Contacts of the helix formed by residues 63 - 69 (chain F) in PDB entry 2Y1T
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 63 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B PHE* 6.5 0.2 - - - -
103B LYS* 4.4 12.2 - - - +
106B ASP* 5.1 1.0 + - - -
143D DUD 4.5 11.8 + - - -
61F ARG* 2.5 25.9 + - - -
62F SER* 1.3 75.6 + - - +
64F THR* 1.3 64.4 + - - -
65F TYR 3.3 2.2 + - - -
66F LYS* 3.4 22.7 + - - +
67F ASN* 3.2 41.5 + - - -
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Residues in contact with THR 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F PRO* 4.2 11.9 - - + -
61F ARG* 2.4 51.3 + - - +
62F SER 3.3 0.2 - - - -
63F SER* 1.3 67.2 + - - +
65F TYR* 1.3 52.7 + - - +
68F PHE* 2.8 49.9 + - + +
70F VAL* 3.8 30.7 - - + +
92F PHE* 4.7 3.6 - - + -
107F ARG 4.9 0.5 + - - -
108F ILE* 3.0 32.3 + - + +
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Residues in contact with TYR 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D PHE* 3.8 41.1 - + + +
73D THR* 3.7 32.8 - - + +
74D ASN* 6.0 1.7 - - + +
95D TYR* 3.2 28.3 - + - -
62F SER 4.6 4.2 + - - +
63F SER 3.4 0.4 - - - -
64F THR* 1.3 75.6 - - - +
66F LYS* 1.3 65.2 + - - +
69F GLY* 2.8 48.8 + - - +
70F VAL 3.7 23.1 + - - +
71F ILE* 4.5 2.0 - - + -
97F LEU* 3.7 25.9 - - + +
98F ARG* 5.5 2.6 - - - +
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Residues in contact with LYS 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LYS* 3.5 15.9 + - + +
67B ASN* 3.1 49.4 + - - +
68B PHE* 4.5 10.0 - - - -
98B ARG* 5.1 6.7 - - - +
100B THR* 5.8 0.8 + - - -
101B LYS 4.6 6.5 + - - -
39D PHE* 6.1 6.9 - - + -
62F SER 5.3 1.2 + - - +
63F SER* 3.4 23.5 + - - +
65F TYR* 1.3 84.9 - - - +
67F ASN* 1.3 80.4 + - - +
98F ARG* 4.1 2.1 + - - -
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Residues in contact with ASN 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ASN* 3.6 28.1 + - - +
68B PHE* 4.1 8.0 - - - -
106B ASP* 4.1 22.4 + - - -
61F ARG* 6.0 0.6 - - - +
63F SER* 3.2 35.2 + - - +
66F LYS* 1.3 96.8 - - - +
68F PHE* 1.4 87.3 + - + +
98F ARG* 3.0 13.4 + - - -
100F THR* 4.8 0.3 + - - -
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Residues in contact with PHE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 3.6 14.6 - - - -
61F ARG* 5.8 0.9 - - - -
64F THR* 2.8 37.2 + - + +
67F ASN* 1.4 96.5 - - + +
69F GLY* 1.3 62.8 + - - +
70F VAL* 3.1 15.6 + - + +
98F ARG* 3.4 8.6 + - - +
100F THR* 2.7 34.2 + - - +
101F LYS 3.9 10.1 - - - -
102F ILE* 3.9 21.5 - - + -
106F ASP* 3.4 38.1 - - + -
107F ARG 3.9 19.1 - - - -
108F ILE* 4.5 8.3 - - + -
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Residues in contact with GLY 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F TYR* 2.8 34.5 + - - -
68F PHE* 1.3 78.7 - - - +
70F VAL* 1.3 54.4 + - - +
96F ALA* 3.6 2.4 - - - +
97F LEU* 2.7 35.3 + - - +
98F ARG* 3.6 23.6 + - - +
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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