Contacts of the helix formed by residues 53 - 68 (chain A) in PDB entry 1P27
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 HIS 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR 4.2 0.4 + - - -
52A VAL* 1.3 76.9 - - - +
54A LYS* 1.3 88.8 + - + +
55A SER* 2.9 27.6 + - - +
56A VAL* 2.9 20.9 + - + +
57A MET* 3.4 4.0 + - - +
147B ASP* 3.8 23.4 + - - +
148B TRP* 3.0 51.8 + + + +
149B CYS* 2.9 15.0 + - - +
151B VAL* 4.0 22.7 - - + +
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Residues in contact with LYS 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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52A VAL 3.9 0.8 + - - -
53A HIS* 1.3 90.1 + - + +
55A SER* 1.3 56.4 + - - +
57A MET* 3.2 13.1 + - + +
58A GLU* 2.9 40.8 + - + +
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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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53A HIS* 2.9 21.1 + - - -
54A LYS* 1.3 79.5 - - - +
56A VAL* 1.3 62.1 + - - +
58A GLU* 3.4 6.8 + - - +
59A GLU* 3.0 23.6 + - - +
76B PHE* 3.8 18.6 + - - -
78B THR* 4.7 8.5 + - - -
145B SER* 5.8 0.5 - - - -
147B ASP* 3.1 32.8 + - - +
148B TRP 4.6 0.2 - - - -
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Residues in contact with VAL 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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26A PHE* 4.6 7.2 - - + -
52A VAL* 3.9 20.4 - - + -
53A HIS* 2.9 11.4 + - + +
55A SER* 1.3 78.5 - - - +
57A MET* 1.3 56.5 + - - +
59A GLU* 3.3 3.3 + - - +
60A LEU* 2.9 27.8 + - - +
132A LEU* 4.8 6.3 - - + +
136A LEU* 4.1 23.8 - - + -
76B PHE* 3.7 40.2 - - + -
149B CYS* 3.7 29.6 - - - +
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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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5A PHE* 3.5 36.7 - - + +
26A PHE* 3.9 24.0 - - + -
27A ARG 3.2 28.0 - - - +
28A PRO* 4.6 5.8 - - + +
30A GLY* 4.2 13.9 - - - +
52A VAL* 3.9 22.4 - - + -
53A HIS 3.4 9.8 + - - +
54A LYS* 3.2 13.6 + - + +
56A VAL* 1.3 76.6 - - - +
58A GLU* 1.3 62.1 + - + +
60A LEU* 3.4 6.7 + - - +
61A LYS* 3.0 22.7 + - - +
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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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54A LYS* 2.9 31.1 + - + +
55A SER* 3.6 8.3 - - - +
56A VAL 3.2 0.2 - - - -
57A MET* 1.3 79.1 - - + +
59A GLU* 1.3 58.1 + - - +
61A LYS* 3.3 21.4 + - - +
62A ARG* 3.0 24.9 + - - +
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Residues in contact with GLU 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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55A SER 3.0 16.8 + - - +
56A VAL 3.7 4.5 - - - +
58A GLU* 1.3 75.4 - - - +
60A LEU* 1.3 66.2 + - - +
62A ARG* 2.7 48.8 + - - +
63A ILE* 2.9 31.5 + - + +
132A LEU* 5.7 2.5 - - + -
76B PHE* 3.8 24.0 - - + -
78B THR* 4.0 20.1 - - + +
114B LYS* 4.8 0.2 - - - +
115B GLY 4.2 1.0 + - - -
116B TYR* 3.3 33.7 + - + +
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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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5A PHE* 3.8 20.4 - - + -
7A LEU* 4.4 8.5 - - + -
26A PHE* 3.5 47.3 - - + -
56A VAL 2.9 16.3 + - - +
57A MET* 3.6 6.3 - - - +
59A GLU* 1.3 74.7 - - - +
61A LYS* 1.3 62.4 + - - +
63A ILE* 3.3 10.3 + - + +
64A ILE* 3.0 37.6 + - + +
129A LEU* 3.3 33.7 - - + -
132A LEU* 4.3 19.2 - - + +
