Contacts of the helix formed by residues 96 - 101 (chain D) in PDB entry 1O94
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 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C GLU* 3.4 12.6 - - - -
8D GLU* 2.6 41.2 + - - -
15D ARG* 5.2 3.8 - - - -
17D VAL* 5.7 1.1 - - - -
94D PRO* 3.1 11.8 + - - -
95D HIS* 1.3 75.8 + - - +
97D VAL* 1.3 64.9 + - - +
98D ASP 3.5 0.7 + - - -
99D SER* 2.9 17.9 + - - -
100D LEU* 2.9 26.7 + - - +
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ALA 4.4 3.4 - - - +
145C VAL* 3.9 27.1 - - + +
162C ARG* 3.7 20.4 + - + +
163C GLU 3.5 27.1 - - - +
164C LEU* 4.1 12.3 - - + -
165C GLU* 2.9 35.4 + - + +
96D SER* 1.3 70.9 - - - +
98D ASP* 1.3 63.8 + - - +
100D LEU* 3.2 20.5 + - + +
101D GLY* 3.5 6.6 + - - -
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Residues in contact with ASP 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ARG* 2.8 28.1 + - - +
8D GLU* 3.6 29.7 - - - +
9D HIS 4.4 6.8 - - - +
10D ARG* 2.7 33.7 + - - +
70D PHE* 3.0 52.7 + - + +
75D PHE* 5.6 3.1 - - + -
96D SER* 3.1 1.8 + - - -
97D VAL* 1.3 75.7 - - - +
99D SER* 1.3 60.1 + - - +
101D GLY 2.9 16.8 + - - -
102D TYR* 3.6 1.7 - - + -
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Residues in contact with SER 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLU* 4.3 1.2 + - - -
93D LEU* 3.7 17.6 - - - +
94D PRO* 2.8 42.6 + - - +
95D HIS* 4.8 0.2 - - - -
96D SER* 2.9 14.1 + - - -
98D ASP* 1.3 80.8 - - - +
100D LEU* 1.3 58.5 + - - +
102D TYR* 3.1 14.8 + - - -
103D ALA* 2.8 37.0 + - - +
154D THR* 4.7 3.6 - - - -
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C VAL* 4.2 14.8 - - + +
121C GLN* 5.2 2.5 - - - +
128C ALA* 3.7 43.7 - - + +
132C ILE* 3.4 24.4 - - - +
144C ALA* 3.5 12.5 - - + +
145C VAL* 3.8 21.3 - - + -
181C THR* 6.0 0.4 - - - +
95D HIS* 3.8 25.4 - - + +
96D SER 2.9 20.1 + - - +
97D VAL* 3.2 13.4 + - + +
99D SER* 1.3 77.7 - - - +
101D GLY* 1.3 61.0 + - - +
102D TYR 3.3 0.9 + - - -
103D ALA* 4.6 1.8 + - - -
104D SER* 5.0 1.4 + - - -
116D THR* 6.4 0.4 - - + -
154D THR* 6.2 1.1 - - + -
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Residues in contact with GLY 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ILE* 3.8 3.9 - - - +
142C HIS* 3.2 28.9 - - - -
144C ALA* 3.7 17.9 - - - +
162C ARG* 6.0 0.2 - - - -
70D PHE* 4.0 12.8 - - - -
72D PRO* 3.5 6.0 - - - +
97D VAL 3.5 3.7 + - - -
98D ASP 2.9 13.4 + - - -
100D LEU* 1.3 80.5 - - - +
102D TYR* 1.3 59.0 + - - +
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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