Contacts of the helix formed by residues 45 - 57 (chain A) in PDB entry 1RPJ
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 PHE 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU 3.7 13.7 - - - -
43A GLY* 3.1 22.5 + - - -
44A ASP* 1.3 72.9 - - - +
46A GLN* 1.3 68.0 + - + +
49A LEU* 3.0 20.8 + - - +
68A LEU* 3.5 29.8 - - + -
69A SER* 3.7 15.7 - - - -
72A ASN* 3.2 30.5 + - + +
142A LYS* 3.3 46.2 - - + -
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Residues in contact with GLN 46 (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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44A ASP 3.2 0.8 - - - -
45A PHE* 1.3 82.4 - - + +
47A SER* 1.3 57.0 + - - +
49A LEU* 3.1 9.4 + - - +
50A GLN* 3.0 43.0 + - - +
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Residues in contact with SER 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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39A SER* 5.5 0.7 - - - -
40A PRO* 4.1 11.2 - - - +
44A ASP* 3.1 33.6 + - - +
46A GLN* 1.3 77.6 - - - +
48A GLN* 1.3 56.0 + - - +
50A GLN* 3.3 12.4 + - - +
51A LEU* 2.8 29.7 + - - +
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Residues in contact with GLN 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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7A VAL* 3.6 24.7 - - + +
8A LEU 3.8 6.1 + - - -
9A LYS* 4.3 0.8 - - - +
39A SER* 3.3 24.9 + - - +
44A ASP 2.9 15.9 + - - +
45A PHE 3.7 4.0 - - - +
47A SER* 1.3 73.2 + - - +
49A LEU* 1.3 67.9 + - - +
51A LEU* 3.6 7.4 - - + +
52A PHE* 2.9 24.3 + - - +
66A ALA 2.9 26.3 + - - -
67A PRO* 3.6 3.0 - - - +
68A LEU* 2.9 33.5 + - + +
72A ASN* 2.9 15.1 + - - +
73A LEU* 3.6 11.4 - - + +
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Residues in contact with LEU 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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45A PHE 3.0 13.3 + - - +
46A GLN* 3.1 8.9 + - - +
48A GLN* 1.3 78.3 - - - +
50A GLN* 1.3 84.3 + - - +
52A PHE* 3.2 1.7 + - - +
53A GLU* 2.8 46.9 + - + +
72A ASN 3.5 16.8 - - - +
73A LEU* 3.5 10.7 - - - +
75A MET* 5.0 3.6 - - + -
76A PRO* 3.4 34.5 - - + -
79A ARG* 4.9 2.2 - - - +
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Residues in contact with GLN 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 GLN* 3.0 32.6 + - - +
47A SER* 3.6 13.0 - - - +
48A GLN 3.2 0.2 - - - -
49A LEU* 1.3 95.5 - - - +
51A LEU* 1.3 57.1 + - - +
53A GLU* 3.3 7.5 + - - +
54A ASP* 2.8 30.3 + - - +
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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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7A VAL* 4.3 16.6 - - + -
37A PHE* 3.8 33.4 - - + -
38A ALA 4.0 23.6 - - - +
39A SER* 4.3 5.6 - - - +
47A SER 2.8 20.3 + - - +
48A GLN* 3.6 6.7 - - + +
49A LEU 3.3 0.2 - - - -
50A GLN* 1.3 72.9 - - - +
52A PHE* 1.3 63.1 + - - +
54A ASP* 3.1 8.9 + - + +
55A LEU* 3.0 52.1 + - + +
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Residues in contact with PHE 52 (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 VAL* 4.3 15.2 - - + +
48A GLN 2.9 17.0 + - - +
49A LEU 3.5 3.6 - - - +
51A LEU* 1.3 76.2 - - - +
53A GLU* 1.3 58.3 + - - +
55A LEU* 3.3 8.4 + - - +
56A SER* 2.8 29.0 + - - -
63A ILE* 3.8 26.6 - - + +
65A PHE* 3.9 14.1 - + + -
73A LEU* 4.0 24.5 - - + -
76A PRO* 3.5 41.3 - - + -
77A VAL* 3.5 23.6 - - + -
80A ALA* 4.0 10.8 - - + -
87A LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 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 LEU* 2.8 36.0 + - + +
50A GLN* 3.7 7.9 - - - +
51A LEU 3.2 0.2 - - - -
52A PHE* 1.3 77.2 - - - +
54A ASP* 1.3 56.1 + - - +
56A SER* 3.3 8.3 + - - -
57A ASN* 2.9 49.1 + - - +
76A PRO* 3.6 15.0 - - + +
79A ARG* 2.4 52.8 + - - +
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Residues in contact with ASP 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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50A GLN 2.8 21.1 + - - +
51A LEU* 3.1 8.6 + - + +
53A GLU* 1.3 73.7 - - - +
55A LEU* 1.3 66.3 + - + +
57A ASN* 3.5 9.1 + - - +
58A LYS* 3.0 57.9 + - - +
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Residues in contact with LEU 55 (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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5A ALA* 4.1 12.3 - - + -
7A VAL* 3.3 34.1 - - + -
37A PHE* 3.4 45.1 - - + -
51A LEU* 3.0 27.1 + - + +
52A PHE* 3.9 3.4 - - - +
54A ASP* 1.3 82.6 - - - +
56A SER* 1.3 66.9 + - - +
57A ASN 3.1 0.2 - - - -
58A LYS* 3.0 17.4 + - + +
60A TYR* 3.3 39.7 + - + +
63A ILE* 4.2 8.6 - - + +
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Residues in contact with SER 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 PHE* 2.8 27.8 + - - -
53A GLU* 3.6 13.1 + - - -
55A LEU* 1.3 76.4 - - - +
57A ASN* 1.3 60.0 + - - +
58A LYS 3.0 11.3 - - - +
63A ILE* 3.7 17.6 - - - +
76A PRO 4.8 1.8 + - - -
79A ARG* 5.1 3.3 - - - +
80A ALA* 3.7 11.3 + - - +
83A LYS* 3.1 35.0 + - - -
85A ILE* 3.7 10.4 - - - +
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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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53A GLU* 2.9 34.8 + - - +
54A ASP* 3.7 9.2 - - - +
55A LEU 3.1 0.4 - - - -
56A SER* 1.3 78.4 + - - +
58A LYS* 1.3 64.0 + - + +
79A ARG* 6.0 1.2 - - - -
83A LYS* 5.1 6.7 - - - +
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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