Contacts of the helix formed by residues 47 - 58 (chain A) in PDB entry 2PK9
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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A TYR* 3.8 22.9 - - + -
38A VAL* 3.6 15.7 - - + -
39A LYS 3.3 26.7 - - - +
40A LEU* 4.7 6.3 - - + -
42A SER* 5.6 0.9 - - - +
44A GLU* 4.1 28.5 - - + +
45A GLY 3.4 11.0 - - - +
46A THR* 1.3 85.0 - - + +
48A SER* 1.3 57.6 + - - +
49A THR* 3.0 4.0 - - - +
50A ALA* 2.7 33.9 + - + +
51A ILE 3.3 2.9 + - - -
78A LEU* 5.8 0.7 - - + -
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Residues in contact with SER 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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44A GLU* 4.6 5.3 + - - -
46A THR 2.8 7.7 + - - -
47A PRO* 1.3 69.8 - - - +
49A THR* 1.3 63.4 + - - +
51A ILE* 3.3 6.9 + - - +
52A ARG* 3.0 28.2 + - - +
132B LYS* 3.1 41.6 + - - +
138B PHE* 3.4 41.9 - - - -
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Residues in contact with THR 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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18A TYR* 4.6 31.1 - - + +
47A PRO* 2.9 3.4 + - - +
48A SER* 1.3 78.7 + - - +
50A ALA* 1.3 57.3 + - - +
52A ARG* 3.6 6.5 + - - +
53A GLU* 3.1 27.1 + - - +
151A ASP* 5.9 0.2 - - - +
153A GLY* 3.7 32.5 - - - +
154A LEU* 6.2 1.6 - - + -
138B PHE* 5.9 1.2 - - - -
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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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18A TYR* 2.9 28.3 + - + +
38A VAL* 4.2 2.9 - - + -
46A THR* 5.0 2.5 - - + -
47A PRO* 2.7 19.3 + - + +
49A THR* 1.3 69.6 - - - +
51A ILE* 1.3 66.9 + - - +
52A ARG 3.0 1.1 - - - -
53A GLU* 2.8 6.0 + - - +
54A ILE* 2.8 38.1 + - + +
78A LEU* 3.9 24.5 - - + -
80A LEU* 4.8 0.9 - - + -
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Residues in contact with ILE 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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46A THR* 3.4 31.2 - - + +
47A PRO 3.3 2.4 + - - +
48A SER* 3.3 6.0 + - - +
50A ALA* 1.3 74.4 - - - +
52A ARG* 1.3 49.3 + - - +
54A ILE* 4.3 6.8 - - - +
55A SER* 2.7 36.7 + - - -
129B VAL* 4.7 6.7 - - + -
132B LYS* 3.9 18.6 - - + +
133B GLY* 3.9 9.9 - - - -
159B GLU* 3.7 18.6 - - - +
163B LEU* 3.9 35.9 - - + -
168B TYR* 4.6 5.5 - - + -
170B ILE* 3.4 25.6 - - + -
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Residues in contact with ARG 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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48A SER* 3.0 19.7 + - - +
49A THR* 3.7 6.3 - - - +
50A ALA 3.0 0.8 - - - -
51A ILE* 1.3 76.5 - - - +
53A GLU* 1.3 64.9 + - - +
55A SER* 3.6 3.1 - - - -
56A LEU* 3.1 34.2 + - + +
132A ARG* 5.9 1.6 - - - +
152A PHE 4.4 1.1 - - - +
153A GLY 3.4 20.2 - - - +
154A LEU* 4.6 1.6 - - - +
155A ALA 2.9 23.9 + - - +
156A ARG* 3.3 33.1 - - - +
157A ALA 4.7 1.4 - - - +
132B LYS 3.9 7.5 + - - +
133B GLY 3.1 28.0 + - - +
134B LEU* 3.2 3.0 + - - +
135B CYS 2.7 45.2 + - - +
136B ASP* 5.7 2.0 - - - -
138B PHE* 6.0 1.0 - - - -
