Contacts of the helix formed by residues 59 - 75 (chain A) in PDB entry 6H60
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 SER 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A VAL* 1.3 74.5 - - - +
60A VAL* 1.3 63.6 + - - +
61A ASN 3.4 2.5 - - - +
62A ASP* 3.6 12.0 + - - +
63A PHE 4.0 5.0 + - - -
122A ALA* 6.0 1.2 - - - +
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Residues in contact with VAL 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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59A SER* 1.3 68.3 - - - +
61A ASN* 1.3 59.3 + - - +
62A ASP 3.0 2.2 - - - -
63A PHE* 2.7 24.7 + - - +
64A ILE* 2.9 9.9 + - - -
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Residues in contact with ASN 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 SER* 3.4 1.0 - - - +
60A VAL* 1.3 75.4 - - - +
62A ASP* 1.3 55.6 + - - +
64A ILE* 3.4 3.7 + - - +
65A ILE* 2.9 25.1 + - - -
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Residues in contact with ASP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.6 11.6 + - - +
60A VAL 3.0 1.6 - - - -
61A ASN* 1.3 73.9 - - - +
63A PHE* 1.3 58.6 + - - +
65A ILE* 3.3 1.3 + - - +
66A LYS* 2.9 26.9 + - - -
121A ILE 5.9 4.0 - - - -
122A ALA* 5.9 7.4 - - - +
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Residues in contact with PHE 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 SER 4.0 4.4 + - - -
60A VAL* 2.7 16.1 + - - +
62A ASP* 1.3 69.2 - - - +
64A ILE* 1.3 58.5 + - - +
66A LYS* 3.4 1.2 + - - +
67A ALA* 2.8 28.9 + - - -
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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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60A VAL 2.9 12.0 + - - -
61A ASN* 3.8 4.0 - - - +
63A PHE* 1.3 75.3 - - - +
65A ILE* 1.3 57.3 + - - +
67A ALA* 3.4 1.7 + - - +
68A ALA* 2.9 24.6 + - - -
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Residues in contact with ILE 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 ASN 2.9 14.5 + - - -
62A ASP* 3.7 2.9 - - - +
63A PHE 3.2 0.2 - - - -
64A ILE* 1.3 74.1 - - - +
66A LYS* 1.3 65.2 + - - +
68A ALA* 2.9 12.9 + - - +
69A ALA* 2.9 10.9 + - - -
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Residues in contact with LYS 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 ASP 2.9 17.9 + - - -
63A PHE* 3.9 1.3 - - - +
65A ILE* 1.3 71.9 - - - +
67A ALA* 1.3 57.3 + - - +
69A ALA* 3.3 3.5 + - - +
70A VAL* 2.9 24.6 + - - -
113A ALA 6.0 1.8 - - - -
232A LEU* 5.4 4.4 - - - +
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Residues in contact with ALA 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 PHE 2.8 17.2 + - - -
64A ILE* 3.7 1.8 - - - +
66A LYS* 1.3 74.5 - - - +
68A ALA* 1.3 60.7 + - - +
70A VAL* 4.3 1.6 - - - +
71A THR* 2.9 25.1 + - - -
222A PHE* 5.6 6.5 - - - -
225A ASN 6.5 0.9 - - - -
232A LEU* 6.0 5.8 - - - +
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Residues in contact with ALA 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 2.9 12.0 + - - -
65A ILE* 2.9 8.0 + - - +
67A ALA* 1.3 76.6 - - - +
69A ALA* 1.3 57.4 + - - +
71A THR* 4.5 0.9 - - - +
72A LEU* 2.9 27.2 + - - -
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Residues in contact with ALA 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 ILE 2.9 12.5 + - - -
66A LYS* 3.3 4.5 + - - +
68A ALA* 1.3 75.7 - - - +
70A VAL* 1.3 57.8 + - - +
72A LEU* 5.2 0.2 - - - +
73A LYS* 2.9 24.8 + - - +
93A ILE* 6.2 4.0 - - - +
113A ALA 6.1 0.2 - - - -
114A ALA* 5.1 18.6 - - - +
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Residues in contact with VAL 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 LYS 2.9 16.1 + - - -
67A ALA* 3.9 2.5 - - - +
68A ALA 3.3 0.2 - - - -
69A ALA* 1.3 74.6 - - - +
71A THR* 1.3 58.9 + - - +
73A LYS* 3.8 1.4 - - - +
74A GLN* 2.9 24.3 + - - -
232A LEU* 5.5 8.5 - - - +
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Residues in contact with THR 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 ALA 2.9 16.7 + - - -
68A ALA* 4.0 0.7 - - - +
70A VAL* 1.3 77.1 - - - +
72A LEU* 1.3 49.8 + - - +
74A GLN* 3.0 2.9 + - - +
75A MET* 2.4 36.7 + - - +
218A PHE* 5.8 5.4 - - - +
221A SER 5.8 6.3 - - - -
222A PHE* 6.2 1.3 - - - +
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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 ALA 2.9 16.5 + - - -
69A ALA* 4.7 0.4 - - - +
71A THR* 1.3 71.1 - - - +
73A LYS* 1.3 60.5 + - - +
75A MET 2.9 11.3 - - - -
76A PRO* 2.8 32.6 - - - +
79A ASN* 5.6 4.3 - - - +
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Residues in contact with LYS 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 ALA 2.9 21.0 + - - -
70A VAL* 3.8 2.0 - - - +
72A LEU* 1.3 76.3 - - - +
74A GLN* 1.3 60.1 + - - +
76A PRO 4.7 1.4 - - - -
91A PRO 6.0 2.2 - - - -
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Residues in contact with GLN 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 VAL 2.9 14.9 + - - -
71A THR* 3.4 3.4 - - - +
73A LYS* 1.3 79.3 - - - +
75A MET* 1.3 55.2 + - - +
76A PRO 3.8 1.3 - - - -
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Residues in contact with MET 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 THR 2.4 22.5 + - - +
72A LEU* 2.9 16.6 - - - +
74A GLN* 1.3 69.3 - - - +
76A PRO* 1.3 63.7 - - - +
77A ASP 3.1 4.5 + - - +
78A VAL* 3.4 12.3 + - - -
79A ASN 4.1 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