Contacts of the helix formed by residues 60 - 74 (chain A) in PDB entry 1TYI
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A THR* 5.3 0.2 - - - -
58A TYR 4.0 0.6 + - - -
59A HIS* 1.4 73.1 - - - +
61A ASP* 1.3 66.0 + - - +
62A ASP* 2.7 23.5 + - - -
63A TYR* 3.1 2.8 + - - +
64A ILE* 3.1 21.8 + - - +
135A LYS* 3.3 9.2 + - - +
136A SER* 3.2 25.8 - - - -
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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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52A ALA 5.4 0.3 - - - +
56A THR* 3.3 27.6 + - - -
59A HIS 4.6 0.2 - - - +
60A SER* 1.3 73.5 - - - +
62A ASP* 1.3 58.8 + - - +
64A ILE* 3.0 11.1 + - - +
65A LYS* 2.7 32.5 + - + +
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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
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60A SER* 2.7 28.1 + - - -
61A ASP* 1.3 74.8 - - - +
63A TYR* 1.3 50.1 + - - -
65A LYS* 2.9 9.2 + - - +
66A PHE* 2.7 52.9 + - + -
84A ARG* 2.6 26.2 + - - -
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Residues in contact with TYR 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 HIS* 4.3 8.7 - + - -
60A SER* 3.1 15.0 + - - +
62A ASP* 1.3 81.8 + - - +
64A ILE* 1.3 71.9 + - + +
66A PHE* 3.2 7.5 + - - +
67A LEU* 3.1 49.8 + - + +
84A ARG* 3.0 35.9 - - + +
86A ASN* 3.5 19.8 + - - -
135A LYS 4.0 5.8 - - - +
136A SER* 3.3 15.9 - - - -
137A GLU* 3.0 23.7 - - - -
138A ALA* 2.8 27.2 + - - +
143A TYR* 3.0 26.0 + - - -
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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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52A ALA* 5.9 7.6 - - + +
55A MET* 4.3 25.4 - - + -
56A THR 5.5 0.7 - - - +
59A HIS* 3.4 38.8 - - + +
60A SER 3.1 16.6 + - - +
61A ASP* 3.0 12.7 + - - +
63A TYR* 1.3 80.6 - - + +
65A LYS* 1.3 66.9 + - + +
67A LEU* 2.9 23.3 + - + +
68A ARG* 2.9 17.8 + - + +
98A PHE* 3.4 27.4 - - + -
144A VAL* 5.4 1.1 - - + -
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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* 2.7 17.7 + - + +
62A ASP* 3.4 11.4 - - - +
64A ILE* 1.3 70.6 - - + +
66A PHE* 1.3 69.4 + - + +
68A ARG* 3.2 33.4 + - - +
69A SER* 2.8 26.6 + - - -
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Residues in contact with PHE 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* 2.7 39.9 + - + -
63A TYR* 3.5 4.7 - - - +
64A ILE 3.1 0.2 - - - -
65A LYS* 1.3 79.5 - - + +
67A LEU* 1.3 63.9 + - - +
69A SER* 3.0 6.5 + - - -
70A ILE* 2.8 27.5 + - - +
77A GLU* 4.4 16.4 - - + -
78A TYR 5.7 2.7 - - - -
80A LYS* 3.2 29.4 - - + +
83A GLN* 4.4 15.0 - - - -
84A ARG* 3.3 45.1 - - + -
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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 TYR* 3.1 45.0 + - + +
64A ILE* 2.9 18.9 + - + +
66A PHE* 1.3 76.0 - - - +
68A ARG* 1.3 62.3 + - - +
70A ILE* 3.3 3.4 + - - +
71A ARG* 3.1 22.5 + - - +
80A LYS* 3.7 10.8 - - - +
86A ASN* 3.4 30.7 - - - +
97A LEU* 3.7 14.7 - - + +
98A PHE* 3.7 21.3 - - + +
143A TYR* 4.2 22.4 - - + +
144A VAL* 4.5 8.5 - - + -
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Residues in contact with ARG 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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52A ALA* 5.7 7.1 - - - +
55A MET* 6.0 0.2 - - - +
64A ILE* 2.9 19.3 + - - +
65A LYS* 3.6 42.5 - - + +
67A LEU* 1.3 77.1 - - - +
69A SER* 1.3 58.3 + - - +
71A ARG* 5.9 0.2 - - - +
72A PRO* 2.8 30.8 - - - +
98A PHE* 3.2 57.9 - - + -
102A GLN* 4.7 3.4 - - - +
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Residues in contact with SER 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* 2.8 19.4 + - - -
66A PHE* 3.4 8.5 - - - -
68A ARG* 1.3 76.2 - - - +
70A ILE* 1.3 59.2 + - - +
71A ARG 3.4 0.2 + - - -
72A PRO* 3.8 1.2 - - - +
73A ASP* 2.5 42.2 + - - +
77A GLU* 3.9 15.9 - - - +
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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 PHE 2.8 14.8 + - - +
67A LEU 3.5 4.9 - - - +
69A SER* 1.3 76.6 - - - +
71A ARG* 1.3 51.7 + - - +
73A ASP* 2.7 2.6 - - - +
74A ASN* 2.6 31.2 + - - -
75A MET 2.9 16.0 + - - +
76A SER* 3.6 5.6 - - - -
77A GLU* 2.7 43.1 - - - +
80A LYS* 2.9 43.3 - - + +
86A ASN* 4.8 2.0 - - + -
87A VAL* 4.2 5.4 - - + -
93A VAL* 3.7 19.1 - - + -
97A LEU* 3.1 22.0 - - + -
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Residues in contact with ARG 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 LEU 3.1 7.3 + - - +
68A ARG* 5.8 0.4 + - - +
70A ILE* 1.3 81.4 - - - +
72A PRO* 1.3 82.7 - - + +
74A ASN* 2.8 20.3 + - - +
94A PHE 3.0 15.7 - - - +
95A ASP* 2.9 42.9 + - - +
97A LEU* 3.0 23.1 - - + -
98A PHE* 3.5 31.7 - - - +
99A GLU* 2.7 47.1 + - - +
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Residues in contact with PRO 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 ARG* 2.8 29.4 - - - +
69A SER 3.9 1.8 - - - +
71A ARG* 1.3 107.3 - - + +
73A ASP* 1.3 62.2 + - - +
74A ASN* 3.3 3.3 + - - +
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Residues in contact with ASP 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 SER* 2.5 35.9 + - - +
70A ILE 2.7 9.2 - - - +
72A PRO* 1.3 77.1 - - - +
74A ASN* 1.3 68.8 + - - +
75A MET* 2.6 69.4 + - + +
77A GLU* 3.6 7.4 - - - +
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Residues in contact with ASN 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 ILE 2.6 14.0 + - - -
71A ARG 2.8 13.3 + - - +
72A PRO 4.2 3.1 - - - +
73A ASP* 1.3 82.3 - - - +
75A MET* 1.3 58.7 + - - +
93A VAL* 3.5 27.9 + - - +
94A PHE* 4.5 10.7 - - - +
95A ASP* 4.6 8.3 + - - -
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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