Contacts of the helix formed by residues 151 - 159 (chain H) in PDB entry 1O1F
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 151 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H MET* 4.5 26.6 - - + +
101H PHE* 5.2 0.8 - - - -
102H LYS* 5.4 8.2 - - - +
109H LYS* 4.6 21.8 + - - +
149H ASP* 4.5 0.2 - - - +
150H TYR* 1.3 122.6 - - + +
152H ASN* 1.3 68.0 + - - +
153H ILE* 3.1 6.1 - - - +
154H CYS* 3.3 21.2 + - - +
155H TYR* 3.2 33.7 + - + -
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Residues in contact with ASN 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H PHE* 5.4 0.4 - - - -
143H ASP* 6.1 0.4 - - - +
144H VAL* 4.4 16.8 - - + +
149H ASP* 3.3 29.8 + - - +
150H TYR 3.3 1.5 - - - +
151H LYS* 1.3 80.4 - - - +
153H ILE* 1.3 58.9 + - - +
155H TYR* 3.4 13.4 + - - +
156H VAL* 3.1 36.6 + - + +
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Residues in contact with ILE 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H PHE* 5.0 18.6 - - + -
117H LEU* 6.5 0.2 - - + -
140H PHE* 4.0 21.3 - - + -
144H VAL* 2.0 74.0 - - + +
147H ASN* 5.9 0.2 - - - -
149H ASP 5.0 6.5 - - - +
150H TYR* 5.5 2.9 - - - -
151H LYS 5.0 4.9 - - - +
152H ASN* 1.3 76.9 - - - +
154H CYS* 1.3 57.1 + - - +
156H VAL* 3.3 1.9 + - - +
157H ILE* 2.9 53.1 + - + +
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Residues in contact with CYS 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H GLU* 3.4 12.6 - - + +
97H ILE* 3.5 40.5 - - + +
98H MET* 3.6 28.9 - - + -
101H PHE* 3.6 20.9 - - - -
150H TYR* 5.6 0.2 - - - -
151H LYS* 3.3 19.5 + - - +
153H ILE* 1.3 75.4 - - - +
155H TYR* 1.3 67.2 + - + +
157H ILE* 3.5 1.6 + - - +
158H THR* 3.2 24.9 + - - -
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Residues in contact with TYR 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H GLU* 3.2 27.4 - - + -
98H MET* 5.2 11.4 - - - -
151H LYS* 3.2 20.3 + - + -
152H ASN* 3.4 17.5 - - - +
154H CYS* 1.3 79.8 - - + +
156H VAL* 1.3 60.1 + - + +
158H THR* 3.0 5.5 + - - -
159H HIS* 2.8 53.1 + + + +
163H ALA* 5.7 7.9 - - + -
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Residues in contact with VAL 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823G PHE* 2.3 52.7 - - + -
140H PHE* 3.6 21.5 - - + -
152H ASN* 3.1 17.7 + - + +
153H ILE 3.3 0.4 + - - -
155H TYR* 1.3 78.2 - - + +
157H ILE* 1.3 51.6 + - - +
158H THR 3.4 0.2 - - - -
159H HIS* 3.0 9.2 - - - +
160H GLY* 3.3 7.1 - - - -
161H GLU 3.7 34.8 - - - +
162H ASP* 5.4 1.8 - - - -
163H ALA* 5.1 11.0 - - + +
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Residues in contact with ILE 157 (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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819G ASN* 4.1 24.5 - - + +
820G VAL* 4.4 22.4 - - + -
823G PHE* 3.4 27.2 - - + +
836G PHE* 5.1 1.6 - - - -
91H ALA* 6.1 1.6 - - - +
92H ASP 4.4 6.8 + - - +
97H ILE* 3.9 30.3 - - + -
101H PHE* 5.9 1.3 - - + -
140H PHE* 3.9 17.7 - - + -
153H ILE* 2.9 37.3 + - + +
154H CYS 3.9 4.3 - - - +
155H TYR 3.3 0.2 - - - -
156H VAL* 1.3 78.0 - - - +
158H THR* 1.3 59.5 + - - +
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Residues in contact with THR 158 (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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832G MET* 4.5 5.5 - - - +
836G PHE* 3.0 15.7 - - - -
839G MLY 3.5 41.7 + - - +
92H ASP 3.3 20.3 + - - +
93H PRO* 4.9 5.4 - - + -
94H GLU* 3.2 38.5 + - + +
97H ILE* 4.0 0.2 - - - +
154H CYS 3.2 5.0 + - - -
155H TYR 3.0 2.9 + - - -
157H ILE* 1.3 77.6 - - - +
159H HIS* 1.3 61.2 + - - +
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Residues in contact with HIS 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836G PHE* 2.6 24.7 - - + +
839G MLY 4.5 22.0 - - + -
94H GLU* 3.3 23.6 + - - -
155H TYR* 2.8 45.6 + + + +
156H VAL* 3.0 18.3 - - + +
158H THR* 1.3 78.9 - - - +
160H GLY* 1.3 70.9 + - - +
161H GLU 4.2 0.9 + - - +
163H ALA* 5.2 13.1 - - + +
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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