Contacts of the helix formed by residues 47 - 64 (chain A) in PDB entry 2X9D
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 ASN 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 3.7 15.5 - - - -
45A VAL* 3.4 4.3 - - - +
46A LYS* 1.3 86.4 + - - +
48A LYS* 1.3 60.1 + - - +
49A ARG* 3.0 14.8 + - - +
50A ALA* 2.9 36.1 + - - +
51A LEU* 3.1 27.0 + - - +
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Residues in contact with LYS 48 (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 ILE* 2.8 28.7 + - - -
23A ASP* 3.1 15.0 + - - +
25A LEU* 2.9 35.2 + - + +
26A THR* 4.9 5.5 - - + +
27A THR* 3.7 16.2 - - + +
47A ASN* 1.3 76.0 - - - +
49A ARG* 1.3 58.6 + - - +
51A LEU* 3.5 5.1 + - + +
52A LEU* 3.0 50.5 + - + +
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 3.0 13.0 + - - +
48A LYS* 1.3 76.1 - - - +
50A ALA* 1.3 65.8 + - - +
52A LEU* 3.7 32.1 - - - +
53A ASP* 2.7 64.2 + - - +
99A VAL 4.9 4.6 + - - -
101A LEU 5.0 6.1 + - - -
102A GLY* 4.1 10.1 + - - -
103A THR* 4.0 12.7 - - - +
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Residues in contact with ALA 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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45A VAL* 4.1 10.5 - - + -
46A LYS* 4.3 10.3 - - + +
47A ASN* 2.9 28.8 + - - +
49A ARG* 1.3 76.1 - - - +
51A LEU* 1.3 64.6 - - - +
53A ASP* 3.4 8.7 - - - +
54A ALA* 3.1 22.2 + - - +
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Residues in contact with LEU 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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9A VAL* 4.8 8.5 - - + -
10A ILE* 5.0 5.8 - - + -
13A ALA* 3.6 25.8 - - + -
25A LEU* 3.6 30.5 - - + -
26A THR 4.9 7.0 - - - +
27A THR* 5.0 9.2 - - + -
30A LEU* 3.8 26.7 - - + -
45A VAL* 4.0 17.0 - - + +
47A ASN 3.1 15.9 + - - +
48A LYS* 3.7 8.1 - - - +
49A ARG 3.3 0.2 - - - -
50A ALA* 1.3 77.5 - - - +
52A LEU* 1.3 57.1 + - - +
54A ALA* 3.1 8.0 + - - +
55A LEU* 2.8 40.5 + - + +
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Residues in contact with LEU 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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17A LEU* 5.5 0.7 - - + -
22A ILE* 4.0 33.7 - - + -
25A LEU* 4.1 22.2 - - + -
48A LYS* 3.0 45.9 + - + +
49A ARG* 3.7 28.3 - - - +
51A LEU* 1.3 72.2 - - - +
53A ASP* 1.3 57.5 + - - +
55A LEU* 3.2 9.5 + - + +
56A ALA* 2.8 35.9 + - - +
99A VAL* 3.7 22.0 - - + +
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Residues in contact with ASP 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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49A ARG* 2.7 59.5 + - - +
50A ALA* 3.4 9.0 - - - +
52A LEU* 1.3 77.3 - - - +
54A ALA* 1.3 59.5 + - - +
56A ALA* 3.4 2.3 + - - +
57A VAL* 3.2 29.6 + - - +
102A GLY 4.5 0.5 - - - +
103A THR* 3.4 19.9 - - + +
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Residues in contact with ALA 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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6A ARG* 4.0 22.6 + - - +
10A ILE* 3.9 20.2 - - + -
45A VAL* 6.4 0.4 - - + -
50A ALA 3.1 9.4 + - - +
51A LEU* 3.1 11.2 + - + +
53A ASP* 1.3 75.7 - - - +
55A LEU* 1.3 60.3 + - - +
57A VAL* 3.5 5.1 + - - +
58A GLU* 2.9 35.0 + - - +
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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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10A ILE* 3.8 29.4 - - + -
13A ALA* 3.6 42.0 - - + +
14A LEU* 3.9 17.6 - - + +
17A LEU* 4.9 12.8 - - + -
25A LEU* 4.2 14.8 - - + -
51A LEU* 2.8 29.7 + - + +
52A LEU* 3.2 13.6 + - + +
54A ALA* 1.3 76.2 - - - +
56A ALA* 1.3 54.1 + - - +
58A GLU* 3.3 3.1 + - - +
59A ILE* 2.8 39.8 + - - +
99A VAL* 4.0 11.0 - - + -
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Residues in contact with ALA 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 LEU 2.8 17.0 + - - +
53A ASP 3.5 5.6 - - - +
54A ALA 3.3 0.2 - - - -
