Contacts of the helix formed by residues 60 - 75 (chain A) in PDB entry 2PPQ
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 ASN 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LYS* 1.3 97.0 - - - +
61A ASP* 1.3 67.2 + - - +
63A PRO* 3.3 20.5 - - + +
64A PHE* 3.4 14.7 + - - +
137A ILE* 5.1 5.7 - - + +
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Residues in contact with ASP 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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59A LYS* 3.4 6.8 - - - +
60A ASN* 1.3 82.2 + - - +
62A LEU* 1.3 63.2 + - + +
64A PHE* 2.9 11.6 + - - +
65A PHE* 2.8 46.6 + - + -
139A ARG* 3.3 41.7 + - - +
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Residues in contact with LEU 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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53A TYR* 3.9 48.7 - - + -
55A LYS* 6.1 2.5 - - + -
59A LYS 4.9 1.9 + - - +
61A ASP* 1.3 79.9 - - + +
63A PRO* 1.3 69.3 - - + +
65A PHE* 4.1 19.7 - - + -
66A LEU* 2.8 33.5 + - + +
90A LEU* 4.0 2.2 - - - -
91A LEU* 3.4 37.0 - - + -
98A PRO* 4.2 11.0 - - + -
213A TYR* 5.2 1.8 - - + -
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Residues in contact with PRO 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 LYS 3.9 7.2 - - - +
60A ASN* 3.3 27.4 - - + +
62A LEU* 1.3 92.8 - - + +
64A PHE* 1.3 57.3 + - - +
67A GLY* 2.9 27.9 + - - -
90A LEU* 3.3 24.0 - - + -
91A LEU* 5.7 1.6 - - + -
137A ILE* 3.8 19.1 - - + +
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Residues in contact with PHE 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 ASN 3.4 11.1 + - - +
61A ASP* 2.9 12.1 + - - +
63A PRO* 1.3 78.3 - - - +
65A PHE* 1.3 67.4 + + - +
68A LEU* 2.8 42.6 + - + +
135A PHE* 3.5 18.9 - + - -
137A ILE* 3.2 46.3 - - + +
138A LYS 5.1 0.7 - - - +
139A ARG* 3.6 35.7 - - + -
189A VAL* 3.9 23.6 - - + -
215A ALA* 3.5 31.2 - - + -
216A CYS* 4.0 7.6 - - - -
217A ASN* 4.0 5.2 - - - -
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Residues in contact with PHE 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 ASP* 2.8 41.0 + - + +
62A LEU* 4.0 14.1 - - + +
64A PHE* 1.3 82.1 - + - +
66A LEU* 1.3 59.3 + - + +
68A LEU* 3.4 5.3 + - - +
69A MSE 3.1 34.0 + - - +
139A ARG* 3.7 28.0 - - - -
212A PHE* 3.0 23.9 - - - +
213A TYR* 3.0 58.1 - + + -
215A ALA* 3.4 23.8 - - + -
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Residues in contact with LEU 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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53A TYR* 3.8 20.0 - - + +
62A LEU* 2.8 25.0 + - + +
65A PHE* 1.3 73.8 - - + +
67A GLY* 1.3 65.3 + - - +
69A MSE 3.4 14.6 + - - -
70A GLN* 3.1 28.3 + - - +
82A PRO* 3.5 30.7 - - + +
90A LEU* 3.7 39.3 - - + +
91A LEU* 3.7 24.0 - - + -
100A ALA* 4.3 10.5 - - + -
102A ILE* 4.7 4.7 - - + -
213A TYR* 4.6 3.1 - - + +
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Residues in contact with GLY 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 PRO 2.9 20.7 + - - -
64A PHE 3.8 0.2 - - - -
66A LEU* 1.3 76.4 - - - +
68A LEU* 1.3 64.0 + - - +
70A GLN* 3.4 13.5 + - - +
71A HIS* 3.0 18.9 + - - +
90A LEU* 5.0 3.2 - - - +
135A PHE* 3.4 19.0 - - - -
137A ILE* 5.2 2.5 - - - -
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Residues in contact with LEU 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 PHE* 2.8 26.1 + - + +
65A PHE* 3.6 4.7 - - - +
66A LEU 3.3 0.2 - - - -
67A GLY* 1.3 73.0 - - - +
69A MSE 1.3 63.7 + - - +
