Contacts of the helix formed by residues 85 - 93 (chain A) in PDB entry 2YSX
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 LYS 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PHE* 4.0 4.1 - - - -
83A PHE* 3.7 7.9 - - - +
84A THR* 1.3 99.2 + - - +
86A LEU* 1.3 65.7 + - - +
87A ASP* 4.6 3.6 - - + +
88A GLN* 3.6 30.2 - - + +
89A LEU* 3.4 17.8 + - - +
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Residues in contact with LEU 86 (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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12A TRP* 4.0 11.2 - - + -
13A ASN* 4.4 11.0 - - - +
37A VAL* 4.7 6.7 - - + -
47A TYR* 3.3 51.1 - - + +
62A ILE* 5.6 2.9 - - + -
70A PHE* 3.7 24.3 - - + -
85A LYS* 1.3 70.1 - - - +
87A ASP* 1.3 67.2 + - - +
89A LEU* 2.7 32.1 + - + +
90A ILE* 3.0 35.8 + - + -
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Residues in contact with ASP 87 (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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10A PRO* 4.3 15.9 - - - +
12A TRP* 3.0 37.2 - - + -
13A ASN* 4.8 2.6 + - - -
85A LYS* 3.6 3.1 - - + +
86A LEU* 1.3 79.9 - - - +
88A GLN* 1.3 64.8 + - + +
89A LEU 3.1 0.3 + - - -
90A ILE* 3.2 1.4 + - - +
91A GLU* 3.1 37.6 + - + +
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Residues in contact with GLN 88 (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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83A PHE* 3.7 17.0 - - + -
85A LYS* 3.6 34.5 - - + +
86A LEU 3.1 0.8 - - - -
87A ASP* 1.3 78.4 - - + +
89A LEU* 1.3 59.8 + - - +
91A GLU* 3.5 23.1 - - - +
92A PHE* 3.6 19.6 + - - +
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Residues in contact with LEU 89 (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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49A LEU* 5.5 4.3 - - + -
62A ILE* 4.7 7.6 - - + -
70A PHE* 2.8 41.3 - - + +
71A THR* 4.2 6.3 - - - +
72A VAL* 4.3 18.2 - - + +
83A PHE* 3.7 24.9 - - + -
85A LYS 3.4 11.2 + - - +
86A LEU* 2.7 17.6 + - + +
88A GLN* 1.3 78.7 - - - +
90A ILE* 1.3 86.9 - - + +
92A PHE* 3.6 3.1 - - - +
93A TYR* 3.3 31.3 + - + -
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Residues in contact with ILE 90 (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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12A TRP* 3.4 30.7 - - + +
35A PHE* 3.4 20.2 - - + -
37A VAL* 3.8 19.3 - - + -
49A LEU* 4.6 13.9 - - + -
86A LEU* 3.0 22.8 + - + +
87A ASP 3.2 4.2 + - - +
89A LEU* 1.3 89.4 - - + +
91A GLU* 1.3 61.1 + - + +
93A TYR* 2.6 35.9 + - - +
94A LYS* 4.2 3.8 - - - -
104A LEU* 3.2 26.9 - - + +
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Residues in contact with GLU 91 (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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12A TRP* 6.1 2.5 - - + +
87A ASP* 3.1 21.7 + - + +
88A GLN* 3.5 23.9 - - - +
90A ILE* 1.3 78.9 - - + +
92A PHE* 1.3 55.1 + - - +
94A LYS* 2.6 52.8 + - + +
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Residues in contact with PHE 92 (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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81A ARG* 3.1 53.4 - - + -
83A PHE* 3.4 21.1 - + + -
88A GLN 3.6 14.6 + - - +
89A LEU 3.6 8.0 + - - +
90A ILE 3.1 0.4 + - - -
91A GLU* 1.3 78.4 - - - +
93A TYR* 1.3 82.1 + + - +
94A LYS 3.1 4.3 + - - -
95A LYS* 4.0 11.6 + - - +
98A MET* 5.0 14.8 - - + +
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Residues in contact with TYR 93 (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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49A LEU* 5.7 2.5 - - + -
72A VAL* 4.1 33.8 + - + +
74A ALA* 6.0 0.7 - - - +
79A SER 4.8 8.8 + - - -
80A MET* 5.0 4.0 - - - +
81A ARG 4.9 8.1 + - - -
83A PHE* 4.5 12.3 - + - -
89A LEU* 3.3 28.2 + - + +
90A ILE* 2.6 20.5 + - - +
92A PHE* 1.3 92.5 - + - +
94A LYS* 1.3 58.8 + - - +
95A LYS 3.4 8.2 - - - +
98A MET* 4.0 31.0 - - + -
99A GLY* 4.5 9.0 - - - -
100A LEU* 4.1 33.6 - - + +
103A HIS* 4.8 0.7 - - - -
104A LEU* 3.3 22.6 + - + +
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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