Contacts of the strand formed by residues 151 - 155 (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 VAL 151 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D SER 3.0 10.6 + - - +
90D VAL* 3.2 4.2 - - - +
91D VAL* 2.7 34.2 + - - +
113D GLY* 3.4 6.7 - - - +
128D LEU* 3.8 22.0 - - + -
145D PHE* 3.6 59.9 - - + +
148D LYS* 4.1 13.5 - - + +
150D THR* 1.3 78.5 - - - +
152D VAL* 1.3 58.9 + - - +
153D LEU* 3.8 16.8 - - + -
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Residues in contact with VAL 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ILE* 4.7 1.1 - - + -
91D VAL* 3.5 28.7 - - + +
93D LEU* 4.3 21.5 - - + -
103D ALA 5.1 1.1 - - - +
106D LEU* 4.3 23.8 - - + -
107D ALA* 5.9 1.8 - - - -
112D TYR* 4.1 24.9 - - + -
113D GLY 2.6 15.8 + - - +
114D PHE* 3.3 27.9 - - + -
115D ALA 3.2 22.3 + - - -
150D THR* 4.9 0.2 - - + -
151D VAL* 1.3 73.1 - - - +
153D LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D VAL* 4.6 3.6 - - + -
91D VAL 2.8 12.4 + - - +
92D LEU* 3.6 24.3 - - + -
93D LEU* 2.9 27.2 + - - +
115D ALA* 3.3 17.3 - - + +
118D VAL* 4.3 3.6 - - + -
121D VAL* 3.5 32.3 - - + -
128D LEU* 4.2 14.1 - - + -
130D ALA* 4.3 5.8 - - + -
145D PHE* 3.6 30.5 - - + -
151D VAL* 3.8 8.5 - - + -
152D VAL* 1.3 83.5 - - - +
154D THR* 1.3 68.4 + - - +
155D ILE* 4.3 6.6 - - + +
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Residues in contact with THR 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LEU* 3.1 15.3 - - + -
94D PRO 3.8 13.5 - - - +
95D HIS* 2.8 30.4 + - - +
99D SER* 4.7 3.1 - - - -
100D LEU* 6.2 1.3 - - + -
103D ALA* 3.9 28.5 - - + -
114D PHE* 4.5 3.8 - - + -
115D ALA 3.1 6.7 + - - -
116D THR* 3.1 15.2 - - + -
117D ASP 3.0 11.7 + - - -
118D VAL* 3.0 28.9 + - - +
153D LEU* 1.3 76.4 - - - +
155D ILE* 1.3 61.3 + - - +
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Residues in contact with ILE 155 (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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17D VAL* 5.2 0.2 - - - +
20D GLU* 6.2 0.9 - - + -
21D LEU* 3.8 36.1 - - + +
24D ALA* 5.1 4.7 - - + -
92D LEU* 4.0 28.0 - - + -
93D LEU 2.9 10.5 + - - +
94D PRO* 3.7 2.4 - - - +
95D HIS* 2.8 23.0 + - - +
118D VAL* 3.5 21.8 - - + +
121D VAL* 4.7 8.7 - - + -
153D LEU* 4.3 5.4 - - + +
154D THR* 1.3 80.3 - - - +
156D ARG* 1.3 77.0 + - - +
157D PRO* 3.4 1.9 - - - +
160D PHE* 3.5 33.0 - - + -
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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