71A HIS* 3.1 4.6 + - + +
72A LEU* 2.9 52.4 + - + +
128A MSE 5.9 0.9 - - - -
132A SER* 4.5 4.0 - - - -
135A PHE* 3.3 32.6 - - + -
189A VAL* 3.6 34.3 - - + -
212A PHE* 3.9 17.7 - - + -
215A ALA* 3.6 23.6 - - + -
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Residues in contact with MSE 69 (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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65A PHE 3.1 21.7 + - - +
66A LEU* 3.5 28.0 - - - +
68A LEU* 1.3 76.4 - - - +
70A GLN* 1.3 62.0 + - - +
72A LEU* 3.5 1.5 + - - -
73A ALA* 3.0 25.3 + - - +
79A CYS* 3.8 11.6 - - - -
80A PRO* 3.5 33.8 - - + +
82A PRO* 3.9 7.6 - - + -
102A ILE* 5.4 5.4 - - + -
211A ASP* 4.0 9.9 - - - +
212A PHE* 3.4 55.6 - - + +
213A TYR* 4.0 23.1 - - + +
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Residues in contact with GLN 70 (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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66A LEU 3.1 14.3 + - - +
67A GLY* 3.5 13.1 - - - +
69A MSE 1.3 76.6 - - - +
71A HIS* 1.3 53.5 + - - +
73A ALA* 3.4 1.6 + - - +
74A ALA* 2.8 37.3 + - - +
81A LEU* 4.2 18.5 - - + +
82A PRO* 3.8 34.1 + - + +
83A LEU 5.8 0.6 + - - -
84A PRO* 6.0 2.8 - - - +
90A LEU* 4.4 16.5 - - - +
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Residues in contact with HIS 71 (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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67A GLY 3.0 12.0 + - - +
68A LEU* 3.4 8.7 - - - +
70A GLN* 1.3 78.5 - - - +
72A LEU* 1.3 63.2 + - - +
74A ALA* 3.4 7.7 + - + +
75A LYS* 3.2 39.7 + - + +
131A ALA 3.1 27.5 + - - -
132A SER* 4.0 4.7 - - - -
133A GLU 3.2 16.9 + - - -
134A GLY* 3.6 6.0 - - - -
135A PHE* 3.5 45.9 + + + +
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Residues in contact with LEU 72 (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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68A LEU* 2.9 36.2 + - + +
69A MSE 4.7 0.2 - - - -
71A HIS* 1.3 75.5 - - - +
73A ALA* 1.3 65.0 + - - +
75A LYS* 3.0 16.4 + - - +
76A GLY 3.3 0.2 + - - -
77A LEU* 3.1 43.6 + - + +
79A CYS* 3.9 8.5 - - - -
128A MSE 3.8 14.6 - - + +
131A ALA* 3.8 10.3 - - + +
132A SER* 3.7 37.9 - - - +
212A PHE* 3.6 33.0 - - + -
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Residues in contact with ALA 73 (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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69A MSE 3.0 18.5 + - - +
70A GLN 3.7 3.1 - - - +
72A LEU* 1.3 74.7 - - - +
74A ALA* 1.3 58.1 + - - +
76A GLY* 2.8 23.4 + - - -
77A LEU 3.7 12.9 - - - +
79A CYS* 4.0 18.9 - - - +
81A LEU* 3.9 23.8 - - + -
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Residues in contact with ALA 74 (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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70A GLN 2.8 21.9 + - - +
71A HIS* 3.5 10.8 - - + +
73A ALA* 1.3 71.9 - - - +
75A LYS* 1.3 59.5 + - + +
76A GLY 3.4 1.6 + - - -
81A LEU* 5.4 0.8 - - - +
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Residues in contact with LYS 75 (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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71A HIS* 3.2 26.4 + - + +
72A LEU 3.0 10.0 + - - +
74A ALA* 1.3 79.4 - - + +
76A GLY* 1.3 59.2 + - - +
77A LEU 3.4 2.6 + - - -
130A LEU 5.0 2.5 - - - -
131A ALA* 3.0 44.7 - - + +
133A GLU* 4.0 12.6 + - - -
134A GLY* 6.0 0.2 - - - -
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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