Contacts of the helix formed by residues 63 - 76 (chain A) in PDB entry 5C6P
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 PHE 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLY 2.9 14.6 + - - +
60A SER* 3.9 14.8 - - - +
61A SER 2.3 18.9 + - - +
62A ALA* 1.3 65.7 - - - +
64A ALA* 1.3 65.0 + - + +
65A THR 2.8 1.6 - - - -
66A VAL* 2.6 32.1 + - + +
67A TYR* 3.2 38.8 + + + -
115A MET* 3.3 36.1 - - + -
145A LEU* 3.8 24.9 - - + +
146A ALA* 4.5 2.5 - - - -
148A PRO* 5.0 6.5 - - + -
149A ALA* 4.0 25.4 - - + -
152A VAL* 5.4 1.6 - - + -
210A PHE* 4.8 20.2 - + - -
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Residues in contact with ALA 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 SER 3.8 6.7 + - - +
61A SER 2.7 12.9 + - - +
63A PHE* 1.3 79.0 - - + +
65A THR* 1.3 58.7 + - - +
67A TYR* 4.0 19.1 - - + -
68A ILE* 2.5 44.3 + - + +
601A 4YH 4.4 17.7 - - - -
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Residues in contact with THR 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 SER 3.7 1.8 + - - -
62A ALA* 3.5 32.9 - - + +
63A PHE 2.8 0.2 - - - -
64A ALA* 1.3 78.8 - - - +
66A VAL* 1.3 75.1 + - + +
68A ILE* 4.7 1.2 - - - +
69A THR* 3.0 26.5 + - + +
265A PHE* 3.7 27.4 - - + -
601A 4YH 5.7 1.0 - - - -
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Residues in contact with VAL 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 ALA 5.2 1.8 - - - +
63A PHE* 2.6 20.8 + - + +
65A THR* 1.3 85.5 - - + +
67A TYR* 1.3 61.5 + - - +
69A THR* 3.3 10.8 - - + -
70A PHE* 3.3 32.5 - - + +
111A GLY* 4.8 12.8 - - - +
112A MET* 5.1 1.6 - - - +
114A LEU* 3.7 28.5 - - + -
115A MET* 3.5 33.9 - - + -
149A ALA* 5.6 3.4 - - + +
153A HIS* 4.6 1.4 + - - -
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Residues in contact with TYR 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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37A ILE* 4.1 24.4 - - + +
63A PHE* 3.2 35.8 + + + -
64A ALA* 2.9 17.2 + - + +
66A VAL* 1.3 77.7 - - - +
68A ILE* 1.3 78.2 + - + +
70A PHE* 3.0 4.0 + - - +
71A MET* 2.6 59.6 + - + +
149A ALA* 5.8 2.9 - - + -
152A VAL* 4.6 19.3 - - + -
153A HIS* 4.4 7.9 + + - -
156A LEU* 3.8 23.3 - - + +
210A PHE* 5.1 15.6 - + - -
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Residues in contact with ILE 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 ALA* 2.5 27.5 + - + +
65A THR* 5.1 0.9 - - - +
67A TYR* 1.3 93.6 - - + +
69A THR* 1.3 70.0 + - - +
71A MET* 3.3 42.8 - - + +
72A GLY 3.2 11.4 + - - -
258A TYR* 3.9 30.7 - - + +
261A GLU* 5.2 7.4 - - + +
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Residues in contact with THR 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 THR* 3.0 28.0 + - + +
66A VAL* 3.3 19.1 - - + -
68A ILE* 1.3 75.7 - - - +
70A PHE* 1.3 77.6 + - + +
71A MET 2.7 0.3 + - - -
72A GLY* 2.5 35.3 + - - -
73A ILE* 3.6 4.4 - - - +
255A GLY* 3.6 28.9 + - - -
256A LEU* 5.2 3.3 - - - +
258A TYR* 4.5 5.2 - - - -
259A PHE* 4.6 15.7 - - + -
262A ALA* 6.1 3.8 - - - -
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Residues in contact with PHE 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 VAL* 3.3 27.8 - - + +
67A TYR 3.0 2.6 + - - -
69A THR* 1.3 91.2 - - + +
71A MET* 1.3 56.2 + - - +
72A GLY 3.1 0.2 - - - -