55A LEU* 1.3 78.0 - - - +
57A VAL* 1.3 61.4 + - + +
59A ILE* 3.6 10.5 + - - +
60A LEU* 3.6 19.2 + - - +
99A VAL* 3.6 29.7 - - + +
100A HIS* 4.3 11.7 + - - +
103A THR* 3.8 24.0 - - + +
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Residues in contact with VAL 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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6A ARG* 4.6 6.7 - - - +
53A ASP* 3.2 18.3 + - + +
54A ALA* 3.8 8.5 - - - +
56A ALA* 1.3 75.7 - - + +
58A GLU* 1.3 73.8 + - - +
60A LEU* 3.3 8.9 + - - +
61A ALA* 3.1 22.8 + - + +
103A THR* 6.1 2.9 - - - +
104A ARG 5.5 4.0 - - - +
106A ASP* 3.7 46.2 - - + +
108A LYS* 5.4 10.8 - - + -
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Residues in contact with GLU 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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6A ARG* 3.1 32.6 + - - +
10A ILE* 3.8 31.2 - - + -
14A LEU* 4.8 3.1 - - + -
54A ALA 2.9 21.3 + - - +
55A LEU* 3.3 3.8 + - - +
57A VAL* 1.3 81.2 - - - +
59A ILE* 1.3 64.1 + - - +
61A ALA* 3.9 10.6 - - - +
62A ARG* 3.1 56.5 + - - +
108A LYS* 5.6 5.7 - - - +
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Residues in contact with ILE 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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14A LEU* 3.8 28.7 - - + -
17A LEU* 4.7 2.2 - - + -
55A LEU* 2.8 24.4 + - + +
56A ALA* 3.9 6.5 - - - +
57A VAL 3.2 0.6 - - - -
58A GLU* 1.3 73.6 - - - +
60A LEU* 1.3 70.9 + - + +
63A HIS* 3.3 30.4 + - + +
64A HIS 3.9 0.9 + - - -
89A ALA* 3.4 31.7 - - + +
90A LEU* 4.7 7.6 - - + +
93A TYR* 3.9 17.9 - - + -
96A GLY* 4.5 13.7 - - - +
99A VAL* 4.1 25.4 - - + -
100A HIS* 6.3 1.8 - - + -
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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
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56A ALA 3.6 11.4 + - - +
57A VAL* 3.3 8.6 + - - +
58A GLU 3.3 0.4 - - - -
59A ILE* 1.3 85.0 - - + +
61A ALA* 1.3 63.6 + - - +
64A HIS* 2.9 48.9 + - + +
86A PHE* 4.1 26.5 - - + -
89A ALA* 4.8 3.1 - - + -
90A LEU* 5.6 1.6 - - + -
100A HIS* 3.8 26.7 - - + +
105A PRO* 6.2 2.7 - - + -
109A GLN* 6.4 0.7 - - + -
1209A ITC 3.7 36.3 - - - +
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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 VAL* 3.1 19.2 + - + +
58A GLU* 4.2 18.6 - - - +
60A LEU* 1.3 76.2 - - - +
62A ARG* 1.3 62.3 + - + +
64A HIS 5.0 1.1 - - - +
65A ASP* 4.0 9.7 - - - +
108A LYS* 6.3 2.9 - - + -
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Residues in contact with ARG 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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7A GLU* 3.5 30.7 + - - +
10A ILE* 3.8 21.0 - - - +
11A ASP* 2.7 34.1 + - - +
14A LEU* 4.1 18.8 - - - +
58A GLU* 3.1 38.7 + - - +
61A ALA* 1.3 79.7 - - + +
63A HIS* 1.3 89.1 + - + +
64A HIS 4.0 0.2 - - - -
65A ASP* 3.9 11.7 - - - +
93A TYR* 5.2 2.4 + - - -
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Residues in contact with HIS 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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14A LEU* 5.6 0.2 - - + -
59A ILE* 3.3 20.1 + - + +
62A ARG* 1.3 115.2 + - + +
64A HIS* 1.3 60.7 + - - +
65A ASP* 3.4 13.9 + - - +
85A SER* 4.3 4.7 + - - +
88A ARG* 5.2 8.3 + - - +
89A ALA* 3.9 22.2 + - + +
92A ARG* 3.3 43.8 + - + -
93A TYR* 3.0 34.2 + + - -
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Residues in contact with HIS 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* 2.9 38.9 + - + +
61A ALA* 5.0 0.9 - - - +
63A HIS* 1.3 74.2 - - - +
65A ASP* 1.3 61.1 + - - +
66A TYR 3.3 11.9 - - - -
67A SER* 4.2 10.8 + - - -
82A ASN* 3.3 24.6 + - - -
85A SER* 2.6 27.1 + - - -
86A PHE* 3.5 26.9 + + - +
89A ALA* 3.8 12.2 - - + +
1209A ITC 3.2 48.6 + - + -
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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