Contacts of the helix formed by residues 48 - 65 (chain A) in PDB entry 2W7N
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 ARG 48 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLN* 4.3 2.6 - - - +
38A ALA* 6.2 3.4 - - - -
41A ALA* 4.6 16.6 - - + -
46A LEU 3.9 0.2 + - - -
47A THR* 1.3 72.9 - - - +
49A GLY* 1.3 57.9 + - - +
51A VAL* 3.3 5.2 + - - +
52A SER* 3.0 29.4 + - - -
3F BRU 3.7 59.2 + - - +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 3.2 5.6 + - - -
48A ARG* 1.3 77.3 - - - +
50A ALA* 1.3 59.0 + - - +
52A SER* 3.4 7.4 + - - -
53A GLN* 3.0 40.8 + - - +
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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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46A LEU* 4.2 26.2 - - + -
47A THR* 3.2 25.2 + - - +
49A GLY* 1.3 74.4 - - - +
51A VAL* 1.3 61.8 + - - +
53A GLN* 3.4 9.6 + - - +
54A ALA* 3.0 22.5 + - - +
57A ARG* 4.8 2.8 + - - -
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Residues in contact with VAL 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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26A ILE* 3.8 23.8 - - + -
37A GLN* 3.6 38.4 - - + +
40A PHE* 4.2 5.2 - - + -
41A ALA* 3.6 33.7 - - + +
46A LEU* 4.0 18.4 - - + -
47A THR 3.3 8.9 + - - +
48A ARG* 3.3 7.2 + - - +
50A ALA* 1.3 73.2 - - - +
52A SER* 1.3 66.3 + - - +
54A ALA* 3.2 6.7 + - - +
55A VAL* 3.0 23.0 + - - +
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Residues in contact with SER 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN* 3.2 22.7 + - - +
48A ARG 3.0 16.8 + - - -
49A GLY* 3.6 8.7 - - - -
51A VAL* 1.3 78.0 - - - +
53A GLN* 1.3 56.4 + - - +
55A VAL* 3.4 2.9 + - - +
56A HIS* 3.0 28.2 + - - +
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Residues in contact with GLN 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 GLY* 3.0 25.1 + - - +
50A ALA* 3.7 7.5 - - - +
51A VAL 3.3 0.2 - - - -
52A SER* 1.3 74.2 - - - +
54A ALA* 1.3 60.5 + - - +
56A HIS* 3.2 8.0 + - - +
57A ARG* 2.8 53.2 + - + +
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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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23A THR* 3.8 18.8 - - + +
26A ILE* 4.1 28.5 - - + -
27A ALA* 4.5 2.1 - - - +
50A ALA 3.0 12.7 + - - +
51A VAL 3.2 8.9 + - - +
53A GLN* 1.3 71.1 - - - +
55A VAL* 1.3 68.1 + - - +
57A ARG* 3.3 36.2 + - - +
58A VAL* 3.5 10.0 + - - +
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Residues in contact with VAL 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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3A LYS* 6.2 2.0 - - + -
26A ILE* 3.9 21.3 - - + +
27A ALA* 4.7 7.0 - - - -
30A VAL* 4.0 25.8 - - + -
31A LEU* 3.8 31.8 - - + +
37A GLN* 4.0 19.7 - - + +
51A VAL 3.0 13.9 + - - +
52A SER 3.8 6.1 - - - +
54A ALA* 1.3 75.0 - - - +
56A HIS* 1.3 59.1 + - - +
58A VAL* 3.3 5.4 + - - +
59A TRP* 3.0 27.2 + - + +
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Residues in contact with HIS 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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3A LYS* 5.3 6.9 + - - -
52A SER* 3.0 19.8 + - - +
53A GLN* 3.2 8.9 + - - +
55A VAL* 1.3 75.6 - - - +
57A ARG* 1.3 63.0 + - + +
59A TRP* 4.2 16.8 - + - -
60A ALA* 2.8 46.6 + - + +
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Residues in contact with ARG 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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17A LEU* 4.4 9.1 - - + +