73A ILE* 3.1 22.2 - - + +
74A MET 3.0 21.8 + - - -
107A LEU* 3.8 48.9 - - + -
110A PHE* 4.3 19.5 - + - -
111A GLY* 3.9 19.3 - - - -
114A LEU* 6.2 6.5 - - + -
153A HIS* 3.0 29.6 - + + +
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Residues in contact with MET 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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34A GLN* 4.2 14.8 - - - +
37A ILE* 6.1 1.1 - - + -
67A TYR* 2.6 41.8 + - + +
68A ILE* 3.3 30.3 - - + +
70A PHE* 1.3 69.9 - - - +
72A GLY* 1.3 56.6 + - - +
74A MET* 3.2 3.0 + - - +
75A ALA* 2.4 41.2 + - - +
153A HIS* 3.9 4.0 - - - -
156A LEU* 3.3 28.9 - - + -
159A TYR* 3.3 23.6 - - - +
258A TYR* 4.2 16.4 - - + +
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Residues in contact with GLY 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 ILE 3.2 5.3 + - - -
69A THR 2.5 18.5 + - - -
71A MET* 1.3 63.7 - - - +
73A ILE* 1.3 66.0 + - - +
74A MET 3.0 0.4 - - - -
75A ALA* 2.8 15.0 + - - -
76A ALA 3.2 2.9 + - - -
254A ILE* 2.8 21.3 - - - +
255A GLY 3.7 1.1 - - - -
258A TYR* 3.2 32.9 - - - -
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Residues in contact with ILE 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 THR* 3.6 13.0 - - - +
70A PHE* 3.1 22.4 - - + +
72A GLY* 1.3 67.2 - - - +
74A MET* 1.3 56.1 + - + +
76A ALA* 2.5 28.9 - - - +
77A LEU* 3.9 4.3 - - - +
103A PHE* 4.2 13.7 - - + -
107A LEU* 3.7 29.4 - - + -
247A ILE* 4.6 1.8 - - - +
248A TRP* 6.3 0.2 - - + -
250A ILE* 4.4 0.2 - - - +
251A GLY* 3.1 26.8 - - - -
252A ALA* 4.0 11.7 - - - +
254A ILE* 3.4 2.2 - - - +
255A GLY* 3.5 26.7 - - - +
256A LEU* 5.1 5.2 - - + -
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Residues in contact with MET 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 PHE 3.0 10.5 + - - +
71A MET 3.6 6.1 - - - +
72A GLY 2.8 3.4 + - - -
73A ILE* 1.3 73.7 - - + +
75A ALA* 1.3 52.8 + - - +
76A ALA 2.4 18.1 + - - -
77A LEU* 3.1 27.1 + - - +
100A GLY 4.2 4.3 - - - +
103A PHE* 3.4 14.6 - - + -
104A GLY* 3.1 43.3 - - - +
107A LEU* 3.1 30.1 - - + -
153A HIS* 3.2 32.8 - - + +
156A LEU* 3.8 17.9 - - + -
157A HIS* 4.7 14.0 - - - +
159A TYR* 5.3 0.4 - - - -
160A ALA* 4.6 7.6 - - - +
247A ILE* 6.0 0.2 - - - -
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Residues in contact with ALA 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 MET* 2.4 36.7 + - - +
72A GLY* 2.8 12.1 + - - +
74A MET* 1.3 63.6 - - - +
76A ALA* 1.3 57.8 + - - +
77A LEU 3.3 0.9 - - - -
78A ASN* 3.3 30.9 + - - +
79A PRO* 4.4 0.7 - - - +
156A LEU* 4.2 1.0 - - - +
159A TYR* 3.6 24.7 - - - +
254A ILE* 4.9 0.4 - - + -
258A TYR* 4.3 6.3 - - + +
302A SER* 5.1 1.8 - - - +
388A ARG* 3.9 26.5 + - - +
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Residues in contact with ALA 76 (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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72A GLY 3.2 2.6 + - - +
73A ILE 2.5 24.9 - - - +
74A MET 2.4 10.3 + - - -
75A ALA* 1.3 68.7 - - - +
77A LEU* 1.3 56.5 + - + +
78A ASN 3.2 4.7 - - - -
79A PRO* 2.8 22.9 - - - +
80A MET* 3.3 0.9 - - - +
250A ILE* 2.9 40.0 - - + +
251A GLY* 3.3 13.0 - - - +
394A LYS* 3.9 11.0 - - - +
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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