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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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18A TYR* 4.1 9.2 + - - -
36A LYS* 3.0 35.7 + - - +
49A THR* 3.1 15.5 + - - +
50A ALA* 2.8 6.0 + - - +
52A ARG* 1.3 74.0 - - - +
54A ILE* 1.3 65.4 + - - +
55A SER 3.2 0.5 + - - -
56A LEU* 3.2 2.9 + - - +
57A MET* 2.9 36.1 + - + +
80A LEU* 4.3 7.7 - - + +
82A PHE* 3.4 28.8 - - + -
151A ASP* 3.6 6.6 - - - +
152A PHE* 3.5 37.9 + - - +
153A GLY* 4.4 6.1 - - - -
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Residues in contact with ILE 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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46A THR* 6.0 0.2 - - + -
50A ALA* 2.8 38.6 + - + +
53A GLU* 1.3 73.7 - - - +
55A SER* 1.3 61.7 + - - +
57A MET* 3.4 1.7 + - - +
58A LYS* 3.4 29.8 + - - +
68A LEU* 3.9 12.5 - - + +
71A VAL* 3.8 24.0 - - + -
78A LEU* 4.1 6.1 - - + -
80A LEU* 3.4 31.6 - - + -
168B TYR* 3.6 54.5 - - + -
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Residues in contact with SER 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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51A ILE 2.7 22.0 + - - -
52A ARG* 3.6 7.0 - - - -
54A ILE* 1.3 81.3 - - - +
56A LEU* 1.3 61.6 + - - +
58A LYS* 3.8 13.6 - - - +
59A GLU* 3.9 5.7 + - - +
133B GLY 5.2 1.7 + - - -
168B TYR* 3.6 19.6 + - - +
169B ARG* 5.8 1.6 - - - -
170B ILE* 3.2 24.9 + - - +
171B ILE* 3.2 27.8 - - - +
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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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52A ARG* 3.1 24.2 + - + +
53A GLU* 4.0 2.2 - - - +
55A SER* 1.3 77.7 - - - +
57A MET* 1.3 63.8 + - + +
59A GLU* 2.9 24.6 + - - +
60A LEU* 3.2 20.0 + - + +
129A ILE* 3.5 35.7 - - + -
152A PHE* 4.4 5.4 - - + +
155A ALA* 3.7 43.7 - - + +
156A ARG* 4.1 3.4 - - - +
157A ALA* 3.9 13.0 - - + +
171B ILE* 3.8 18.2 - - + -
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Residues in contact with MET 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 38.8 + - + +
54A ILE 3.9 0.2 - - - +
55A SER 3.4 0.2 - - - -
56A LEU* 1.3 72.3 - - - +
58A LYS* 1.3 55.6 + - - +
59A GLU 2.9 4.5 - - - -
60A LEU* 2.8 64.7 + - + +
61A LYS* 4.2 5.4 + - - +
65A ILE* 4.0 6.1 - - + -
66A VAL 4.1 13.7 - - - +
68A LEU* 3.7 32.2 + - + +
82A PHE* 4.0 19.5 - - + -
150A GLY* 6.3 0.4 - - - -
151A ASP 6.0 0.7 - - - -
152A PHE* 3.6 34.3 - - + -
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Residues in contact with LYS 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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54A ILE* 3.4 24.1 + - + +
55A SER 3.8 11.0 - - - +
57A MET* 1.3 75.9 - - - +
59A GLU* 1.3 58.9 + - - +
61A LYS* 2.8 31.4 + - - +
68A LEU* 5.4 4.9 - - + +
71A VAL* 5.5 5.4 - - - -
167B ASN* 3.1 42.3 + - - +
168B TYR* 4.8 6.1 - - + -
169B ARG* 4.0 28.6 + - + +
183B GLU* 2.7 30.8 + - - +
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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