Contacts of the helix formed by residues 49 - 60 (chain A) in PDB entry 2X2P
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 PRO 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ASP* 5.5 0.2 - - - +
40A THR* 3.3 12.6 - - - +
41A TYR* 3.2 69.1 - - + +
43A THR* 3.7 15.9 - - + -
47A ASN 3.8 2.4 - - - +
48A VAL* 1.3 87.2 - - + +
50A GLU* 1.3 66.6 + - - +
51A ARG* 4.5 4.9 - - + +
52A VAL* 3.0 15.7 + - + +
53A LEU* 2.9 18.4 + - - +
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Residues in contact with GLU 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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43A THR* 5.3 0.2 - - - +
48A VAL 3.5 2.7 + - - -
49A PRO* 1.3 72.5 - - - +
51A ARG* 1.3 59.4 + - - +
53A LEU* 3.1 22.8 + - - +
54A ASP* 2.9 33.6 + - - +
1121A ZN 2.2 38.0 - - - -
1123A ZN 3.7 4.9 - - - -
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Residues in contact with ARG 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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6A ASP* 3.3 25.6 + - - +
25A GLN* 3.5 23.2 - - - +
26A ILE* 3.4 16.3 + - + -
27A ASP* 3.5 18.8 - - - +
28A GLU* 2.9 42.6 + - - +
49A PRO* 3.2 3.2 - - + +
50A GLU* 1.3 79.1 - - - +
52A VAL* 1.3 58.1 + - - +
54A ASP* 3.4 8.8 + - + +
55A PHE* 3.0 27.5 + - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASP* 3.9 28.5 - - + +
26A ILE* 4.3 8.1 - - + -
38A LEU* 3.8 31.6 - - + -
40A THR* 3.6 22.2 - - - +
41A TYR* 5.4 0.2 - - + -
48A VAL* 3.7 19.1 - - + -
49A PRO* 3.0 19.2 + - + +
51A ARG* 1.3 75.1 - - - +
53A LEU* 1.3 65.3 + - - +
55A PHE* 3.3 6.4 + - - +
56A LEU* 2.9 28.2 + - + +
85A ILE* 4.4 0.2 - - + -
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Residues in contact with LEU 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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48A VAL* 3.6 48.5 - - + +
49A PRO 2.9 8.8 + - - +
50A GLU* 3.5 26.2 - - - +
52A VAL* 1.3 77.4 - - - +
54A ASP* 1.3 60.5 + - - +
56A LEU* 3.3 9.9 + - + +
57A GLU* 2.9 32.3 + - - +
85A ILE* 5.7 1.3 - - + -
88A LYS* 5.9 6.7 - - + +
89A TYR* 5.1 4.0 + - + +
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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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28A GLU* 5.7 7.5 - - + +
50A GLU* 2.9 25.9 + - - +
51A ARG* 3.7 8.0 - - - +
53A LEU* 1.3 73.5 - - - +
55A PHE* 1.3 69.9 + - - +
57A GLU* 3.3 18.0 + - - +
58A ARG* 3.4 17.0 + - - +
1121A ZN 1.9 38.6 - - - -
1123A ZN 2.9 10.3 - - - -
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Residues in contact with PHE 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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4A ALA* 4.5 1.6 - - + -
26A ILE* 3.7 42.0 - - + -
27A ASP 4.1 2.0 - - - +
30A LEU* 3.6 26.9 - - + -
32A ILE* 3.7 24.9 - - + -
36A PHE* 4.0 22.7 - + - -
38A LEU* 5.1 1.6 - - + -
51A ARG 3.0 18.2 + - - +
52A VAL 3.3 4.7 + - - +
54A ASP* 1.3 77.8 - - - +
56A LEU* 1.3 68.3 + - + +
58A ARG* 3.0 21.5 + - - +
59A ASN* 2.9 61.6 + - + +
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Residues in contact with LEU 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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36A PHE* 4.7 7.4 - - + -
38A LEU* 3.8 30.1 - - + -
48A VAL* 5.2 0.7 - - + -
52A VAL* 2.9 22.8 + - + +
53A LEU* 3.9 9.0 - - + +
55A PHE* 1.3 82.4 - - + +
57A GLU* 1.3 67.5 + - - +
58A ARG 3.1 0.5 + - - -
59A ASN 4.2 1.8 - - - +
60A ASN* 2.8 35.0 + - + +
63A LEU* 3.9 28.9 - - + -
85A ILE* 3.8 27.4 - - + -
89A TYR* 3.8 23.3 - - + +
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Residues in contact with GLU 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 LEU* 2.9 20.7 + - + +
54A ASP* 3.5 10.2 - - - +
55A PHE 3.3 0.4 - - - -
56A LEU* 1.3 76.6 - - - +
58A ARG* 1.3 63.2 + - + +
60A ASN* 3.6 11.8 + - - +
88A LYS* 6.3 1.3 - - - +
89A TYR* 4.1 6.8 + - - +
1123A ZN 3.7 23.7 - - - -
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Residues in contact with ARG 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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27A ASP 3.1 23.6 + - - -
28A GLU* 3.6 22.2 + - - +
29A ASP* 3.9 4.6 - - - +
30A LEU 2.9 32.2 + - - -
31A VAL* 4.0 10.7 - - - +
54A ASP 3.4 13.4 + - - +
55A PHE* 3.0 14.6 + - - +
57A GLU* 1.3 84.1 - - + +
59A ASN* 1.3 69.5 + - - +
60A ASN* 3.7 1.5 + - - -
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Residues in contact with ASN 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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30A LEU 3.4 12.5 + - - -
31A VAL* 3.5 11.3 - - - +
32A ILE* 2.9 32.7 + - + +
36A PHE* 3.3 26.2 - - + -
55A PHE* 2.9 56.0 + - + +
56A LEU* 3.3 2.9 + - - -
58A ARG* 1.3 86.7 - - - +
60A ASN* 1.3 64.3 + - - +
61A GLU* 3.3 3.9 + - - -
62A LYS 3.9 1.4 + - - -
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Residues in contact with ASN 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 LEU* 2.8 30.8 + - + +
57A GLU* 3.6 13.3 + - - +
58A ARG 3.7 1.2 - - - -
59A ASN* 1.3 78.7 - - - +
61A GLU* 1.3 69.3 + - - +
62A LYS 3.2 1.1 + - - -
63A LEU* 3.2 22.1 + - + +
89A TYR* 3.5 43.2 + - + +
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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