Contacts of the helix formed by residues 57 - 70 (chain A) in PDB entry 3W8I
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 GLY 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A SER* 4.6 1.3 + - - -
21A PRO* 6.5 0.2 - - - -
52A GLU* 2.7 12.9 + - - -
55A ASN* 5.2 0.4 - - - -
56A PRO* 1.3 72.3 - - - +
58A LEU* 1.3 62.1 + - - +
59A THR 3.4 2.5 - - - -
60A GLN* 3.5 13.7 + - - +
61A ASP* 3.3 27.1 + - - +
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Residues in contact with LEU 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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51A ALA* 3.7 33.7 - - + +
52A GLU* 3.2 4.4 + - - +
55A ASN* 3.0 22.2 - - + +
56A PRO 3.2 2.2 + - - -
57A GLY* 1.3 77.0 - - - +
59A THR* 1.3 60.9 + - - +
61A ASP* 3.1 7.6 + - + +
62A ILE* 2.9 49.4 + - + +
364B LEU* 4.8 2.2 - - + -
374B ARG* 3.9 32.5 - - + +
377B ALA* 4.2 11.4 - - + -
378B ILE* 4.0 31.0 - - + +
381B LEU* 5.3 0.7 - - + -
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Residues in contact with THR 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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19A SER* 5.6 0.2 - - - -
21A PRO* 4.2 5.2 - - + -
22A LEU* 3.9 25.5 - - + +
26A MET* 3.8 28.7 - - + -
48A PHE* 4.5 14.2 + - + -
52A GLU* 2.8 43.6 + - - +
58A LEU* 1.3 71.9 - - - +
60A GLN* 1.3 58.3 + - - +
62A ILE* 3.3 11.1 + - - +
63A ILE* 2.9 37.7 + - + +
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Residues in contact with GLN 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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21A PRO* 4.1 20.4 - - + +
57A GLY* 3.5 15.4 + - - +
58A LEU 3.2 0.4 - - - -
59A THR* 1.3 79.4 - - - +
61A ASP* 1.3 57.8 + - - +
63A ILE* 3.3 1.7 + - - +
64A MET* 2.9 56.5 + - + +
76A PHE* 3.3 42.9 - - + -
77A THR* 5.1 7.1 - - - +
80A LEU* 5.8 0.3 - - - +
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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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57A GLY 3.3 15.5 + - - +
58A LEU* 3.1 10.9 + - + +
60A GLN* 1.3 77.4 - - - +
62A ILE* 1.3 57.9 + - - +
64A MET* 3.7 19.9 - - - +
65A LYS* 2.9 32.4 + - - +
364B LEU* 3.7 17.8 - - + +
367B GLN* 3.9 9.6 + - - +
374B ARG* 3.0 27.1 + - - +
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Residues in contact with ILE 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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26A MET* 6.3 0.4 - - - -
48A PHE* 4.1 24.5 - - + -
51A ALA* 5.5 1.3 - - + -
58A LEU* 2.9 37.4 + - + +
59A THR* 3.5 9.4 - - - +
61A ASP* 1.3 76.5 - - - +
63A ILE* 1.3 58.9 + - + +
65A LYS* 3.3 1.8 + - - +
66A ILE* 2.9 54.3 + - + +
360B ALA* 5.7 0.2 - - - +
361B PHE* 4.1 16.8 - - + -
364B LEU* 3.6 24.2 - - + -
378B ILE* 6.2 0.7 - - + -
381B LEU* 3.5 30.3 - - + -
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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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21A PRO* 4.1 7.2 - - + +
25A VAL* 3.9 28.3 - - + -
26A MET* 3.9 19.7 - - + -
48A PHE* 6.1 0.2 - - + -
59A THR* 2.9 36.5 + - + +
60A GLN 3.8 3.4 - - - +
62A ILE* 1.3 78.2 - - + +
