Contacts of the strand formed by residues 78 - 85 (chain H) in PDB entry 5Y39
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 TYR 78 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G GLY* 3.2 16.8 + - - -
63G ALA* 3.1 36.7 - - + +
64G PHE* 3.4 24.2 - - + +
67G ASP* 3.5 6.7 - - - -
20H HIS* 5.7 1.6 - - + -
41H PRO* 4.7 19.5 - - + -
44H ALA* 4.6 5.4 - - + -
49H PHE* 4.7 0.4 - + - -
75H TYR* 2.9 61.6 + + + +
77H THR* 1.3 98.9 - - - +
79H GLN* 1.3 60.3 + - - +
80H VAL* 3.8 21.5 - - + -
93H ILE* 4.7 8.1 - - + -
94H ALA 3.3 15.5 - - - +
95H SER* 4.7 0.7 - - - -
96H SER* 3.5 10.5 - - - +
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Residues in contact with GLN 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H ILE* 4.6 1.1 - - + +
73H CYS 3.4 5.6 - - - +
74H TYR* 3.5 25.9 - - + -
78H TYR* 1.3 74.5 - - - +
80H VAL* 1.3 66.9 + - - +
81H VAL* 3.8 10.0 - - + +
92H PHE 3.8 1.0 - - - +
93H ILE* 3.8 0.9 - - - +
94H ALA* 2.9 39.8 + - + +
95H SER 3.4 19.3 + - - +
96H SER* 4.0 3.2 + - - +
98H ALA* 2.7 32.9 + - - +
100H THR* 2.7 34.3 + - - +
103H ILE* 4.2 8.1 - - + -
109J GLN* 3.8 9.9 - - - +
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Residues in contact with VAL 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G TYR* 5.8 0.9 - - + -
49H PHE* 3.6 33.9 - - + -
71H ILE 3.7 1.7 - - - +
72H ILE* 3.5 3.1 - - - +
73H CYS* 2.9 41.1 + - + +
75H TYR* 4.3 2.7 - - + -
78H TYR* 3.8 20.4 - - + -
79H GLN* 1.3 78.1 - - - +
81H VAL* 1.3 64.3 + - - +
82H GLN* 3.6 30.0 - - + +
91H SER* 5.1 0.7 - - - -
92H PHE 3.5 3.1 - - - +
93H ILE* 3.8 27.4 - - + -
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Residues in contact with VAL 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H SER* 5.4 2.0 - - - -
71H ILE 3.6 3.1 - - - +
72H ILE* 4.1 25.6 - - + -
79H GLN* 3.8 22.7 - - + +
80H VAL* 1.3 77.4 - - - +
82H GLN* 1.3 62.5 + - - +
83H PHE* 3.5 28.4 - - + -
90H VAL 3.7 0.5 - - - +
91H SER* 3.6 0.9 - - - -
92H PHE* 2.9 43.8 + - - +
100H THR* 4.2 7.4 - - + -
103H ILE* 4.2 25.1 - - + -
104H VAL* 4.8 7.6 - - + -
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Residues in contact with GLN 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G TYR* 2.8 35.2 + - + +
49H PHE* 4.8 4.8 - - - +
50H LEU* 3.9 21.2 + - - +
53H PHE* 3.3 37.6 + - + +
70H SER* 3.1 4.6 - - - -
71H ILE 2.9 41.2 + - - +
73H CYS* 6.4 0.9 - - - -
80H VAL* 3.6 26.2 - - + +
81H VAL* 1.3 73.1 - - - +
83H PHE* 1.3 61.7 + - - +
89H VAL* 4.1 3.0 - - + +
90H VAL 3.4 5.6 - - - +
91H SER* 3.2 25.7 + - - +
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Residues in contact with PHE 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H PHE* 3.9 3.9 - - - -
69H LYS* 3.7 2.2 - - + -
70H SER* 3.7 20.4 - - - -
81H VAL* 3.5 30.5 - - + -
82H GLN* 1.3 75.4 - - - +
84H ASN* 1.3 60.1 + - - +
85H ARG* 3.4 34.7 + - - +
89H VAL* 3.6 5.2 - - - +
90H VAL* 2.7 49.9 + - + +
92H PHE* 4.0 11.7 - + - -
103H ILE* 5.0 1.3 - - + -
104H VAL* 4.1 21.8 - - + -
107H GLU* 3.4 44.2 - - + +
108H LYS* 4.1 9.2 - - - -
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Residues in contact with ASN 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H PHE* 3.5 19.5 - - + -
57H THR* 3.5 30.1 + - - +
68H ASN 3.7 13.9 + - - +
69H LYS* 2.7 20.3 + - - +
83H PHE* 1.3 68.7 - - - +
85H ARG* 1.3 82.2 + - - +
86H LEU* 3.1 41.6 + - - +
88H LEU 4.3 1.3 - - - -
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Residues in contact with ARG 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H LYS* 3.8 23.4 + - - +
83H PHE* 3.4 30.6 + - + +
84H ASN* 1.3 102.7 + - - +
86H LEU* 1.3 66.9 + - - +
88H LEU* 2.9 38.6 + - + +
90H VAL* 3.9 21.5 - - + -
107H GLU* 3.5 21.9 + - - +
108H LYS* 5.3 4.6 - - - +
111H ALA* 5.7 3.6 - - - +
114H PHE* 5.1 8.7 - - + +
115H GLU* 6.0 4.0 - - - -
118H ARG* 3.5 19.8 - - - +
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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