61.0 + - - +
60A LEU* 3.1 48.9 + - - +
61A ALA* 3.5 6.6 + - - +
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Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PHE* 4.7 4.5 - - - -
55A GLU* 3.1 13.6 + - - +
57A GLN* 1.3 78.9 - - - +
59A ALA* 1.3 60.5 + - - +
61A ALA* 3.5 7.9 + - - +
62A ASN* 3.4 24.8 + - - +
6C VAL* 4.3 20.3 - - - +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.4 42.3 - - + -
34A VAL* 3.6 24.0 - - + -
36A MET* 4.5 2.2 - - + -
54A PHE* 4.2 4.2 - - + -
56A ALA 3.0 13.1 + - - +
58A GLY* 1.3 73.9 - - - +
60A LEU* 1.3 60.5 + - - +
62A ASN* 3.2 3.6 + - - +
63A ILE* 2.9 33.4 + - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.5 6.1 - - + -
36A MET* 4.3 22.2 - - - +
39A LYS* 3.8 46.7 - - + +
56A ALA 3.7 15.7 - - - +
57A GLN* 3.1 33.7 + - - +
59A ALA* 1.3 77.0 - - - +
61A ALA* 1.3 61.2 + - - +
63A ILE* 3.3 7.2 + - - +
64A ALA* 3.0 23.0 + - - +
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Residues in contact with ALA 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 GLN 3.5 6.6 + - - +
58A GLY* 3.8 10.1 - - - +
59A ALA 3.3 0.2 - - - -
60A LEU* 1.3 77.7 - - - +
62A ASN* 1.3 66.4 + - - +
64A ALA* 3.3 9.3 + - - +
65A VAL* 3.2 25.2 + - - +
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Residues in contact with ASN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.2 5.3 - - - +
11A GLU* 2.7 31.1 + - - +
22A PHE* 4.3 4.9 - - + -
58A GLY 3.4 9.6 + - - +
59A ALA 3.2 8.4 + - - +
61A ALA* 1.3 80.0 - - - +
63A ILE* 1.3 59.0 + - - +
65A VAL* 3.2 4.1 + - - +
66A ASP* 2.9 26.6 + - - -
6C VAL* 3.7 14.7 - - - +
7C CIR 3.0 22.0 + - - -
8C VAL* 3.9 15.2 - - - +
9C ASN* 2.9 31.0 + - - +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 4.7 2.2 - - + +
12A PHE 3.5 17.7 - - - +
13A TYR* 4.0 21.5 - - + -
20A GLY* 4.0 4.3 - - - -
21A GLU 3.5 32.1 - - - +
22A PHE* 4.8 2.9 - - + -
36A MET* 3.6 24.7 - - + -
59A ALA 2.9 19.1 + - - +
60A LEU* 3.8 6.5 - - - +
62A ASN* 1.3 75.4 - - - +
64A ALA* 1.3 58.0 + - - +
66A ASP* 3.2 15.2 + - + +
67A LYS* 2.9 29.1 + - + +
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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 LEU 3.0 14.4 + - - +
61A ALA* 3.4 13.2 - - - +
62A ASN 3.2 0.2 - - - -
63A ILE* 1.3 77.6 - - - +
65A VAL* 1.3 58.1 + - + +
67A LYS* 3.3 10.9 + - - +
68A ALA* 3.0 25.6 + - - +
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Residues in contact with VAL 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 ALA 3.2 12.1 + - - +
62A ASN* 3.2 8.7 + - - +
64A ALA* 1.3 73.4 - - + +
66A ASP* 1.3 56.5 + - - +
68A ALA* 3.1 6.9 + - - +
69A ASN* 2.7 50.2 + - - +
8C VAL* 5.9 2.7 - - + -
9C ASN* 3.5 37.2 - - + +
10C SER 3.8 7.0 - - - +
11C ALA* 3.9 17.9 - - + -
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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
----------------------------------------------------------
11A GLU* 2.6 32.5 - - - +
12A PHE* 4.5 3.0 + - - -
13A TYR* 3.9 17.9 - - + +
62A ASN 2.9 14.7 + - - +
63A ILE* 3.4 18.4 - - - +
65A VAL* 1.3 78.4 - - - +
67A LYS* 1.3 56.9 + - - +
69A ASN* 4.5 3.1 + - - +
70A LEU* 2.9 29.6 + - - +
9B GLU* 3.7 15.4 - - + +
11B VAL* 3.2 24.9 - - - +
9C ASN* 3.1 15.6 + - - +
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.3 51.3 - - + +
15A ASN* 5.4 3.4 + - - +
18A GLN* 4.0 17.7 - - - +
63A ILE* 2.9 13.4 + - + +
64A ALA* 3.4 13.2 - - - +
66A ASP* 1.3 76.0 - - - +
68A ALA* 1.3 64.5 + - - +
70A LEU* 3.3 3.5 + - - +
71A GLU* 3.2 43.0 + - + +
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Residues in contact with ALA 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 3.0 14.0 + - - +
65A VAL* 3.1 11.0 + - + +
67A LYS* 1.3 76.7 - - - +
69A ASN* 1.3 65.8 + - - +
71A GLU* 3.3 15.3 + - - +
72A ILE* 3.3 27.5 + - + +
11C ALA* 5.9 4.0 - - + -
12C TYR 6.1 0.2 - - - +
