Contacts of the helix formed by residues 110 - 116 (chain N) in PDB entry 2O5J
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 110 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104N PHE 4.2 4.0 - - - -
105N VAL 3.8 13.9 + - - -
107N ASP 3.9 7.0 - - - -
108N VAL 3.1 8.2 + - - -
109N PRO* 1.3 65.3 - - - +
111N LYS* 1.3 51.1 + - - +
112N ILE* 2.8 14.3 + - - +
113N GLY* 2.5 29.4 + - - -
114N THR* 2.6 39.9 + - - -
120N ALA* 2.9 30.8 + - - +
121N THR* 5.1 1.6 - - - -
124N GLU* 4.3 4.5 - - - +
10Z A 4.8 2.0 + - - -
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Residues in contact with LYS 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N PHE* 3.3 21.4 + - + +
107N ASP* 5.5 1.1 - - + +
109N PRO* 2.7 14.0 + - + +
110N SER* 1.3 70.5 - - - +
112N ILE* 1.3 56.4 + - - +
114N THR* 4.2 4.2 - - - +
115N LEU* 3.5 24.3 + - - +
497N GLU* 6.2 0.2 - - - +
498N VAL* 4.0 36.9 - - + +
512N MET* 3.8 18.7 - - + +
1448N THR* 4.6 9.0 - - + -
1449N GLU* 2.9 34.1 + - - +
1452N ILE* 3.4 47.3 - - + +
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Residues in contact with ILE 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N PHE 2.9 28.5 - - - +
105N VAL* 3.8 16.2 - - + -
110N SER* 3.5 9.2 - - - +
111N LYS* 1.3 74.2 - - - +
113N GLY* 1.3 60.5 + - - +
114N THR 3.3 2.0 - - - -
115N LEU* 4.7 5.2 - - + +
116N LEU* 3.0 38.3 + - + +
118N LEU* 4.3 1.8 - - + -
124N GLU* 4.4 0.9 - - + -
128N TYR* 2.9 29.8 - - + +
461N ILE* 3.6 25.8 - - + -
465N LEU* 6.2 2.2 - - + -
512N MET* 4.0 21.5 - - - -
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Residues in contact with GLY 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N SER* 2.5 31.1 + - - -
112N ILE* 1.3 74.4 - - - +
114N THR* 1.3 56.3 + - - +
116N LEU 2.6 20.8 - - - +
117N ASP* 4.2 1.6 - - - -
118N LEU 3.6 13.0 + - - +
120N ALA* 3.9 20.1 - - - +
124N GLU* 4.4 10.3 - - - -
491N LYS* 5.2 3.5 + - - -
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Residues in contact with THR 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109N PRO* 3.9 4.0 - - - +
110N SER 2.6 38.0 + - - -
111N LYS* 4.2 4.6 - - - -
113N GLY* 1.3 73.8 - - - +
115N LEU* 1.3 66.6 + - - +
116N LEU 4.1 1.7 - - - -
117N ASP* 4.4 0.7 + - - -
120N ALA* 5.5 4.3 - - - +
491N LYS* 4.4 17.1 - - - +
494N LYS* 3.7 44.1 + - + +
495N ARG* 3.4 35.3 + - + +
498N VAL* 4.7 7.6 - - + -
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Residues in contact with LEU 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111N LYS 3.5 18.5 + - - +
112N ILE* 4.4 4.3 - - + +
114N THR* 1.3 81.6 - - - +
116N LEU* 1.3 73.1 + - + +
117N ASP 3.4 2.9 + - - -
150N ARG* 5.8 0.3 + - - -
465N LEU* 5.1 13.7 - - + -
468N LEU* 4.4 17.8 - - + +
470N LEU* 6.5 0.7 - - + -
473N LEU* 5.1 6.9 - - - +
495N ARG* 3.8 21.1 + - - +
498N VAL* 3.5 19.4 - - + +
499N VAL* 4.9 13.4 - - + +
502N PHE* 3.3 37.7 - - + -
509N PRO* 4.5 7.4 - - + -
512N MET* 5.2 5.4 - - + -
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Residues in contact with LEU 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N ILE* 3.0 17.6 + - + +
113N GLY* 2.6 27.8 - - - +
114N THR 4.1 0.2 - - - -
115N LEU* 1.3 85.2 - - + +
117N ASP* 1.3 59.0 + - - +
118N LEU* 2.7 43.8 + - + +
150N ARG* 4.1 14.4 - - - +
461N ILE* 3.9 26.9 - - + -
464N LEU* 3.5 42.6 - - + -
465N LEU* 5.2 2.9 - - + +
468N LEU* 4.4 12.6 - - + -
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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