Contacts of the helix formed by residues 88 - 97 (chain A) in PDB entry 5HVO
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 ASP 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLU* 3.3 23.4 - - - +
87A MET* 1.3 76.9 - - - +
89A ASP* 1.3 65.6 + - - +
90A LYS* 3.2 13.3 - - + +
91A LEU* 3.3 14.1 + - + +
92A ALA* 3.0 22.2 + - - +
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Residues in contact with ASP 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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59A TRP* 4.8 8.0 - - - -
62A LEU* 4.5 4.5 - - - -
63A GLU* 3.0 46.3 + - - +
87A MET 3.9 0.4 + - - +
88A ASP* 1.3 72.3 - - - +
90A LYS* 1.3 60.0 + - + +
92A ALA* 3.9 3.5 - - - +
93A ASP* 2.9 32.4 + - - +
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Residues in contact with LYS 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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63A GLU* 6.1 0.4 - - - +
88A ASP* 3.2 7.9 - - + +
89A ASP* 1.3 79.4 - - + +
91A LEU* 1.3 60.7 + - - +
93A ASP* 3.7 4.7 + - - +
94A ARG* 3.3 31.8 + - - +
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Residues in contact with LEU 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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87A MET* 3.6 29.4 - - + -
88A ASP* 3.3 17.0 + - + +
90A LYS* 1.3 75.9 - - - +
92A ALA* 1.3 61.8 + - - +
94A ARG* 3.2 15.7 + - - +
95A HIS* 2.9 26.7 + - - +
124A ALA* 3.8 26.7 - - + +
127A GLU* 3.7 37.0 - - + +
128A ALA* 4.4 4.0 - - + -
131A LEU* 3.7 23.6 - - + -
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Residues in contact with ALA 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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59A TRP* 3.7 38.4 - - + +
87A MET* 4.3 14.3 - - + -
88A ASP 3.0 17.7 + - - +
89A ASP* 3.9 6.1 - - - +
91A LEU* 1.3 76.6 - - - +
93A ASP* 1.3 57.3 + - - +
95A HIS* 3.7 5.6 - - - +
96A TYR* 2.8 36.5 + - + +
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Residues in contact with ASP 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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89A ASP 2.9 18.9 + - - +
90A LYS* 3.9 6.1 - - - +
92A ALA* 1.3 78.3 - - - +
94A ARG* 1.3 60.4 + - - +
96A TYR* 5.3 0.4 - - - -
97A ASN* 2.4 69.3 + - - +
98A GLY 3.1 5.5 + - - -
327A ASP* 4.8 3.5 - - - +
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Residues in contact with ARG 94 (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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90A LYS* 3.3 15.6 + - - +
91A LEU* 3.2 28.4 + - - +
93A ASP* 1.3 84.0 - - - +
95A HIS* 1.3 61.2 + - - +
98A GLY* 3.1 24.8 - - - +
99A PHE 3.2 4.5 + - - -
120A GLY* 3.3 31.9 + - - -
121A ALA* 3.9 10.0 - - + +
123A ASP* 4.6 6.3 - - - +
124A ALA* 3.4 26.2 - - + +
127A GLU* 4.0 11.1 + - - -
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Residues in contact with HIS 95 (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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18A ASN* 3.7 26.7 + - - -
87A MET* 4.3 13.0 - - + -
91A LEU 2.9 16.6 + - - +
92A ALA* 3.7 5.4 - - - +
94A ARG* 1.3 79.8 - - - +
96A TYR* 1.3 66.7 - - + +
99A PHE* 3.5 1.8 + - - +
100A SER* 3.1 31.9 + - - -
124A ALA* 4.0 8.9 - - - +
125A TYR* 3.4 34.9 - + - +
128A ALA* 3.6 24.4 - - + +
129A ASN* 3.8 8.3 - - - -
132A PHE* 5.5 1.8 - + - -
152A HIS* 3.3 30.7 + - - +
153A LEU* 5.1 4.4 - - + +
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Residues in contact with TYR 96 (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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18A ASN* 3.6 17.9 - - - +
19A ARG* 3.3 33.7 + - - -
59A TRP* 5.7 7.6 - + + -
92A ALA* 2.8 20.6 + - + +
93A ASP* 5.3 0.4 - - - -
95A HIS* 1.3 76.7 - - + +
97A ASN* 1.3 67.5 + - - +
100A SER* 3.7 3.0 - - - -
101A ASN* 3.0 59.8 + - - -
152A HIS* 2.9 38.9 + + - -
325A ARG* 3.8 18.3 + - + -
502A VDM 3.8 24.6 + - - -
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Residues in contact with ASN 97 (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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93A ASP* 2.4 46.3 + - - +
96A TYR* 1.3 88.1 - - - +
98A GLY* 1.3 59.0 + - - +
101A ASN* 4.2 6.5 + - - +
102A SER* 2.4 36.0 + - - -
325A ARG* 5.2 4.9 - - - -
327A ASP* 3.8 30.9 + - + +
328A VAL* 3.9 18.1 - - + +
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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