64A MET* 1.3 58.2 + - - +
66A ILE* 3.3 6.4 + - - +
67A LEU* 2.9 34.3 + - + +
76A PHE* 3.6 26.0 - - + -
403B LEU* 4.1 12.5 - - + +
407B PHE* 3.7 21.5 - - + -
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Residues in contact with MET 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 GLN* 2.9 47.0 + - + +
61A ASP* 3.7 19.7 - - - +
63A ILE* 1.3 73.8 - - - +
65A LYS* 1.3 58.4 + - - +
67A LEU* 3.4 9.8 + - + +
68A GLU* 2.9 29.1 + - - +
76A PHE* 3.7 37.5 - - + -
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Residues in contact with LYS 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 2.9 19.5 + - - +
62A ILE* 3.7 3.6 - - - +
64A MET* 1.3 77.1 - - - +
66A ILE* 1.3 57.7 + - - +
68A GLU* 3.2 32.3 + - - +
69A LYS* 2.9 30.1 + - + +
360B ALA* 3.5 33.4 - - + +
363B GLU* 2.7 44.0 + - - +
364B LEU* 3.9 9.4 - - + -
367B GLN* 4.0 21.7 - - - +
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Residues in contact with ILE 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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48A PHE* 6.0 1.8 - - + -
62A ILE* 2.9 39.2 + - + +
63A ILE 3.7 3.6 - - - +
65A LYS* 1.3 75.2 - - - +
67A LEU* 1.3 64.2 + - - +
69A LYS* 3.3 6.0 + - - +
70A LYS* 3.1 25.4 + - + +
356B ILE* 4.2 20.6 - - + -
357B ILE* 4.0 23.6 - - + -
360B ALA* 4.7 9.4 - - + -
361B PHE* 5.5 0.2 - - + -
399B MET* 5.4 4.9 - - + -
400B VAL* 4.3 21.8 - - + -
403B LEU* 4.0 28.9 - - + -
404B ILE* 4.9 4.3 - - + -
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Residues in contact with LEU 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* 2.9 39.4 + - + +
64A MET* 3.6 9.9 - - + +
66A ILE* 1.3 76.2 - - + +
68A GLU* 1.3 60.4 + - - +
70A LYS 3.5 1.1 + - - +
71A SER 3.1 2.4 + - - -
72A VAL* 2.9 51.1 + - + +
74A VAL* 5.3 8.3 - - + +
76A PHE* 4.5 8.3 - - + -
403B LEU* 5.3 2.7 - - + -
404B ILE* 3.8 26.2 - - + -
407B PHE* 3.9 46.4 - - + -
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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 MET 2.9 13.5 + - - +
65A LYS* 3.2 44.8 + - + +
67A LEU* 1.3 78.4 - - - +
69A LYS* 1.3 65.2 + - + +
70A LYS 3.1 0.2 - - - -
71A SER* 2.9 23.4 + - - +
72A VAL 5.1 1.6 - - - -
363B GLU* 4.1 4.3 - - - +
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Residues in contact with LYS 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 LYS* 2.9 22.0 + - + +
66A ILE* 3.3 5.6 + - - +
68A GLU* 1.3 84.7 + - + +
70A LYS* 1.3 59.5 + - - +
71A SER* 3.4 3.3 + - - -
355B MET 5.0 2.5 - - - +
356B ILE* 4.0 42.5 - - + +
359B PRO* 4.5 14.1 - - + -
360B ALA* 5.0 3.8 - - + +
363B GLU* 2.4 39.4 + - - +
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Residues in contact with LYS 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 ILE* 3.1 18.8 + - + +
67A LEU 4.2 2.2 - - - +
68A GLU 3.1 0.2 - - - -
69A LYS* 1.3 78.4 - - - +
71A SER* 1.3 70.0 + - - +
72A VAL* 3.1 17.9 + - + +
352B CYS* 4.4 15.0 - - - -
355B MET* 5.2 8.3 - - - +
356B ILE* 4.2 19.9 - - + +
400B VAL* 3.6 27.9 - - + +
404B ILE* 3.7 24.1 - - + +
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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