Contacts of the helix formed by residues 88 - 96 (chain I) in PDB entry 4HOK
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 88 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I GLY 3.9 0.6 + - - -
87I PRO* 1.3 76.6 - - - +
89I LEU* 1.3 61.5 + - - +
90I GLU 3.4 1.6 + - - -
91I ASP* 3.0 23.5 + - - +
92I LEU* 2.9 25.5 + - - +
131I PRO 4.0 1.8 - - - -
132I ASP* 3.1 31.8 + - - -
134I PHE 3.1 15.5 - - - -
135I LEU* 3.8 16.1 - - - +
293K LEU* 5.5 0.4 - - - +
294K LYS 5.6 0.4 - - - +
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Residues in contact with LEU 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I SER* 1.3 74.6 - - - +
90I GLU* 1.3 54.3 + - - +
92I LEU* 4.0 14.3 - - + +
93I PHE* 2.8 35.2 + - - +
100I PHE* 4.1 3.5 - - + -
108I LEU* 4.0 35.2 - - + -
112I MET* 4.0 25.1 - - + -
131I PRO* 3.4 10.3 + - + +
134I PHE* 3.0 35.7 + - + +
136I MET* 4.2 17.5 - - + -
145I VAL* 4.7 3.1 - - + -
206I PHE* 4.0 18.3 - - + -
290I TRP* 4.4 4.9 - - + -
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Residues in contact with GLU 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I SER* 3.1 0.6 + - - -
89I LEU* 1.3 80.0 - - - +
91I ASP* 1.3 61.6 + - - +
93I PHE* 4.2 3.5 - - - -
94I ASN* 3.2 44.8 + - - +
98I ARG* 3.3 24.5 + - - -
131I PRO* 3.6 16.9 + - + +
132I ASP* 3.1 49.6 - - - +
179I TYR* 5.1 0.2 + - - -
205I TYR* 2.8 23.8 + - - -
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Residues in contact with ASP 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I PRO* 4.4 7.9 - - + -
88I SER* 3.0 26.7 + - - +
90I GLU* 1.3 83.6 - - - +
92I LEU* 1.3 59.8 + - - +
94I ASN* 4.0 9.2 + - - +
95I PHE* 3.0 26.3 + - - +
132I ASP* 4.4 5.9 - - - +
95K PHE* 3.4 13.8 - - + -
294K LYS* 3.6 34.0 + - + +
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Residues in contact with LEU 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I PRO* 4.0 26.7 - - + +
88I SER 2.9 19.0 + - - +
89I LEU* 4.0 9.2 - - + +
91I ASP* 1.3 73.4 - - - +
93I PHE* 1.3 66.9 + - - +
95I PHE* 2.9 8.9 + - + +
96I CYS* 2.8 23.9 + - - -
100I PHE* 4.2 3.1 - - - -
136I MET* 3.7 23.1 - - + -
290I TRP* 3.6 63.3 - - + +
95K PHE* 4.1 13.2 - - + -
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Residues in contact with PHE 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I LEU 2.8 19.3 + - - +
90I GLU* 3.7 7.6 - - - +
92I LEU* 1.3 74.6 - - - +
94I ASN* 1.3 55.1 + - - +
96I CYS* 2.7 23.7 + - - +
98I ARG* 3.0 53.7 + - + -
99I LYS* 3.0 30.7 - - - -
100I PHE* 3.5 31.7 - + + -
205I TYR* 3.3 61.0 - + - -
206I PHE* 3.6 18.2 - + + -
209I GLY* 3.9 6.5 - - - -
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Residues in contact with ASN 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I GLU* 3.2 31.2 + - - +
91I ASP* 4.0 9.6 + - - +
93I PHE* 1.3 77.6 - - - +
95I PHE* 1.3 65.4 + - - +
96I CYS 2.7 2.3 + - - -
97I SER* 2.7 14.9 + - - -
98I ARG* 2.4 42.8 + - - +
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Residues in contact with PHE 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I ASP 3.0 15.9 + - - +
92I LEU* 2.9 12.7 + - + +
94I ASN* 1.3 75.4 - - - +
96I CYS* 1.3 56.0 + - - +
97I SER* 3.4 2.6 + - - -
290I TRP* 3.5 42.2 - - + -
294I LYS* 3.6 35.2 - - + +
87K PRO* 3.6 25.6 - - + -
91K ASP* 4.3 16.6 - - + -
92K LEU* 4.2 7.4 - - + -
95K PHE* 3.2 46.4 - + + -
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Residues in contact with CYS 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I LEU 2.8 11.7 + - - +
93I PHE 2.7 11.3 + - - +
95I PHE* 1.3 77.4 - - - +
97I SER* 1.3 70.9 + - - +
98I ARG 3.2 1.2 + - - -
99I LYS* 3.5 26.0 - - - +
100I PHE* 3.8 17.9 - - + -
289I ASP* 3.9 8.1 - - + -
290I TRP* 3.6 37.0 - - - -
294I LYS* 3.9 14.8 - - - -
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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