Contacts of the helix formed by residues 139 - 147 (chain L) 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 TYR 139 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88L VAL* 4.1 14.4 - - + +
91L LEU* 3.2 44.4 - - + -
92L ARG* 3.0 43.4 + - - -
95L ASP* 2.8 40.9 + - - -
100L GLY* 2.9 34.8 + - - -
101L THR 3.5 0.4 - - - -
102L VAL* 3.2 23.6 - - + -
137L ILE* 3.2 4.0 + - + +
138L ASN* 1.3 69.2 - - - +
140L GLU* 1.3 64.9 + - + +
141L ALA 3.4 0.2 - - - -
142L PHE* 3.5 17.0 - - + -
143L VAL* 2.9 31.1 + - + +
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Residues in contact with GLU 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L VAL* 5.3 11.2 - - + +
92L ARG* 3.8 24.0 + - - +
99L ASN* 4.5 5.5 + - - -
100L GLY* 3.3 18.3 + - - -
138L ASN* 3.0 28.1 + - - +
139L TYR* 1.3 84.7 - - + +
141L ALA* 1.3 61.6 + - - +
143L VAL* 4.4 1.2 - - - +
144L LYS* 3.3 26.2 + - - +
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Residues in contact with ALA 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L GLN* 5.5 1.3 - - + -
138L ASN* 3.1 15.4 + - + +
140L GLU* 1.3 77.3 - - - +
142L PHE* 1.3 60.1 + - - +
144L LYS* 3.3 15.1 + - + +
145L HIS* 2.9 53.2 + - + -
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Residues in contact with PHE 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794J CYS* 5.7 7.0 - - - -
91L LEU* 4.5 8.3 - - + -
107L LEU* 3.9 25.6 - - + -
111L LEU* 5.9 2.2 - - + -
126L LEU* 3.2 26.7 - - + -
127L MET* 3.7 26.0 - - + -
130L GLN* 3.6 31.1 - - + +
137L ILE* 4.2 7.6 - - + -
138L ASN 2.9 20.2 + - - +
139L TYR* 3.5 15.0 - - + -
141L ALA* 1.3 75.1 - - - +
143L VAL* 1.3 70.0 + - + +
145L HIS* 3.2 4.3 + - - +
146L ILE* 3.0 50.5 + - + +
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Residues in contact with VAL 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790J THR* 6.1 4.0 - - + -
84L PHE* 5.4 0.2 - - + -
87L PHE* 4.2 16.6 - - + +
88L VAL* 4.0 27.6 - - + -
91L LEU* 3.8 28.3 - - + -
139L TYR 2.9 21.7 + - - +
140L GLU 4.4 0.7 - - - +
142L PHE* 1.3 80.5 - - + +
144L LYS* 1.3 65.4 + - - +
146L ILE* 3.2 7.2 + - + +
147L MET* 3.0 45.8 + - + +
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Residues in contact with LYS 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L GLU* 3.3 18.7 + - - +
141L ALA* 3.3 17.8 + - + +
143L VAL* 1.3 79.7 - - - +
145L HIS* 1.3 75.5 + - + +
147L MET* 3.2 6.5 + - - +
148L SER* 2.8 24.5 + - - +
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Residues in contact with HIS 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797J PHE* 3.2 20.6 - - + -
130L GLN* 4.0 27.4 - - + +
141L ALA* 2.9 37.4 + - + +
142L PHE 3.2 4.0 + - - +
144L LYS* 1.3 88.8 - - + +
146L ILE* 1.3 64.6 + - - +
148L SER* 3.1 24.9 + - - -
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Residues in contact with ILE 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793J ARG* 2.9 33.6 - - + -
794J CYS* 3.7 31.2 - - - -
797J PHE* 3.2 37.2 - - + -
126L LEU* 4.1 8.1 - - + -
130L GLN* 4.3 4.5 - - - +
142L PHE* 3.0 51.0 + - + +
143L VAL* 3.2 9.8 + - + +
145L HIS* 1.3 76.5 - - - +
147L MET* 1.3 58.6 + - + +
149L VAL* 3.1 17.8 - - - +
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Residues in contact with MET 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793J ARG* 2.6 55.3 + - + +
82L GLY 4.8 7.4 - - - +
84L PHE* 3.6 39.0 - - + +
87L PHE* 4.0 17.5 - - + -
143L VAL* 3.0 31.8 + - + +
144L LYS* 3.5 6.5 - - - +
146L ILE* 1.3 74.3 - - + +
148L SER* 1.3 59.2 + - - +
149L VAL 4.0 0.3 - - - +
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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