Contacts of the helix formed by residues 60 - 72 (chain A) in PDB entry 1SHZ
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLU 3.4 1.0 + - - -
59A SER* 1.3 79.8 - - - +
61A LYS* 1.3 66.1 + - - +
63A THR* 2.9 14.4 + - - -
64A PHE* 3.0 22.2 + - - -
291A ASN* 4.0 3.4 - - - -
475A GDP 2.9 41.0 + - - -
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.4 21.0 - - + +
54A LEU* 3.2 40.8 - - - +
55A GLY 3.2 8.0 + - - -
56A ALA 2.8 24.7 + - - -
59A SER* 3.4 5.5 + - - +
60A GLY* 1.3 73.8 - - - +
62A SER* 1.3 58.8 + - - +
64A PHE* 3.0 30.9 + - - +
65A LEU 3.4 3.8 + - - -
222A ASP* 3.5 13.5 - - - +
223A VAL* 3.1 27.4 - - - +
224A GLY 4.3 0.2 - - - -
225A GLY* 3.7 5.8 - - - +
246A CYS* 4.3 9.3 - - - -
378A ALF 2.9 17.5 - - - -
475A GDP 2.7 25.0 + - - +
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Residues in contact with SER 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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61A LYS* 1.3 74.4 - - - +
63A THR* 1.3 68.2 + - - +
64A PHE 3.0 2.2 + - - -
65A LEU* 3.2 14.1 + - - +
66A LYS* 3.3 26.0 + - - +
201A ARG 5.8 1.1 - - - -
203A THR* 3.3 8.4 + - - -
222A ASP* 2.7 21.7 + - - -
377A MG 2.6 24.1 - - - -
475A GDP 3.1 12.3 + - - -
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Residues in contact with THR 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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60A GLY 2.9 10.0 + - - -
62A SER* 1.3 78.4 - - - +
64A PHE* 1.3 62.5 + - - +
66A LYS* 3.4 13.0 + - - +
67A GLN* 3.2 19.6 + - - +
197A LEU* 4.0 20.5 + - + +
348A ALA* 3.4 37.5 - - + +
349A THR* 4.0 6.5 - - + +
475A GDP 3.1 42.2 + - + -
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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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53A LEU* 4.1 15.5 - - + -
60A GLY 3.0 28.3 + - - -
61A LYS 3.0 8.6 + - - +
63A THR* 1.3 76.4 - - - +
65A LEU* 1.3 66.3 + - - +
67A GLN* 2.9 18.3 + - - +
68A MET* 2.9 21.3 + - + +
220A MET* 6.1 0.4 - - + -
244A ILE* 6.0 0.9 - - + -
246A CYS* 4.0 23.1 - - - -
289A PHE* 3.6 36.3 - + - -
291A ASN* 3.9 14.1 - - + -
346A THR* 3.8 18.2 - - + -
348A ALA* 3.5 29.6 - - + -
354A VAL* 4.3 22.7 - - + -
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Residues in contact with LEU 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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53A LEU* 3.5 23.3 - - + -
61A LYS 3.4 1.9 + - - +
62A SER* 3.2 9.2 + - - +
64A PHE* 1.3 76.4 - - - +
66A LYS* 1.3 60.2 + - + +
68A MET* 2.9 8.0 + - + +
69A ARG* 2.8 28.9 + - - +
207A HIS* 4.5 7.0 - - + +
209A THR* 3.6 26.9 - - + +
220A MET* 3.5 26.9 - - + +
222A ASP* 3.3 39.5 - - + +
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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 SER* 3.3 22.4 + - - +
63A THR* 3.6 9.8 + - - +
64A PHE 3.2 0.2 - - - -
65A LEU* 1.3 76.2 - - + +
67A GLN* 1.3 58.0 + - - +
69A ARG* 3.1 8.2 + - - +
70A ILE* 2.8 34.8 + - - +
76A PHE* 4.2 18.2 - - + -
84A PHE* 3.7 22.1 - - - -
196A ILE* 3.1 40.0 + - + +
197A LEU* 3.7 19.4 + - + -
199A ALA* 3.7 16.4 + - - +
201A ARG* 6.3 1.6 - - - +
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Residues in contact with GLN 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 THR 3.2 12.7 + - - +
64A PHE* 2.9 10.2 + - - +
66A LYS* 1.3 77.9 - - - +
68A MET* 1.3 58.2 + - - +
70A ILE* 3.1 7.8 + - - +
71A ILE* 2.8 37.8 + - + +
197A LEU* 3.2 30.5 - - - +
348A ALA 2.6 30.3 + - - +
349A THR 3.3 10.3 + - - -
351A THR* 3.1 38.5 + - - +
354A VAL* 3.5 27.1 - - + -
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Residues in contact with MET 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* 2.9 23.2 + - + +
65A LEU* 2.9 9.8 + - + +
67A GLN* 1.3 76.3 - - - +
69A ARG* 1.3 54.5 + - - +
71A ILE* 3.5 22.4 - - + -
72A HIS* 2.7 45.2 + - - +
73A GLY 3.5 0.6 + - - -
209A THR* 6.3 2.5 - - + -
211A PHE* 4.2 15.9 - - + -
220A MET* 3.7 26.7 - - + -
354A VAL* 3.6 24.5 - - + -
358A PHE* 4.0 44.9 - - + -
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Residues in contact with ARG 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 LEU 2.8 15.4 + - - +
66A LYS* 3.4 9.2 - - - +
68A MET* 1.3 72.8 - - - +
70A ILE* 1.3 58.2 + - - +
73A GLY* 3.1 32.5 + - - +
74A GLN* 3.0 55.0 + - - +
76A PHE* 3.2 48.4 - - + -
80A ALA* 4.7 6.9 - - - +
209A THR* 6.2 4.7 - - + -
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Residues in contact with ILE 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 2.8 26.7 + - - +
67A GLN* 3.5 10.1 - - - +
69A ARG* 1.3 79.4 - - - +
71A ILE* 1.3 67.9 + - + +
73A GLY 4.9 1.2 - - - +
75A ASP* 3.0 38.7 - - - +
76A PHE* 3.6 30.5 - - + -
193A GLN* 3.9 30.7 - - + +
196A ILE* 5.5 0.4 - - + -
197A LEU* 4.0 26.9 - - + -
351A THR* 4.7 6.1 - - + -
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Residues in contact with ILE 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 GLN* 2.8 20.9 + - + +
68A MET* 3.5 33.4 - - + +
70A ILE* 1.3 79.3 - - + +
72A HIS* 1.3 93.9 + - + +
73A GLY 5.1 0.2 - - - -
351A THR* 3.6 31.2 - - + +
354A VAL* 4.9 0.7 - - + -
355A GLN* 4.3 42.9 - - + +
358A PHE* 4.8 2.0 - - + -
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Residues in contact with HIS 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 MET* 2.7 19.9 + - - +
70A ILE 3.5 0.2 - - - -
71A ILE* 1.3 114.5 - - + +
73A GLY* 1.3 65.3 + - - +
211A PHE* 3.6 35.8 - + + -
212A THR 5.3 5.2 - - - +
213A PHE* 3.9 32.0 - + + -
355A GLN* 5.6 4.2 + - - +
358A PHE* 3.4 36.5 - + - -
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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