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Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 2.7 31.0 + - - +
66A ASP* 3.9 5.9 + - - +
68A ALA* 1.3 73.6 - - - +
70A LEU* 1.3 57.6 + - - +
72A ILE* 3.1 9.0 + - - +
73A MET* 2.8 34.1 + - + +
9B GLU* 3.8 18.9 + - + +
11B VAL* 5.6 0.2 - - - +
30B TYR* 4.3 16.2 - - - -
37B TYR* 4.5 6.4 + - - +
61B TRP* 4.8 3.1 - - - -
9C ASN* 5.2 0.2 - - - +
10C SER 2.9 24.0 + - - -
11C ALA* 3.5 5.2 - - - +
12C TYR* 3.2 28.7 + - - +
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Residues in contact with LEU 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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13A TYR* 3.4 27.8 - - + +
15A ASN* 3.6 26.7 - - + +
66A ASP 2.9 18.1 + - - +
67A LYS* 3.6 5.8 - - - +
68A ALA 3.3 0.2 - - - -
69A ASN* 1.3 77.6 - - - +
71A GLU* 1.3 52.0 + - - +
73A MET* 4.5 0.4 - - - +
74A THR* 2.7 54.5 + - - +
7B PHE 3.3 24.0 - - - +
8B LEU 3.7 7.2 - - - -
9B GLU* 3.7 28.2 + - + +
32B TYR* 3.8 15.7 - - + -
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Residues in contact with GLU 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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15A ASN* 5.1 11.0 - - - +
67A LYS* 3.2 34.6 + - + +
68A ALA* 3.5 13.1 - - - +
69A ASN 3.3 0.2 - - - -
70A LEU* 1.3 77.5 - - - +
72A ILE* 1.3 63.9 + - + +
74A THR* 3.7 5.3 - - - -
75A LYS* 3.2 45.1 + - - +
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Residues in contact with ILE 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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68A ALA* 3.3 16.3 + - + +
69A ASN* 3.1 13.1 + - - +
71A GLU* 1.3 81.1 - - + +
73A MET* 1.3 61.7 + - - +
75A LYS* 3.3 11.6 + - + +
76A ARG* 2.9 57.2 + - - +
12C TYR* 3.2 51.1 - - + +
13C GLN* 4.9 3.8 - - - +
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Residues in contact with MET 73 (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 ASN* 2.8 24.5 + - + +
70A LEU 4.1 0.9 - - - +
72A ILE* 1.3 72.8 - - - +
74A THR* 1.3 66.4 + - - +
76A ARG* 3.4 38.6 - - - +
77A SER* 3.0 27.7 + - - -
9B GLU* 3.5 15.3 - - - +
32B TYR* 3.6 21.8 - - + -
37B TYR* 3.6 36.1 - - + +
53B LEU* 3.5 38.6 - - + -
57B ASP* 4.0 2.2 - - - +
12C TYR* 6.2 0.2 - - - -
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Residues in contact with THR 74 (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 ASN* 5.5 1.4 + - - -
70A LEU* 2.7 44.6 + - - +
71A GLU* 3.7 7.0 - - - -
73A MET* 1.3 72.3 - - - +
75A LYS* 1.3 59.2 + - - +
77A SER* 2.9 8.5 + - - -
79A TYR* 2.9 55.4 + - + -
7B PHE* 3.7 35.2 - - + +
32B TYR* 3.5 8.6 + - - -
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Residues in contact with LYS 75 (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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71A GLU* 3.2 31.3 + - - +
72A ILE* 3.7 10.1 - - + +
74A THR* 1.3 74.2 - - - +
76A ARG* 1.3 67.6 + - - +
78A ASN* 2.9 19.8 + - - +
79A TYR* 3.4 34.7 - - + +
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Residues in contact with ARG 76 (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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72A ILE* 2.9 25.8 + - - +
73A MET* 3.4 20.8 - - - +
74A THR 3.3 0.2 - - - -
75A LYS* 1.3 77.4 - - - +
77A SER* 1.3 57.2 + - - +
78A ASN* 3.2 7.0 + - - +
201A NAG 3.9 16.5 + - - +
53B LEU* 2.8 49.0 + - + +
56B PRO* 3.9 21.1 - - - +
57B ASP* 2.7 43.9 + - - -
12C TYR* 3.3 34.1 - - - -
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET 3.0 12.2 + - - -
74A THR 2.9 15.9 + - - -
75A LYS 3.1 0.2 - - - -
76A ARG* 1.3 74.8 - - - +
78A ASN* 1.3 64.7 + - - +
80A THR* 2.7 40.1 + - - -
201A NAG 3.9 17.5 - - - +
32B TYR* 3.0 34.5 + - - -
53B LEU* 4.3 9.4 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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