Contacts of the helix formed by residues 88 - 97 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C GLU* 3.5 20.6 - - - +
87C MET* 1.3 76.1 - - - +
89C ASP* 1.3 66.1 + - - +
90C LYS* 4.2 18.2 + - + +
91C LEU* 3.2 13.3 + - + +
92C ALA* 3.0 20.4 + - - +
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Residues in contact with ASP 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C TRP* 4.9 7.3 - - - -
62C LEU* 4.4 3.3 - - - -
63C GLU* 3.0 51.7 + - - +
87C MET 5.0 0.3 - - - +
88C ASP* 1.3 71.7 - - - +
90C LYS* 1.3 64.0 + - - +
92C ALA* 4.0 4.6 - - - +
93C ASP* 3.0 27.4 + - - +
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Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ASP* 3.2 14.2 + - + +
89C ASP* 1.3 78.8 - - - +
91C LEU* 1.3 59.8 + - - +
93C ASP* 3.8 6.1 + - - +
94C ARG* 3.4 39.1 + - + +
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C MET* 4.0 19.5 - - + -
88C ASP* 3.2 17.3 + - + +
90C LYS* 1.3 77.0 - - - +
92C ALA* 1.3 66.4 + - - +
93C ASP 3.1 1.6 - - - -
94C ARG* 3.1 14.5 + - - +
95C HIS* 2.9 20.4 + - - +
124C ALA* 3.8 28.0 - - + +
127C GLU* 3.6 40.2 - - + +
128C ALA* 4.4 5.4 - - + -
131C LEU* 3.7 29.8 - - + -
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C TRP* 4.0 31.2 - - + -
87C MET* 4.2 21.0 - - + +
88C ASP 3.0 16.3 + - - +
89C ASP* 4.0 6.7 - - - +
91C LEU* 1.3 75.7 - - - +
93C ASP* 1.3 54.9 + - - +
95C HIS* 4.2 6.5 - - - -
96C TYR* 2.7 39.6 + - + +
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ASP 3.0 18.7 + - - +
90C LYS* 3.8 8.5 - - - +
92C ALA* 1.3 77.1 - - - +
94C ARG* 1.3 62.4 + - - +
96C TYR* 5.2 0.4 - - - -
97C ASN* 3.0 54.8 + - - +
98C GLY 3.1 5.4 + - - -
327C ASP* 5.6 0.5 - - - +
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Residues in contact with ARG 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LYS* 3.4 26.3 + - + +
91C LEU* 3.1 25.2 + - - +
93C ASP* 1.3 84.1 - - - +
95C HIS* 1.3 57.5 + - - +
98C GLY* 3.0 26.9 - - - +
99C PHE* 3.1 5.7 + - - +
120C GLY* 3.5 30.4 + - - -
121C ALA* 3.7 11.2 - - + +
123C ASP* 4.8 5.1 - - - +
124C ALA* 3.4 19.6 - - + +
127C GLU* 4.0 11.1 + - - -
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Residues in contact with HIS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASN* 3.5 27.6 + - - -
87C MET* 4.3 11.9 - - + +
91C LEU 2.9 16.3 + - - +
92C ALA* 3.6 5.4 - - - +
94C ARG* 1.3 76.8 - - - +
96C TYR* 1.3 65.1 - - + +
99C PHE* 3.5 3.6 + - - +
100C SER* 3.0 39.8 + - - -
124C ALA* 3.9 10.3 - - - +
125C TYR* 3.5 26.4 - + - +
128C ALA* 3.7 33.7 - - + +
129C ASN* 4.2 2.0 - - - -
132C PHE* 5.5 1.0 - - - -
152C HIS* 3.5 29.1 + - + +
153C LEU* 5.4 4.0 - - + +
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Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASN* 3.6 23.3 - - - +
19C ARG* 3.2 34.3 + - - -
59C TRP* 5.6 6.5 - + + -
92C ALA* 2.7 21.4 + - + +
93C ASP* 5.2 0.7 - - - -
95C HIS* 1.3 78.2 - - + +
97C ASN* 1.3 68.2 + - - +
100C SER* 3.6 2.3 - - - -
101C ASN* 3.0 59.4 + - - +
151C TYR* 4.9 0.2 - - - -
152C HIS* 3.3 33.6 + + - -
325C ARG* 4.0 23.6 + - + +
502C VDM 4.3 13.5 + - - -
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Residues in contact with ASN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ASP* 3.0 34.4 + - - +
96C TYR* 1.3 91.8 - - - +
98C GLY* 1.3 58.3 + - - +
101C ASN* 4.1 6.0 + - - -
102C SER* 2.4 38.1 + - - -
325C ARG* 5.2 4.2 - - - +
327C ASP* 3.9 29.5 + - + +
328C VAL* 3.6 22.0 - - + +
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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