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Residues in contact with LYS 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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5A PHE* 4.0 30.0 - - + -
57A MET 3.0 15.1 + - - +
58A GLU* 3.6 22.6 + - - +
59A GLU 3.2 0.4 - - - -
60A LEU* 1.3 77.4 - - - +
62A ARG* 1.3 57.1 + - - +
64A ILE* 3.4 3.8 + - - +
65A ASP* 2.8 50.6 + - - +
92A ILE* 4.6 20.6 - - + -
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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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58A GLU 3.0 13.5 + - - +
59A GLU* 2.7 48.0 + - - +
61A LYS* 1.3 77.2 - - - +
63A ILE* 1.3 60.3 + - - +
65A ASP* 3.8 5.6 - - + +
66A ASP* 2.8 66.0 + - - +
78B THR* 5.6 3.2 - - - +
114B LYS* 4.7 8.1 - - - +
115B GLY* 3.4 26.3 - - - +
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Residues in contact with ILE 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 GLU* 2.9 34.6 + - + +
60A LEU* 3.3 13.4 + - + +
62A ARG* 1.3 78.1 - - - +
64A ILE* 1.3 61.5 + - - +
66A ASP* 3.8 6.9 - - - +
67A SER* 3.1 23.1 + - - -
125A LEU* 4.3 19.5 - - + -
128A ASP* 4.4 15.7 - - + +
129A LEU* 4.4 9.2 - - + -
132A LEU* 4.8 14.6 - - + -
114B LYS* 4.1 30.7 + - + +
116B TYR* 4.1 26.7 - - + -
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Residues in contact with ILE 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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5A PHE* 4.0 27.4 - - + -
7A LEU* 4.0 24.7 - - + -
60A LEU* 3.0 24.6 + - + +
61A LYS* 3.7 4.5 - - - +
63A ILE* 1.3 75.3 - - - +
65A ASP* 1.3 63.3 + - - +
67A SER* 2.5 26.5 + - - -
68A GLU* 3.5 2.1 + - - -
69A ILE* 3.9 21.8 - - + +
70A THR* 4.9 5.2 - - + +
90A ILE* 4.3 17.7 - - + -
92A ILE* 4.2 21.1 - - + -
125A LEU* 4.9 6.7 - - + -
129A LEU* 4.7 10.5 - - + -
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Residues in contact with ASP 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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61A LYS* 2.8 51.8 + - - +
62A ARG* 3.9 6.3 - - - +
64A ILE* 1.3 70.6 - - - +
66A ASP* 1.3 65.9 + - - +
68A GLU* 3.0 20.8 + - - +
70A THR* 5.8 2.5 - - - +
92A ILE* 3.9 22.0 - - - +
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Residues in contact with ASP 66 (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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62A ARG* 2.8 66.8 + - - +
63A ILE* 3.8 6.1 + - - +
65A ASP* 1.3 75.8 - - - +
67A SER* 1.3 60.9 + - - +
68A GLU* 3.4 11.1 + - - +
114B LYS* 5.5 8.3 + - - +
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Residues in contact with SER 67 (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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63A ILE* 3.1 13.4 + - - -
64A ILE* 2.5 22.8 + - - -
66A ASP* 1.3 75.0 - - - +
68A GLU* 1.3 67.3 + - - +
69A ILE* 3.0 19.4 + - - +
121A VAL* 3.0 27.4 - - - +
125A LEU* 3.9 23.1 - - - +
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Residues in contact with GLU 68 (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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64A ILE 3.5 1.3 + - - -
65A ASP 3.0 16.0 + - - +
66A ASP* 3.6 11.3 - - - +
67A SER* 1.3 81.0 + - - +
69A ILE* 1.3 61.2 + - - +
70A THR* 3.2 8.8 + - - +
71A LYS* 2.6 49.6 + - + +
72A GLU* 3.0 21.3 - - - +
121A VAL* 4.3 0.7 - - + -
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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