19A VAL* 5.8 2.1 - - + +
23A THR* 3.0 34.7 + - + +
50A ALA 4.8 2.2 + - - -
53A GLN* 2.8 51.0 + - + +
54A ALA* 3.4 23.5 - - - +
55A VAL 3.3 0.4 - - - -
56A HIS* 1.3 74.3 - - + +
58A VAL* 1.3 62.6 + - + +
60A ALA* 3.9 5.1 - - - +
61A ALA* 3.3 21.3 + - - +
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Residues in contact with VAL 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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5A LEU* 4.6 0.7 - - + -
10A PHE* 3.8 25.4 - - + -
13A ALA* 3.8 11.3 - - + +
14A ILE* 3.9 25.1 - - + -
17A LEU* 4.4 8.1 - - + -
19A VAL* 4.7 2.5 - - + -
23A THR* 4.2 14.8 - - + +
24A ILE* 5.3 0.4 - - - -
27A ALA* 3.4 27.6 - - + -
31A LEU* 4.0 9.2 - - + -
54A ALA 3.5 6.4 + - - +
55A VAL 3.3 4.5 + - - +
56A HIS 3.2 0.6 - - - -
57A ARG* 1.3 76.0 - - - +
59A TRP* 1.3 65.0 + - - +
61A ALA* 3.2 7.5 + - - +
62A PHE* 3.0 20.8 + - - +
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Residues in contact with TRP 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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3A LYS* 3.6 63.5 - - + +
4A ARG 4.0 9.6 - - - -
5A LEU* 3.6 32.8 - - + -
31A LEU* 4.2 18.5 - - + +
55A VAL* 3.0 19.0 + - + +
56A HIS* 3.8 17.5 - + - +
58A VAL* 1.3 76.7 - - - +
60A ALA* 1.3 58.1 + - - +
62A PHE* 3.2 11.9 + + - +
63A GLU* 2.9 65.0 + - + +
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A HIS* 2.8 41.0 + - + +
57A ARG* 3.9 5.6 - - - +
59A TRP* 1.3 75.9 - - - +
61A ALA* 1.3 57.3 + - - +
63A GLU* 3.3 8.7 + - - +
64A ASP* 3.0 37.0 + - - +
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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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13A ALA* 3.4 24.0 - - - +
17A LEU* 3.9 23.8 - - + -
57A ARG 3.3 11.9 + - - +
58A VAL 3.2 9.6 + - - +
59A TRP 3.2 0.2 - - - -
60A ALA* 1.3 76.6 - - - +
62A PHE* 1.3 64.0 + - - +
64A ASP* 3.4 9.6 + - - +
65A LYS* 3.3 26.0 + - - +
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Residues in contact with PHE 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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5A LEU* 3.6 25.8 - - + -
9A GLN* 3.6 57.4 - - + -
12A GLU* 3.7 9.2 - - - -
13A ALA* 3.7 19.4 - - + +
58A VAL 3.0 8.7 + - - +
59A TRP* 3.5 19.1 - + - +
61A ALA* 1.3 74.5 - - - +
63A GLU* 1.3 83.3 + - - +
65A LYS* 3.1 6.4 + - - -
66A ASN* 2.8 59.2 + - + +
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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 TRP* 2.9 54.0 + - + +
60A ALA* 3.6 10.5 - - - +
62A PHE* 1.3 92.9 - - - +
64A ASP* 1.3 65.7 + - - +
66A ASN* 3.1 17.5 + - - +
67A LEU* 3.6 18.3 + - + +
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Residues in contact with ASP 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* 3.0 24.7 + - - +
61A ALA* 3.7 9.0 - - - +
62A PHE 3.2 0.2 - - - -
63A GLU* 1.3 77.8 - - - +
65A LYS* 1.3 61.4 + - + +
66A ASN 3.3 0.7 + - - -
67A LEU* 3.8 20.3 + - - +
73A ARG* 3.0 31.9 + - - +
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Residues in contact with LYS 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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12A GLU* 2.7 50.9 + - + +
13A ALA* 4.5 4.2 + - - +
15A GLN* 2.7 35.2 + - - +
61A ALA 3.3 12.2 + - - +
62A PHE 3.1 9.6 + - - +
64A ASP* 1.3 78.1 - - + +
66A ASN* 1.3 70.2 + - - +
67A LEU 3.8 1.1 - - - -
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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